Urinary tract infection with Corynebacterium aurimucosum after urethroplasty stricture of the urethra: a case report

Preanalytical, Analytical and Postanalytical Analyses on Corynebacterium spp. and Actinomycetaceae in Urine Samples of Patients with Suspected Urinary Tract Infection-A Hypothesis-Forming Observational Study

A hypothesis-forming exploratory cross-sectional assessment was conducted to assess the occurrence and relevance of Gram-positive rod-shaped bacteria like Corynebacterium spp. and Actinomycetaceae in human urine samples. In total, 1170 urine samples from 1031 inpatients with suspected urinary tract infection were assessed for culture-based growth of Gram-positive rod-shaped bacteria applying API Coryne assays, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS), and in-house 16S rRNA gene sequencing. Overall, 502 different bacterial colonies from 346 urine samples taken from 324 inpatients were observed. The three quantitatively most abundant genera or genus clusters were Corynebacterium (254 isolates, 62%), Actinomyces/Winkia (79 isolates, 19%), and Actinotignum/Actinobaculum (29 isolates, 7%). Compared to sequencing, the diagnostic accuracy of all assessed competitor assays from the diagnostic routine was <80% for differentiation on the genus level and <30% for differentiation on the species level. Prolongated incubation for 4 days compared to 2 days resulted in additional detection of 15% of the totally recorded Gram-positive rod-shaped bacteria. An approximately 5-fold increased detection rate in mid-stream urine compared to urine acquired applying alternative sampling strategies was observed. In conclusion, in the rare event of the suspected clinical relevance of such findings, confirmatory testing with invasively sampled urine should be considered due to the high contamination rate observed in mid-stream urine. Confirmatory testing by DNA-sequencing methods should be considered if an exact identification of genus or species is regarded as relevant for the individual choice of the therapeutic strategy.

Unmasking the invisible enemy: A case report of metagenomics-guided diagnosis and treatment of neonatal septic meningitis caused by Corynebacterium aurimucosum in a preterm infant with neonatal lupus erythematosus

RATIONALE

Neonatal septic meningitis is a serious condition that can be caused by various pathogens, including Corynebacterium aurimucosum, a rare and opportunistic bacterium. We reports a case of infectious meningitis in a premature infant with neonatal lupus erythematosus caused by C aurimucosum. The purpose of this study is to explore the occurrence of meningitis caused by C aurimucosum in preterm infants with neonatal lupus erythematosus. We found that early diagnosis and treatment are crucial for this type of meningitis, especially for infants with impaired immunity or mothers receiving immunosuppressive therapy. This bacterium is rare in clinical practice, but it needs to be taken seriously.

PATIENT CONCERNS

The infant was born to a mother with systemic lupus erythematosus who had a history of long-term immunosuppressive therapy. The infant presented with preterm birth, purplish-red skin, fever, and widespread scarlet dermatitis. He also had positive anti-Ro/SSA and anti-La/SSB antibodies.

DIAGNOSIS

The infant was diagnosed with neonatal lupus erythematosus based on clinical and serological features. A lumbar puncture revealed septic meningitis with high levels of total nucleated cells, protein, and Pan's test in the CSF. The macrogenic examination identified C aurimucosum as the causative agent. The culture of the mother's vaginal secretion also revealed the same bacterium.

INTERVENTIONS

The infant was treated with anti-infective therapy with ceftriaxone, ampicillin, vancomycin, and meropenem. He also received prednisone and gammaglobulin infusion for neonatal lupus erythematosus.

OUTCOMES

The infant's temperature returned to normal, and his general condition and responsiveness improved. The CSF cytology and biochemistry normalized, and the culture was negative. The cranial MRI examination showed no abnormalities. The red rash disappeared, and the follow-ups after discharge revealed no complications.

LESSONS

This case highlights the importance of early diagnosis and treatment of neonatal septic meningitis caused by C aurimucosum, especially in infants with immunocompromised conditions or maternal history of immunosuppressive therapy. C aurimucosum should not be overlooked as a potential pathogen in neonatal septic meningitis.

