Role of Tsukamurella species in human infections: first literature review

Mucosal infection with Tsukamurella species following nasal septum procedure: a rare case report

Introduction and importance

Tsukamurella species are rare, aerobic, gram-positive bacteria known to cause infections, primarily in immunocompromised individuals. This case report presents a rare instance of a mucosal infection caused by Tsukamurella species following a nasal septum procedure in an immunocompetent patient.

Case presentation

A 51-year-old man with a history of multiple hereditary exostosis, allergic rhinitis, and recent nasal fracture repair presented with persistent fevers and low back pain. Postoperatively, he developed sinus pain and small oral lesions, initially treated with antibiotics for presumed sinusitis. Despite treatment, his fever persisted, leading to an emergency department visit. Laboratory tests indicated sepsis, but a CT scan of the sinuses showed no sinusitis. Despite broad-spectrum antibiotics, the patient's fever continued. On admission day 9, nasal endoscopy and culture identified Tsukamurella species. The patient was treated with augmentin, fluconazole, and levofloxacin, leading to the resolution of symptoms and discharge with ongoing treatment.

Clinical discussion

Tsukamurella species are uncommon pathogens that are often associated with bacteremia in immunocompromised individuals. This case highlights the diagnostic challenges and the importance of considering unusual pathogens in postprocedural infections, even in immunocompetent patients. Accurate identification and appropriate management are critical in improving outcomes for patients with Tsukamurella infections.

Conclusion

This case underscores the need for vigilance in diagnosing rare infections like Tsukamurella, even in immunocompetent individuals. The successful resolution with combination therapy highlights the importance of appropriate antibiotic selection in managing such infections.

A Case Report of a Rare Pulmonary Opportunistic Infection in an Infant Caused by Tsukamurella tyrosinosolvens

This case report describes the case of a female infant hospitalized for severe pneumonia. During the treatment process, various antibiotics are used to treat and prevent further infection. The child had a weak physical condition, combined with neuroblastoma, paraneoplastic syndrome, and low immune function, leading to Tsukamurella tyrosinosolvens infection. The treatment was eventually abandoned owing to poor prognosis. This study aims to through the medium, dyeing, electron microscope observation, 16s rRNA and high-throughput sequencing investigated the morphological characteristics, staining properties, electron microscope morphology, antibiotic resistance, and genomic characteristics of Tsukamurella tyrosinosolvens. The aim of the study is to provide data reference for clinical laboratory staff in bacteria identification research, and to provide relevant help for clinicians in diagnosis and treatment.

Tsukamurella Bacteremia in a Surgical Patient: Case Report and Review of the Literature

Background: Tsukamurella species were first isolated in 1941. Since then, 48 cases of Tsukamurella bacteremia have been reported, a majority of which were immunosuppressed patients with central venous catheters.A case is described and previous cases of Tsukamurella bacteremia are reviewed. Patients and Methods: A 70-year-old total parenteral nutrition (TPN)-dependent female with recurrent enterocutaneous fistula (ECF), developed leukocytosis one week after a challenging ECF takedown. After starting broad-spectrum antibiotic agents, undergoing percutaneous drainage of intra-abdominal abscess, and subsequent repositioning of the drain, her leukocytosis resolved. Blood and peripherally inserted central catheter (PICC) cultures grew Tsukamurella spp. The patient was discharged to home with 14 days of daily 2 g ceftriaxone, with resolution of bacteremia. Conclusions: Tsukamurella spp. are a rare opportunistic pathogen predominantly affecting immunocompromised patients, with central venous catheters present in most cases. However, there have been few reported cases in immunocompetent individuals with predisposing conditions such as end-stage renal disease and uncontrolled diabetes mellitus.

Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach

Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.

