Molecular characterization and whole-genome sequencing of Corynebacterium diphtheriae causing skin lesion.

We present a case of skin lesion caused by nontoxigenic Corynebacterium diphtheriae. Genomic taxonomy analyses corroborated the preliminary identification provided by mass spectrometry. The strain showed a susceptible phenotype with increased exposure to penicillin, the first drug of choice for the treatment. An empty type 1 class integron carrying only the sul1 gene, which encodes sulfonamide resistance, was found flanked by transposases. Virulence factors involved in adherence and iron uptake, as well as the CRISPR-Cas system, were predicted. MLST analysis revealed the ST-681, previously reported in French Guiana, a European territory.

Molecular characterization and phylogenetic analysis of the first Corynebacterium rouxii strains isolated in Brazil: a recent member of Corynebacterium diphtheriae complex.

BACKGROUND: Corynebacterium diphtheriae complex was formed by the species C. diphtheriae, Corynebacterium ulcerans and Corynebacterium pseudotuberculosis in the recent past. In addition to C. diphtheriae, C. ulcerans and C. pseudotuberculosis species can carry the tox gene, which encodes diphtheria toxin. Currently, three new species have been included in the complex: Corynebacterium rouxii, Corynebacterium silvaticum, and Corynebacterium belfantii. C. rouxii is derived from the ancient Belfanti biovar of C. diptheriae. We provide the complete genome sequences of two non-toxigenic strains C. rouxii isolated from a cat with a purulent infection in Brazil. The taxonomic status and sequence type, as well as the presence of resistance and virulence genes, and CRISPR-Cas system were additionally defined. RESULTS: The genomes showed an average size of 2.4 Mb and 53.2% GC content, similar to the type strain of the species deposited in Genbank/NCBI. Strains were identified as C. rouxii by the rMLST database, with 95% identity. ANI and DDH in silico were consistent with values above the proposed cut-off points for species limit, corroborating the identification of the strains as C. rouxii. MLST analyses revealed a new ST, which differs from ST-537 only by the fusA allele. No horizontal transfer resistance gene was predicted in both genomes and no mutation was detected in the constitutive genes gyrA and rpoB. Some mutations were found in the seven penicillin-binding proteins (PBPs) detected. The tox gene was not found, but its regulatory gene dtxR was present. Among the predicted virulence genes are those involved in iron uptake and adherence, in addition to the DIP0733 protein involved in epithelial cell adhesion and invasion. The CRISPR-Cas type I-E system was detected in both genomes, with 16 spacer sequences each. Of them, half are unknown according to the databases used, indicating that there is an unexplored reservoir of corynebacteriophages and plasmids. CONCLUSIONS: This is the first genomic study of C. rouxii reported in Brazil. Here we performed taxonomic analysis and the prediction of virulence factors. The genomic analyses performed in this study may help to understand the potential pathogenesis of non-toxigenic C. rouxii strains.

Phenotypic and molecular characterization and complete genome sequence of a Corynebacterium diphtheriae strain isolated from cutaneous infection in an immunized individual.

Diphtheria is an infectious disease potentially fatal that constitutes a threat to global health security, with possible local and systemic manifestations that result mainly from the production of diphtheria toxin (DT). In the present work, we report a case of infection by Corynebacterium diphtheriae in a cutaneous lesion of a fully immunized individual and provided an analysis of the complete genome of the isolate. The clinical isolate was first identified by MALDI-TOF Mass Spectrometry. The commercial strip system and mPCR performed phenotypic and genotypic characterization, respectively. The antimicrobial susceptibility profile was determined by the disk diffusion method. Additionally, genomic DNA was sequenced and analyzed for species confirmation and sequence type (ST) determination. Detection of resistance and virulence genes was performed by comparisons against ResFinder and VFDB databases. The isolate was identified as a nontoxigenic C. diphtheriae biovar Gravis strain. Its genome presented a size of 2.46 Mbp and a G + C content of 53.5%. Ribosomal Multilocus Sequence Typing (rMLST) allowed the confirmation of species as C. diphtheriae with 100% identity. DDH in silico corroborated this identification. Moreover, MLST analyses revealed that the isolate belongs to ST-536. No resistance genes were predicted or mutations detected in antimicrobial-related genes. On the other hand, virulence genes, mostly involved in iron uptake and adherence, were found. Presently, we provided sufficient clinical data regarding the C. diphtheriae cutaneous infection in addition to the phenotypic and genomic data of the isolate. Our results indicate a possible circulation of ST-536 in Brazil, causing cutaneous infection. Considering that cases of C. diphtheriae infections, as well as diphtheria outbreaks, have still been reported in several regions of the world, studies focusing on taxonomic analyzes and predictions of resistance genes may help to improve the diagnosis and to monitor the propagation of resistant clones. In addition, they can contribute to understanding the association between variation in genetic factors and resistance to antimicrobials.