Multidrug-Resistant Uropathogens Causing Community Acquired Urinary Tract Infections among Patients Attending Health Facilities in Mwanza and Dar es Salaam, Tanzania

In low-income countries, the empirical treatment of urinary tract infections (UTIs) without laboratory confirmation is very common, especially in primary health facilities. This scenario often leads to unnecessary and ineffective antibiotic prescriptions, prompting the emergence and spread of antimicrobial resistance. We conducted this study to examine the antibiogram of uropathogens causing community-acquired urinary tract infections among outpatients attending selected health facilities in Tanzania.

METHOD

This was a cross-sectional health centre-based survey conducted for a period of five months, from July to November 2021, in the Mwanza and Dar es Salaam regions in Tanzania. We enrolled consecutively a total of 1327 patients aged between 2 and 96 years with a median [IQR] age of 28 [22-39] from Dar es Salaam (n = 649) and Mwanza (n = 678).

RESULTS

Significant bacteriuria was observed in 364 (27.4% [95%CI: 25.0-29.9]) patients, from whom 412 urinary pathogens were isolated. Gram-negative bacteria contributed to 57.8% (238) of the 412 uropathogens isolated, of which 221 were Enterobacterales, and Escherichia coli was the most frequent. Staphylococcus aureus and Staphylococcus haemolyticus were the most frequently isolated among Gram-positive uropathogens (n = 156). Generally, resistance among Escherichia coli ranged from 0.7% (meropenem) to 86.0% (ampicillin) and from 0.0% (meropenem) to 75.6% (ampicillin) in other Enterobacterales. Moreover, about 45.4% (108) of Enterobacterales and 22.4% (35) of Gram-positive bacteria were multidrug resistant (MDR), p = 0.008. We observed 33 MDR patterns among Gram-negative bacteria, predominantly AMP-CIP-TCY (23/108; 21.3%), and 10 MDR patterns among Gram-positive bacteria, most commonly CIP-GEN-TCY (22/35; 62.9%).

CONCLUSION

the presence of a high number of wide-ranging uropathogens that are multidrug resistant to a variety of antibiotics points to the need to strengthen the laboratory diagnostic systems for the regular surveillance of the antimicrobial resistance of uropathogens to guide and update empirical treatment guidelines.

The Complex Role of Lactic Acid Bacteria in Food Detoxification

Toxic ingredients in food can lead to serious food-related diseases. Such compounds are bacterial toxins (Shiga-toxin, listeriolysin, Botulinum toxin), mycotoxins (aflatoxin, ochratoxin, zearalenone, fumonisin), pesticides of different classes (organochlorine, organophosphate, synthetic pyrethroids), heavy metals, and natural antinutrients such as phytates, oxalates, and cyanide-generating glycosides. The generally regarded safe (GRAS) status and long history of lactic acid bacteria (LAB) as essential ingredients of fermented foods and probiotics make them a major biological tool against a great variety of food-related toxins. This state-of-the-art review aims to summarize and discuss the data revealing the involvement of LAB in the detoxification of foods from hazardous agents of microbial and chemical nature. It is focused on the specific properties that allow LAB to counteract toxins and destroy them, as well as on the mechanisms of microbial antagonism toward toxigenic producers. Toxins of microbial origin are either adsorbed or degraded, toxic chemicals are hydrolyzed and then used as a carbon source, while heavy metals are bound and accumulated. Based on these comprehensive data, the prospects for developing new combinations of probiotic starters for food detoxification are considered.

Circulating Antibodies to Skin Bacteria Detected by Serological Lateral Flow Immunoassays Differentially Correlated With Bacterial Abundance

The serological lateral flow immunoassay (LFIA) was used to detect circulating antibodies to skin bacteria. Next-generation sequencing analysis of the skin microbiome revealed a high relative abundance of Cutibacterium acnes but low abundance of Staphylococcus aureus and Corynebacterium aurimucosum on human facial samples. Yet, results from both LFIA and antibody titer quantification in 96-well microplates illustrated antibody titers that were not correspondent, and instead negatively correlated, to their respective abundance with human blood containing higher concentrations of antibodies to both S. aureus and C. aurimucosum than C. acnes. Acne vulgaris develops several unique microbial and cellular features, but its correlation with circulating antibodies to bacteria in the pilosebaceous unit remains unknown. Results here revealed that antibodies to C. acnes and S. aureus were approximately 3-fold higher and 1.5-fold lower, respectively, in acne patients than in healthy subjects. Although the results can be further validated by larger sample sizes, the proof-of-concept study demonstrates a newfound discrepancy between the abundance of skin bacteria and amounts of their corresponding antibodies. And in light of acne-correlated amplified titers of specific anticommensal antibodies, we highlight that profiling these antibodies in the pilosebaceous unit by LFIAs may provide a unique signature for monitoring acne vulgaris.