Systematic investigation of the emerging pathogen of Tsukamurella species in a Chinese tertiary teaching hospital

Tsukamurella species have been clinically regarded as rare but emerging opportunistic pathogens causing various infections in humans. Tsukamurella pneumonia has often been misdiagnosed as pulmonary tuberculosis due to its clinical presentation resembling tuberculosis-like syndromes. Tsukamurella species have also been confused in the laboratory with other phylogenetic bacteria, such as Gordonia. This study aimed to investigate the clinical, microbiological, and molecular characteristics; species distribution; and antimicrobial susceptibility of Tsukamurella species. Immunodeficiency and chronic pulmonary disease appeared to be risk factors for Tsukamurella pneumonia, and the presence of bronchiectasis and pulmonary nodules on imaging was highly correlated with this infection. The study confirmed that groEL (heat shock protein 60) and secA (the secretion ATPase) genes are reliable for identifying Tsukamurella species. Additionally, the ssrA (stable small RNA) gene showed promise as a tool for discriminating between different Tsukamurella species with the shortest sequence length. In terms of antimicrobial susceptibility, quinolones, trimethoprim/sulfamethoxazole, amikacin, minocycline, linezolid, and tigecycline demonstrated potent in vitro activity against Tsukamurella isolates in our study. The study also proposed a resistance mechanism involving a substitution (S91R) within the quinolone-resistance-determining region of the gyrA gene, which confers resistance to levofloxacin and ciprofloxacin. Furthermore, we found that disk diffusion testing is not suitable for testing the susceptibilities of Tsukamurella isolates to ciprofloxacin, imipenem, and minocycline. In conclusion, our systematic investigation may contribute to a better understanding of this rare pathogen. Tsukamurella species are rare but emerging human pathogens that share remarkable similarities with other mycolic acid-containing genera of the order Actinomycetales, especially Mycobacterium tuberculosis. Consequently, misdiagnosis and therapeutic failures can occur in clinical settings. Despite the significance of accurate identification, antimicrobial susceptibility, and understanding the resistance mechanism of this important genus, our knowledge in these areas remains fragmentary and incomplete. In this study, we aimed to address these gaps by investigating promising identification methods, the antimicrobial susceptibility patterns, and a novel quinolone resistance mechanism in Tsukamurella species, utilizing a collection of clinical isolates. The findings of our study will contribute to improve diagnosis and successful management of infections caused by Tsukamurella species, as well as establishing well-defined performance and interpretive criteria for antimicrobial susceptibility testing.

Catheter-related bloodstream infection caused by Tsukamurella tyrosinosolvens identified by secA1sequencing in an immunocompromised child: a case report

BACKGROUND

Tsukamurella spp. are obligate aerobic, gram-positive, non-motile, and slightly acid-fast bacilli belonging to the Actinomycetes family. They share many characteristics with Nocardia, Rhodococcus, Gordonia, and the rapidly growing Mycobacterium species. Therefore, standard testing may misidentify Tsukamurella spp. as another species. Accurate and rapid diagnosis is critical for proper infection management, but identification of this bacterium is difficult in the standard laboratory setting.

CASE PRESENTATION

A bloodstream infection caused by a gram-positive bacterium and related to a central venous catheter was identified in an immunocompromised 2-year-old girl. Tsukamurella tyrosinosolvens was identified by modified secA1 sequencing. Antibiotic treatment and removal of the central venous catheter resolved the infection. Inappropriate management of the catheter during an overnight stay outside of the hospital was considered as a possible source of infection.

CONCLUSIONS

SecA1 sequencing may be a useful diagnostic tool in the identification of T. tyrosinosolvens. Providing proper central venous catheter care instructions to patients, their families, and medical staff is important for infection prevention.

Biochemical, Catabolic, and PGP Activity of Microbial Communities and Bacterial Strains from the Root Zone of Baccharis linearis in a Mediterranean Mine Tailing

The management of mine tailings (MT) is commonly workload heavy, intrusive, and expensive. Phytostabilization offers a promising approach for MT management; however, it poses challenges due to the unfavorable physicochemical properties of these wastes. Nevertheless, native microorganisms capable of supporting plant growth and development could enhance the efficacy of phytostabilization. This study assesses the biological activity of microbial communities from the root zone of Baccharis linearis, which is naturally present in MT, in order to evaluate their biotechnological potential for phytostabilization. The root zone and bulk samples were collected from B. linearis plants located within a MT in the Mediterranean zone of Chile. Enzyme activities related to the cycling of C, N, and P were assessed. The community-level physiological profile was evaluated using the MicroRespTM system. Bacterial plant growth-promoting (PGP) traits and colony forming units (CFU) were evaluated through qualitative and microbiological methods, respectively. CFU, enzyme activities, and CLPP were higher in the root zone compared with the bulk samples. Five bacterial strains from the root zone exhibited PGP traits such as P solubilization and N acquisition, among others. The presence of microbial communities in the root zone of B. linearis with PGP traits suggests their potential to enhance the ecological management of MT through phytostabilization programs.