Monitoring fluoroquinolone resistance among ESBL-positive and ESBL-negative Escherichia coli strains isolated from urinary tract infections: An alert for empirical treatment.

BACKGROUND: Bacterial resistance to extended-spectrum beta-lactamases (ESBL) is present worldwide. Empirical antibiotic therapy is often needed, and the use of fluoroquinolones, such as ciprofloxacin and norfloxacin, is common. This study aimed to analyze the urine cultures from 2,680 outpatients in January 2019, 2020, 2021, and 2022, with bacterial counts above 100,000 CFU/mL in which Escherichia coli was the etiological agent. METHODS: We monitored the resistance of ESBL-positive and ESBL-negative strains to ciprofloxacin and norfloxacin and evaluated resistance rates. RESULTS: Significantly higher fluoroquinolone resistance rates were observed among ESBL-positive strains in all years studied. Furthermore, a significant increase in the rate of fluoroquinolone resistance was observed between 2021 and 2022 in ESBL-positive and -negative strains, as well as from 2020 to 2021 among the ESBL-positive strains. CONCLUSIONS: The data obtained in the present study showed a tendency towards an increase in fluoroquinolone resistance among ESBL-positive and -negative E. coli strains isolated from urine cultures in Brazil. Since empirical antibiotic therapy with fluoroquinolones is commonly used to treat diverse types of infections, such as community-acquired urinary tract infections, this work highlights the need for continuous monitoring of fluoroquinolone resistance among E. coli strains circulating in the community, which can mitigate the frequency of therapeutic failures and development of widespread multidrug-resistant strains.

Prosthetic joint infection caused by an imipenem-resistant Mycobacterium senegalense.

Periprosthetic joint infection (PJI) remains one of the most common complications of total knee arthroplasty. Although mainly caused by Staphylococcus aureus and other Gram-positive microorganisms, occasionally, commensal or environmental bacteria are reported as causative agents of these infections. The present work aimed to report a case of PJI caused by an imipenem-resistant Mycobacterium senegalense strain. A bacterial strain isolated from the culture of intraoperative samples was observed by optical microscopy after Gram and Ziehl-Neelsen staining. The species identification was performed by mass spectrometry analysis and partial sequencing of the heat shock protein 65 (hsp65) gene. The antimicrobial profile of the clinical isolate was determined according to the Clinical and Laboratory Standards Institute. Mass spectrometry and gene sequencing analysis identified the bacterial isolate as Mycobacterium fortuitum complex and M. senegalense, respectively. The isolated was found exhibiting an imipenem-resistant profile. The accurate and timely identification, as well as investigation of the antimicrobial susceptibility profile, of fast-growing nontuberculous mycobacteria species are crucial for establishing the prompt and correct treatment of the infection, particularly in cases of patients at greater risk for opportunistic and severe infections.

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.

Monitoring fluoroquinolone resistance among ESBL-positive and ESBL-negative Escherichia coli strains isolated from urinary tract infections: An alert for empirical treatment

ABSTRACT Background: Bacterial resistance to extended-spectrum beta-lactamases (ESBL) is present worldwide. Empirical antibiotic therapy is often needed, and the use of fluoroquinolones, such as ciprofloxacin and norfloxacin, is common. This study aimed to analyze the urine cultures from 2,680 outpatients in January 2019, 2020, 2021, and 2022, with bacterial counts above 100,000 CFU/mL in which Escherichia coli was the etiological agent. Methods: We monitored the resistance of ESBL-positive and ESBL-negative strains to ciprofloxacin and norfloxacin and evaluated resistance rates. Results: Significantly higher fluoroquinolone resistance rates were observed among ESBL-positive strains in all years studied. Furthermore, a significant increase in the rate of fluoroquinolone resistance was observed between 2021 and 2022 in ESBL-positive and -negative strains, as well as from 2020 to 2021 among the ESBL-positive strains. Conclusions: The data obtained in the present study showed a tendency towards an increase in fluoroquinolone resistance among ESBL-positive and -negative E. coli strains isolated from urine cultures in Brazil. Since empirical antibiotic therapy with fluoroquinolones is commonly used to treat diverse types of infections, such as community-acquired urinary tract infections, this work highlights the need for continuous monitoring of fluoroquinolone resistance among E. coli strains circulating in the community, which can mitigate the frequency of therapeutic failures and development of widespread multidrug-resistant strains.