Corynebacterium phoceense, resident member of the urogenital microbiota?

Corynebacterium phoceense is a Gram-positive species previously isolated from human urine. Although other species from the same genus have been associated with urinary tract infections, C. phoceense is currently believed to be a non-pathogenic member of the urogenital microbiota. Prior to our study, only two isolates were described in the literature, and very little is known about the species. Here, we describe C. phoceense UFMG-H7, the first strain of this species isolated from the urine of healthy cattle. The genome for this isolate was produced and compared to the two other publicly available C. phoceense as well as other Corynebacterium genome assemblies. Our in-depth genomic analysis identified four additional publicly available genome assemblies that are representatives of the species, also isolated from the human urogenital tract. Although none of the strains have been associated with symptoms or disease, numerous genes associated with virulence factors are encoded. In contrast to related Corynebacterium species and Corynebacterium species from the bovine vaginal tract, all C. phoceense strains examined code for the SpaD-type pili suggesting adherence is essential for its persistence within the urinary tract. As the other C. phoceense strains analysed were isolated from the human urogenital tract, our results suggest that this species may be specific to this niche.

Corynebacterium phoceense - a rare Corynebacterium species isolated from a urine sample

Corynebacterium spp. are Gram-positive rods that are recognized to cause opportunistic diseases under certain predisposing clinical conditions. Some species have been described in urinary tract infections. In this report we document a new episode of urinary tract infection caused by Corynebacterium phoceense and describe the whole-genome sequencing, phenotypic characteristics and mass spectra obtained by matrix-assisted desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Based on genome identification and DNA-to-DNA hybridization, we can assume that our strain is the second isolate of C. phoceense to be described in a urine sample. No other infectious diseases have been reported to be associated with this species.

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.

The gut-brain axis and beyond: Microbiome control of spinal cord injury pain in humans and rodents

Spinal cord injury (SCI) is a devastating injury to the central nervous system in which 60 to 80% of patients experience chronic pain. Unfortunately, this pain is notoriously difficult to treat, with few effective options currently available. Patients are also commonly faced with various compounding injuries and medical challenges, often requiring frequent hospitalization and antibiotic treatment. Change in the gut microbiome from the "normal" state to one of imbalance, referred to as gut dysbiosis, has been found in both patients and rodent models following SCI. Similarities exist in the bacterial changes observed after SCI and other diseases with chronic pain as an outcome. These changes cause a shift in the regulation of inflammation, causing immune cell activation and secretion of inflammatory mediators that likely contribute to the generation/maintenance of SCI pain. Therefore, correcting gut dysbiosis may be used as a tool towards providing patients with effective pain management and improved quality of life.

Culturable Bacterial Community on Leaves of Assam Tea (Camellia sinensis var. assamica) in Thailand and Human Probiotic Potential of Isolated Bacillus spp

Assam tea plants (Camellia sinensis var. assamica) or Miang are found in plantations and forests of Northern Thailand. Leaf fermentation has been performed for centuries, but little information is available about their associated microbial community. One hundred and fifty-seven bacterial isolates were isolated from 62 Assam tea leaf samples collected from 6 provinces of Northern Thailand and classified within the phyla of Firmicutes, Actinobacteria, and Proteobacteria. Phayao and Phrae provinces exhibited the highest and the lowest bacterial diversities, respectively. The bacterial community structural pattern demonstrated significant differences between the west and the east sides. Since some Bacillus spp. have been reported to be involved in fermented Miang, Bacillus spp. isolated in this study were chosen for further elucidation. Bacillus siamensis ML122-2 exhibited a growth inhibitory effect against Staphylococcus aureus ATCC 25923 and MRSA DMST 20625, and the highest survival ability in simulated gastric and intestinal fluids (32.3 and 99.7%, respectively), autoaggregation (93.2%), cell surface hydrophobicity (50.0%), and bacterial adherence with Vero cells (75.8% of the control Lactiplantibacillusplantarum FM03-1). This B. siamensis ML122-2 is a promising probiotic to be used in the food industry and seems to have potential antibacterial properties relevant for the treatment of antibiotic-resistant infections.