A Pediatric Case of Septic Pulmonary Embolism Caused by Tsukamurella paurometabola

We herein report a three-year-old boy with septic pulmonary embolism caused by Tsukamurella paurometabola bacteremia during chemotherapy for rhabdomyosarcoma. During the interval of chemotherapy, the patient was temporarily discharged with a peripherally inserted central venous catheter but was re-admitted to the hospital with a fever on the same day. A blood culture taken at the time of re-admission showed T. paurometabola. The patient had a persistent fever, and computed tomography performed on the ninth day showed septic pulmonary embolism. We stress the importance of being aware of the possibility of septic pulmonary embolism in patients with Tsukamurella bacteremia.

The Re-Identification of Previously Unidentifiable Clinical Non-Tuberculous Mycobacterial Isolates Shows Great Species Diversity and the Presence of Other Acid-Fast Genera

Non-tuberculous mycobacteria that cannot be identified at the species level represent a challenge for clinical laboratories, as proper species assignment is key to implementing successful treatments or epidemiological studies. We re-identified forty-eight isolates of Ziehl-Neelsen (ZN)-staining-positive "acid-fast bacilli" (AFB), which were isolated in a clinical laboratory and previously identified as Mycobacterium species but were unidentifiable at the species level with the hsp65 PCR restriction fragment length polymorphism analysis (PRA). As most isolates also could not be identified confidently via 16S, hsp65, or rpoB DNA sequencing and a nBLAST search analysis, we employed a phylogenetic method for their identification using the sequences of the 16S rDNA, which resulted in the identification of most AFB and a Mycobacterium species diversity not found before in our laboratory. Most were rare species with only a few clinical reports. Moreover, although selected with the ZN staining as AFB, not all isolates belonged to the genus Mycobacterium, and we report for the first time in Latin America the isolation of Nocardia puris, Tsukamurella pulmosis, and Gordonia sputi from sputum samples of symptomatic patients. We conclude that ZN staining does not differentiate between the genus Mycobacterium and other genera of AFB. Moreover, there is a need for a simple and more accurate tree-based identification method for mycobacterial species. For this purpose, and in development in our lab, is a web-based identification system using a phylogenetic analysis (including all AFB genera) based on 16S rDNA sequences (and in the future multigene datasets) and the closest relatives.

Morganella Phage Mecenats66 Utilizes an Evolutionarily Distinct Subtype of Headful Genome Packaging with a Preferred Packaging Initiation Site

Both recognized species from the genus Morganella (M. morganii and M. psychrotolerans) are Gram-negative facultative anaerobic rod-shaped bacteria that have been documented as sometimes being implicated in human disease. Complete genomes of seven Morganella-infecting phages are publicly available today. Here, we report on the genomic characterization of an insect associated Morganella sp. phage, which we named Mecenats66, isolated from dead worker honeybees. Phage Mecenats66 was propagated, purified, and subjected to whole-genome sequencing with subsequent complete genome annotation. After the genome de novo assembly, it was noted that Mecenats66 might employ a headful packaging with a preferred packaging initiation site, although its terminase amino acid sequence did not fall within any of the currently recognized headful packaging subtype employing phage (that had their packaging strategy experimentally verified) with clusters on a terminase sequence phylogenetic tree. The in silico predicted packaging strategy was verified experimentally, validating the packaging initiation site and suggesting that Mecenats66 represents an evolutionarily distinct headful genome packaging with a preferred packaging initiation site strategy subtype. These findings can possibly be attributed to several of the phages already found within the public biological sequence repositories and could aid newly isolated phage packaging strategy predictions in the future.