Virulence potential of the first Corynebacterium mycetoides strain isolated from human urine: a rare species of Corynebacterium.

For many years, the potential pathogenic of non-diphtheriae corynebacteria were underestimated. Nowadays, a growing number of Corynebacterium species are recognized as opportunistic agents of human infections, mainly in hospital settings. In addition, multidrug-resistant Corynebacterium isolates from clinical specimens, have been reported and the role of Corynebacterium spp. in urinary tract infections (UTIs) has been highlighted. Several studies have reported Corynebacterium species as the agent of UTIs especially in patients with risk factors. Thus, the present work aimed to report the first isolation of Corynebacterium mycetoides from human urine and an initial study on its virulence properties. The isolate, initially characterized by phenotypical tests as a multidrug-resistant Corynebacterium sp., was recovered from the urine of a female transplant patient. Mass spectrometry and 16S rRNA and rpoB genes sequencing identified the isolate as C. mycetoides. The isolate was found able to adhere to and survive into epithelial cells (Vero cells), and its pathogenic potential was confirmed when tested against Caenorhabditis elegans nematode. The results obtained suggest that C. mycetoides is a potential pathogen for the urinary tract in humans and for a better understanding of the multifactorial mechanisms of virulence, studies about this species should be continued.

MALDI-TOF mass spectrometry identification of yeast-form fungi: a comparison between methods

Introduction: Identification of yeast species has clinical and epidemiological value. Different methods can be used, such as chromogenic media, microculture on corn meal agar with Tween 80, as well as conventional biochemical and automated methods. Recently, proteomic studies employing matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry have been a major advance in diagnosis due to speed of execution and accuracy of results. Methods: For this study, 79 yeast samples were submitted to identification using chromogenic medium, microculture on corn meal-Tween 80 agar, VITEK 2 Compact identification, and MALDI-TOF mass spectrometry. Results: Most of the 79 samples were identified, with differences in the performance of the methods used. Colonial morphology and microscopy were compatible with the genus Candida. MALDI-TOF mass spectrometry had the best performance, with 78 strains identified (98.7%), compared to VITEK 2 Compact (92.4%) and microculture on corn meal agar (70.9%). Conclusions: MALDI-TOF mass spectrometry using the VITEK MS instrument performed best and has proven to be a revolutionary method in clinical microbiology laboratories. Regarding the identification of C. albicans and C. tropicalis, the chromogenic medium had excellent performance, thus being a good option to optimize the process. (AU)

Use of MALDI-TOF MS in diagnostic microbiology for identification of species that conventional methods usually fail to identify

(MALDI-TOF MS) has been used in clinical diagnostic laboratories for the identification of microorganisms. It has a relevant advantage compared to other methods in terms of speed to provide results, being an alternative for addressing restrictions in clinical diagnosis as it may replace or complement existing identification techniques. This is especially important because some rare microorganisms would be identified only by higher cost techniques which are not widely available, such as genetic sequencing. Thus, the present paper reports two cases in which uncommon microorganisms were identified effectively and quickly. (AU)

Identification of Chromobacterium violaceum by MALDI-TOF mass spectrometry in blood culture

Report of Chromobacterium violaceum isolation from blood culture. Identification by MALDI-TOF mass spectrometry. Relevant report due to the site affected, infection severity, and importance of correct and rapid identification for a successful treatment and lower risk of morbidity and mortality. (AU)

Identification of Cryptococcus neoformans by MALDI-TOF mass spectrometry in blood culture

This is a report of isolation of Cryptococcus neoformans from blood culture. Identification was conducted by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. The relevance of this report is related to the site affected, the severity of the infection, and the importance of correct and rapid identification of the causative pathogen for a successful treatment and for reducing the risk of morbidity and mortality. (AU)