Draft Genome Sequence of Corynebacterium aurimucosum UMB7769, Isolated from the Female Urinary Tract

Here, we present the draft genome sequence of Corynebacterium aurimucosum UMB7769, isolated from the female urinary tract. The size of the genome is 2,731,818 bp, assembled in 50 contigs, with an observed GC content of 60.9% and an N₅₀ score of 129,518 bp. Annotation revealed 31 antibiotic resistance genes.

Here, we present the draft genome sequence of Corynebacterium aurimucosum UMB7769, isolated from the female urinary tract. The size of the genome is 2,731,818 bp, assembled in 50 contigs, with an observed GC content of 60.9% and an N₅₀ score of 129,518 bp. Annotation revealed 31 antibiotic resistance genes.

A 'pathogenic needle' in a 'commensal haystack': Genetic virulence signatures of Corynebacterium glucuronolyticum that may drive its infectious propensity for the male urogenital system

The predominance of the genus Corynebacterium in the healthy male urogenital system contributes to the resident microbiome of not only the distal urethra, but potentially the proximal urethra and urinary bladder as well. However, for certain species in this genus, pathogenic potential was described, and the salient representative is Corynebacterium glucuronolyticum (C. glucuronolyticum) implicated in cases of urethritis and prostatitis in men. Nonetheless, some still question whether C. glucuronolyticum can actually be considered pathogenic or rather just a commensal species fortuitously isolated in patients with urogenital symptoms and/or syndromes. Although pathogen/commensal dichotomy is not always clear-cut, we hypothesize that specific genetic markers may expose C. glucuronolyticum as a convincingly pathogenic Corynebacterium. More specifically, characteristic pathogenic gene constellation inherent to this species (most notably the presence of specific sortase/SpaA-type pili gene clusters, but also the augmentative role of type VII secretion system) may significantly facilitate host tissue adhesion, with subsequent suppression/evasion of the immune response and acquisition of vitally important nutrients. Consequently, these genetic markers differentiate C. glucuronolyticum from its commensal counterparts, and give this species a pathogenic facet, which can be even further influenced by the Allee effect. In this paper we also propose a specific methodological approach on how to analyze C. glucuronolyticum epithelial colonization capacity and explore inceptive host cell-pathogen interactions that manipulate host environment and immune responses. This entails moving from approaches based primarily on overall homology of primary sequences towards specific structure-function studies to precisely evaluate all stakeholders involved in pili assemblage, cell adhesion and the expression of other virulence traits. In the era of high precision medicine, the hypothesized roles of C. glucuronolyticum adhesion systems in both virulence and nutrient acquisition may also reveal promising targets for future drug developments.

Insight of Genus Corynebacterium: Ascertaining the Role of Pathogenic and Non-pathogenic Species

This review gathers recent information about genomic and transcriptomic studies in the Corynebacterium genus, exploring, for example, prediction of pathogenicity islands and stress response in different pathogenic and non-pathogenic species. In addition, is described several phylogeny studies to Corynebacterium, exploring since the identification of species until biological speciation in one species belonging to the genus Corynebacterium. Important concepts associated with virulence highlighting the role of Pld protein and Tox gene. The adhesion, characteristic of virulence factor, was described using the sortase mechanism that is associated to anchorage to the cell wall. In addition, survival inside the host cell and some diseases, were too addressed for pathogenic corynebacteria, while important biochemical pathways and biotechnological applications retain the focus of this review for non-pathogenic corynebacteria. Concluding, this review broadly explores characteristics in genus Corynebacterium showing to have strong relevance inside the medical, veterinary, and biotechnology field.

Whole metagenome profiles of particulates collected from the International Space Station

BACKGROUND

The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized.