Obligate aerobic, gram-positive, weak acid-fast, nonmotile bacilli, Tsukamurella tyrosinosolvens: Minireview of a rare opportunistic pathogen

Tsukamurella species are obligate aerobic, gram-positive, weak acid-fast, nonmotile bacilli. They are found in various environments, such as soil, water, sludge, and petroleum reservoir wastewater, and belong to the order Actinomycetales. In 2016, there was a reclassification of species within the genus Tsukamurella, merging the species Tsukamurella tyrosinosolvens (T. tyrosinosolvens) and Tsukamurella carboxydivorans. Tsukamurella species are clinically considered to be a rare opportunistic pathogen, because most reported cases have been related to bacteremia and intravascular prosthetic devices and immunosuppression. To date, it has been isolated only from human specimens, and has always been associated with clinical disease; human infections are very rare. Reported infections have included pneumonia, brain abscesses, catheter-related bloodstream infections, ocular infections, bacteremia, and sepsis presenting with septic pulmonary emboli in patients who are immunocompromised. To date, there is no commercially available test for identification. On the other hand, sequence-based identification, including matrix-assisted laser desorption ionization time-of-flight mass spectrometry, is an alternative method for identifying clinical isolates that are either slow growers or difficult to identify through biochemical profiling. The golden standards for diagnosis and optimal management still remain to be determined. However, newer molecular biological techniques can provide accurate identification, and contribute to the appropriate selection of definitive therapy for infections caused by this organism. Combinations of several antimicrobial agents have been proposed for treatment, though the length of treatment for infections has yet to be determined, and should be individualized according to clinical response. Immunocompromised patients often experience severe cases due to infection, and life-threatening T. tyrosinosolvens events associated with dissemination and/or failure of source control have occurred. Favorable prognoses can be achieved through earlier identification of the cause of infection, as well as successful management, including appropriate antibiotic therapy together with source control. Further analyses of similar cases are required to establish the most adequate diagnostic methods and treatment regimens for infections.

A taxonomically representative strain collection to explore xenobiotic and secondary metabolism in bacteria

Bacteria employ secondary metabolism to combat competitors, and xenobiotic metabolism to survive their chemical environment. This project has aimed to introduce a bacterial collection enabling comprehensive comparative investigations of those functions. The collection comprises 120 strains (Proteobacteria, Actinobacteria and Firmicutes), and was compiled on the basis of the broad taxonomic range of isolates and their postulated biosynthetic and/or xenobiotic detoxification capabilities. The utility of the collection was demonstrated in two ways: first, by performing 5144 co-cultures, recording inhibition between isolates and employing bioinformatics to predict biosynthetic gene clusters in sequenced genomes of species; second, by screening for xenobiotic sensitivity of isolates against 2-benzoxazolinone and 2-aminophenol. The co-culture medium of Bacillus siamensis D9 and Lysinibacillus sphaericus DSM 28^T was further analysed for possible antimicrobial compounds, using liquid chromatography-mass spectrometry (LC-MS), and guided by computational predictions and the literature. Finally, LC-MS analysis demonstrated N-acetylation of 3,4-dichloroaniline (a toxic pesticide residue of concern) by the actinobacterium Tsukamurella paurometabola DSM 20162^T which is highly tolerant of the xenobiotic. Microbial collections enable "pipeline" comparative screening of strains: on the one hand, bacterial co-culture is a promising approach for antibiotic discovery; on the other hand, bioremediation is effective in combating pollution, but requires knowledge of microbial xenobiotic metabolism. The presented outcomes are anticipated to pave the way for studies that may identify bacterial strains and/or metabolites of merit in biotechnological applications.

Bacterial Peritonitis Caused by Tsukamurella inchonensis in a Patient Undergoing Continuous Ambulatory Peritoneal Dialysis

Background

Tsukamurella is an environmental saprophyte that potentially causes various infections in humans. It has been reported to cause rare opportunistic infections in immunocompromised patients or patients with indwelling foreign bodies.

Case Presentation

We report a case of continuous ambulatory peritoneal dialysis (CAPD)-related peritonitis caused by Tsukamurella inchonensis (T. inchonensis). The patient was admitted to our hospital while demonstrating a cloudy peritoneal dialysate. Peritoneal fluid sample culturing yielded yellow-greyish, dry and membrane-like colonies. Gram staining showed straight, gram-positive rods. The organism was identified to be Tsukamurella species by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). It was then characterized to be homologous to T. inchonensis in the GenBank database by 16S Ribosomal RNA Sequencing. The strain was susceptible to quinolones, carbapenems and linezolid, but intermediately resistant to vancomycin in drug susceptibility testing. Eventually, the peritonitis was controlled with meropenem and the patient discharged from the hospital.

Conclusion

Here, we describe the first case of CAPD-related peritonitis caused by T. inchonensis in China. Importantly, T. inchonensis show resistance to cephalosporins and heterogeneous resistance to vancomycin, guideline-based empiric therapy occasionally fails. Further analyses of similar cases are required to understand the characteristics and formulate appropriate therapy regimen for T. inchonensis infections.

Tsukamurella inchonensis Isolated from Catheter of an Ecuadorian Patient with Hemodialysis

We report a case of catheter-related bloodstream infection by Tsukamurella inchonensis, identified using 16S rRNA gene sequencing, in a patient with arterial hypertension for 20 years and chronic kidney disease in hemodialysis since 08/07/2019. To our knowledge, this is the first case of T. inchonensis in Ecuador.

Catheter-related bloodstream infection caused by Tsukamurella ocularis: A case report

Tsukamurella spp. causes mainly bacteremia and central venous catheter-related bloodstream infections. To the best of our knowledge, there is no documented evidence that Tsukamurella ocularis causes catheter-related bloodstream infections like other species of Tsukamurella. We present a novel case of T. ocularis bacteremia in a 69-year-old woman with malignant cancer, wherein the patient was successfully treated with a peripherally inserted central venous catheter. We administered combination antimicrobial therapy to the patient, which was terminated only after confirming the absence of infection. We identified T. ocularis by sequencing three housekeeping genes that could not be identified using conventional mass spectrometry and 16S rRNA gene analysis.

Identification of a phosphorus-solubilizing Tsukamurella tyrosinosolvens strain and its effect on the bacterial diversity of the rhizosphere soil of peanuts growth-promoting

Phosphate solubilizing microorganisms widely exist in plant rhizosphere soil, but report about the P solubilization and multiple growth-promoting properties of rare actinomycetes are scarce. In this paper, a phosphate solubilizing Tsukamurella tyrosinosolvens P9 strain was isolated from the rhizosphere soil of tea plants. Phosphorus-dissolving abilities of this strain were different under different carbon and nitrogen sources, the soluble phosphorus content was 442.41 mg/L with glucose and potassium nitrate as nutrient sources. The secretion of various organic acids, such as lactic acid, maleic acid, oxalic acid, etc., was the main mechanism for P solubilization and pH value in culture was very significant negative correlation with soluble P content. In addition, this strain had multiple growth-promoting characteristics with 37.26 μg/mL of IAA and 72.01% of siderophore relative content. Under pot experiments, P9 strain improved obviously the growth of peanut seedlings. The bacterial communities of peanut rhizoshpere soil were assessed after inoculated with P9 strain. It showed that there was no significant difference in alpha-diversity indices between the inoculation and control groups, but the P9 treatment group changed the composition of bacterial communities, which increased the relative abundance of beneficial and functional microbes, which relative abundances of Chitinophagaceae at the family level, and of Flavihumibacter, Ramlibacter and Microvirga at the genus level, were all siginificant increased. Specially, Tsukamurella tyrosinosolvens were only detected in the rhizosphere of the inoculated group. This study not only founded growth-promoting properties of T. tyrosinosolvens P9 strain and its possible phosphate solublizing mechanism, but also expected to afford an excellent strain resource in biological fertilizers.