METHODS

This study examined the whole metagenome of ISS microbes at both species- and gene-level resolution. Air filter and dust samples from the ISS were analyzed and compared to samples collected in a terrestrial cleanroom environment. Furthermore, metagenome mining was carried out to characterize dominant, virulent, and novel microorganisms. The whole genome sequences of select cultivable strains isolated from these samples were extracted from the metagenome and compared.

RESULTS

Species-level composition in the ISS was found to be largely dominated by Corynebacterium ihumii GD7, with overall microbial diversity being lower in the ISS relative to the cleanroom samples. When examining detection of microbial genes relevant to human health such as antimicrobial resistance and virulence genes, it was found that a larger number of relevant gene categories were observed in the ISS relative to the cleanroom. Strain-level cross-sample comparisons were made for Corynebacterium, Bacillus, and Aspergillus showing possible distinctions in the dominant strain between samples.

CONCLUSION

Species-level analyses demonstrated distinct differences between the ISS and cleanroom samples, indicating that the cleanroom population is not necessarily reflective of space habitation environments. The overall population of viable microorganisms and the functional diversity inherent to this unique closed environment are of critical interest with respect to future space habitation. Observations and studies such as these will be important to evaluating the conditions required for long-term health of human occupants in such environments.

Metagenomics analysis of red blood cell and fresh-frozen plasma units

BACKGROUND

Although the risk of transmitting infectious agents by blood transfusion is dramatically reduced after donor selection, leukoreduction, and laboratory testing, some could still be present in donor's blood. A description of metagenomes in blood products eligible for transfusion represents relevant information to evaluate the risk of pathogen transmission by transfusion.

STUDY DESIGN AND METHODS

Detection of viruses, bacteria, and fungi genomes was made by high-throughput sequencing (HTS) of 600 manufactured blood products eligible for transfusion: 300 red blood cell (RBC) and 300 fresh-frozen plasma (FFP) units.

RESULTS

Anelloviruses and human pegivirus, frequent in the blood of healthy individuals, were found. Human papillomavirus type 27 and Merkel cell polyomavirus, present on the skin, were also detected. Unexpectedly, astrovirus MLB2 was identified and characterized in a FFP unit. The presence of astrovirus MLB2 was confirmed in donor's blood and corresponded to an asymptomatic acute viremia. Sequences of bacteria and fungi were also detected; they are likely the result of environmental contamination.

CONCLUSION

This study demonstrates that HTS is a promising tool for detecting common and less frequent infectious pathogens in blood products.

Clinical Significance of Commensal Gram-Positive Rods Routinely Isolated from Patient Samples

Commensal bacteria from the skin and mucosal surfaces are routinely isolated from patient samples and considered contaminants. The majority of these isolates are catalase-positive Gram-positive rods from multiple genera routinely classified as diphtheroids. These organisms can be seen upon Gram staining of clinical specimens or can be isolated as the predominant or pure species in culture, raising a priori suspicion of a possible involvement in infection. With the development and adoption of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), suspicious isolates are now routinely identified to the species level. In this study, we performed a retrospective data review (2012 to 2015) and utilized site-specific laboratory criteria and chart reviews to identify species within the diphtheroid classification representative of true infection versus contamination. Our data set included 762 isolates from 13 genera constituting 41 bacterial species. Only 18% represented true infection, and 82% were deemed contaminants. Clinically significant isolates were identified in anaerobic wounds (18%), aerobic wounds (30%), blood (5.5%), urine (22%), cerebrospinal fluid (24%), ophthalmologic cultures (8%), and sterile sites (20%). Organisms deemed clinically significant included multiple Actinomyces species in wounds, Propionibacterium species in joints and cerebrospinal fluid associated with central nervous system hardware, Corynebacterium kroppenstedtii (100%) in breast, and Corynebacterium striatum in multiple sites. Novel findings include clinically significant urinary tract infections by Actinomyces neuii (21%) and Corynebacterium aurimucosum (21%). Taken together, these findings indicate that species-level identification of diphtheroids isolated with a priori suspicion of infection is essential to accurately determine whether an isolate belongs to a species associated with specific types of infection.