Role of Williamsia and Segniliparus in human infections with the approach taxonomy, cultivation, and identification methods

The genera Williamsia and Segniliparus are of aerobic actinomycetes and at the time of writing, they have 12 and 2 species, respectively. These genera cause various infections in humans. In this review, we surveyed their taxonomy, isolation, identification, as well as their role to cause human infections.

Tsukamurella pulmonis conjunctivitis in patients with an underlying nasolacrimal duct obstruction - report of two cases

Tsukamurella pulmonis (Actinobacteria), a Gram-positive, obligate aerobic and weakly or variably acid-fast bacterium, is an opportunistic pathogen. Here we report two cases of conjunctivitis caused by T. pulmonis. Both patients had a previous history of nasolacrimal duct obstruction (NLDO). Isolation of T. pulmonis was performed on chocolate, tryptic soy blood and Columbia nalidixic agars. After 24 h of incubation, odourless, white-greyish, membrane-like colonies were observed. The VITEK-2 bacterial identifier system failed to identify the species, while Vitek-MS matrix-assisted laser desorption ionization time-of-flight technology, successfully identified the isolate from case 2 but not from case 1. Final identification was verified using 16S rRNA gene sequencing. An antibiogram was performed and according to the results cefazoline in addition to vancomycin eye drops for 5 days, were suggested as a treatment in case 1. In case 2 the infection was ended without treatment. This is the first report of Tsukamurella as a pathogen that causes conjunctivitis in patients with NLDO.

Septic pulmonary emboli caused by Tsukamurella inchonensis: A case report

The genus Tsukamurella is a fastidious, environmental organism that potentially causes various infections in humans. Due to the morphological and biochemical similarities to others pathogens, such as Gordona, Rhodococcus, Corynebacterium, Nocardia, and Mycobacterium, a molecular-based approach is indispensable to correctly identify them. Herein, we describe a case of Tsukamurella inchonensis bacteremia complicated with septic pulmonary emboli (SPE), which is the first in the literature. A 44-year-old Japanese woman diagnosed with tongue cancer had undergone partial tongue resection. While receiving chemotherapy and radiotherapy, she developed high fever. Chest computed tomography suggested multiple emboli at the bilateral, peripheral lungs, indicating SPE. Blood culture detected Gram-positive rods, to which matrix-assisted laser desorption/ionization-time of flight mass spectrometry failed to identify. Then, we attempted to characterize it by 16S rRNA sequence, which suggested the organism to be Tsukamurella species but resulted in low resonance of the species-level identification. Additionally, we employed a confidence gene targeting groEL, leading to 100% matching (753/753 bps) with T. inchonensis NCTC 10741 (GenBank accession no. LR131273.1), which has been incorrectly registered as wrong species name Tsukamurella paurometabola in the database. Under the diagnosis of T. inchonensis-associated SPE, we successfully treated the patient with imipenem/cilastatin administration for 4 weeks. Sequencing analysis of groEL was of great use in identifying the organism in this case. More clinical cases based on molecular diagnosis of the fastidious pathogens need to be accumulated to further understand the characteristics and appropriate treatment regimen.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Tsukamurella pulmonis central venous catheter infection mimicking proteinase 3-antineutrophil cytoplasmic antibody (PR3-ANCA)-associated vasculitis

A 40-year-old Japanese woman, who underwent total thyroidectomy, had suffered from repeated episodes of fever and microscopic hematuria for 3 years, which had started 3 months after central venous port catheter insertion. On admission, she had malaise and low-grade fever, and was found to have microscopic hematuria, urinary red blood cell casts, multiple pulmonary nodules, and positivity of proteinase 3-anti-neutrophil cytoplasmic antibody (PR3-ANCA), which were suggestive to the presence of ANCA-associated small vessel vasculitis. However, her blood culture and subsequent gene analysis revealed the positivity of Tsukamurella pulmonis, and she was diagnosed with Tsukamurella pulmonis bacteremia accompanying PR3-ANCA positivity. Her condition improved after the removal of the catheter and antibiotic treatment. Tsukamurella species are categorized to the order Actinomycetales and can be misidentified as other Actinomycetales without genetic analyses. This case illustrates that chronic Tsukamurella pulmonis infection can cause ANCA production and nephritis, which mimics ANCA-associated vasculitis. Thus, it is critical to diagnose these cases correctly to avoid misdiagnosis and inappropriate treatment, such as immunosuppressive treatment.

First report of Tsukamurella endocarditis in an immunocompromised patient receiving chemotherapy

Tsukamurella spp. are gram-positive rods that can be isolated from the environment in soil and moist areas. In rare instances, they are known to cause infections in immunocompromised hosts. We present the first reported case of Tsukamurella endocarditis in an immunocompromised patient who was successfully treated with a 6-week course of imipenem and trimethoprim-sulfamethoxazole.

[Rare species in the structure of acid-resistent members of the order Actinomycetales isolated from clinical material.]

The article presents data on the structure of acid-resistant members of the order Actinomycetales and rare species that have been isolated and identified using various methods. The study included strains of non-tuberculous mycobacteria (NTM) isolated from clinical material during examination for tuberculosis in the period from 2016 to 2019. The total number of samples with signs of NTMs growth that were included in the study was 316 samples. Primary isolation on Levenshtein-Jensen, Finn II, and MGIT media and NTMs identification by DNA-hybridization. All strains that were not identified prior to the species and culture, identified as microorganisms with a high G+C content (High GC GR +) were re-identified using a MALDI-ToF Microflex LT mass spectrometer (Bruker®). By the method of DNA-hybridization, 188 strains isolated by NTM were successfully identified to form 58.5% of all selected cultures. Among the selected species, representatives of slowly growing NTMs (M. avium complex, M. gordonae, M. kansasii) predominated, which amounted to 67.0% of all NTM strains identified to the species. Among the cultures for which DNA hybridization failed to carry out acceptable identification, predominantly NTMs were found, among which M. gordonae, M. avium, M. kansasii dominated. A number of NTMs were represented by rare species: M. iranicum and M. pseudoshottsii. Among this group of microorganisms, other acid-resistant aerobic actinomycetes were isolated, including those of potential clinical significance: Gordonia spp., Tsukamurella spp., Rhodococcus spp., Nocardia spp. When identifying cultures containing high concentrations of G+C, the maximum number of microbial associations was revealed, including those consisting of two types of NTMs (M. monacense + M. flavescens, M. avium + M. kansasii), as well as associations of M. gordonae with staphylococci. The same group included rare NTM species: M. fredericbergense, M. szulgai, M. malmoense, M. bohemicum, M. septicum, as well as representatives of the genera Nocardia, Gordonia, Tsukamurella.

Ophthalmic Manifestation of Tsukamurella Species: A Case Series and First Report of Ocular Implant Infection After Enucleation

PURPOSE

Tsukamurella is an important and emerging organism that causes opportunistic human infection. We present the largest case series of Tsukamurella species-associated ophthalmic infections, with an emphasis on clinical spectrum, risk factors, treatment, and outcome.

METHODS

A case series of culture-positive Tsukamurella species in ocular microbiological specimens was identified retrospectively from 2005 to 2018. Tsukamurella species were identified by phenotypic, molecular, and genotypic methods. Diagnoses were clinical and were supplemented by microbiological findings. Treatment including antibiotic type, number of antibiotics, treatment duration, and clinical outcome was documented.

RESULTS

Eleven cases of culture-positive Tsukamurella ocular infection were identified. Of these 54.5% (6/11) of cases resulted in conjunctivitis, 18% (2/11) of cases resulted in keratitis, and 9% (1/11) of cases resulted in blepharitis. One case of canaliculitis and 1 case of postenucleation ocular implant-related infection were reported, which were both novel findings. The presence of ocular implant and preexisting ocular surface diseases such as exposure keratopathy and ectropion were thought to be predisposing factors. We have demonstrated that treatment of Tsukamurella ocular conjunctivitis, keratitis, and blepharitis was effective using a combination therapy of 2 antibiotics (fluoroquinolone, fusidic acid, or chloramphenicol). Canaliculitis and ocular implant infection required further addition of oral antibiotics (macrolide or doxycycline), canaliculotomy, and removal of the infected implant for satisfactory management.

CONCLUSIONS

Tsukamurella tyrosinosolvens and Tsukamurella pulmonis were found to be the predominant species that caused ocular infection. Ocular manifestation of Tsukamurella has a wider spectrum than that previously reported. A high-level of suspicion and a low threshold for microbiological sampling in cases with prolonged ocular surface infection are recommended to diagnose Tsukamurella infections.

The actinobacterium Tsukamurella paurometabola has a functionally divergent arylamine N-acetyltransferase (NAT) homolog

Actinobacteria in the Tsukamurella genus are aerobic, high-GC, Gram-positive mycolata, considered as opportunistic pathogens and isolated from various environmental sources, including sites contaminated with oil, urban or industrial waste and pesticides. Although studies look into xenobiotic biotransformation by Tsukamurella isolates, the relevant enzymes remain uncharacterized. We investigated the arylamine N-acetyltransferase (NAT) enzyme family, known for its role in the xenobiotic metabolism of prokaryotes and eukaryotes. Xenobiotic sensitivity of Tsukamurella paurometabola type strain DSM 20162^T was assessed, followed by cloning, recombinant expression and functional characterization of its single NAT homolog (TSUPD)NAT1. The bacterium appeared quite robust against chloroanilines, but more sensitive to 4-anisidine and 2-aminophenol. However, metabolic activity was not evident towards those compounds, presumably due to mechanisms protecting cells from xenobiotic entry. Of the pharmaceutical arylhydrazines tested, hydralazine was toxic, but the bacterium was less sensitive to isoniazid, a drug targeting mycolic acid biosynthesis in mycobacteria. Although (TSUPD)NAT1 protein has an atypical Cys-His-Glu (instead of the expected Cys-His-Asp) catalytic triad, it is enzymatically active, suggesting that this deviation is likely due to evolutionary adaptation potentially serving a different function. The protein was indeed found to use malonyl-CoA, instead of the archetypal acetyl-CoA, as its preferred donor substrate. Malonyl-CoA is important for microbial biosynthesis of fatty acids (including mycolic acids) and polyketide chains, and the corresponding enzymatic systems have common evolutionary histories, also linked to xenobiotic metabolism. This study adds to accummulating evidence suggesting broad phylogenetic and functional divergence of microbial NAT enzymes that goes beyond xenobiotic metabolism and merits investigation.

Antibiotic resistance genes in the Actinobacteria phylum

The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.

Commensal and Pathogenic Members of the Dental Calculus Microbiome of Badia Pozzeveri Individuals from the 11th to 19th Centuries

The concept of the human oral microbiome was applied to understand health and disease, lifestyles, and dietary habits throughout part of human history. In the present study, we augment the understanding of ancient oral microbiomes by characterizing human dental calculus samples recovered from the ancient Abbey of Badia Pozzeveri (central Italy), with differences in socioeconomic status, time period, burial type, and sex. Samples dating from the Middle Ages (11th century) to the Industrial Revolution era (19th century) were characterized using high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. Consistent with previous studies, individuals from Badia Pozzeveri possessed commensal oral bacteria that resembled modern oral microbiomes. These results suggest that members of the oral microbiome are ubiquitous despite differences in geographical regions, time period, sex, and socioeconomic status. The presence of fecal bacteria could be in agreement with poor hygiene practices, consistent with the time period. Respiratory tract, nosocomial, and other rare pathogens detected in the dental calculus samples are intriguing and could suggest subject-specific comorbidities that could be reflected in the oral microbiome.

Pyrosequencing Uncovers a Shift in Bacterial Communities Across Life Stages of Octodonta nipae (Coleoptera: Chrysomelidae)

Bacterial symbionts of insects affect a wide array of host traits including fitness and immunity. Octodonta nipae (Maulik), commonly known as hispid leaf beetle is a destructive palm pest around the world. Understanding the dynamics of microbiota is essential to unravel the complex interplay between O. nipae and its bacterial symbionts. In this study, bacterial 16S rRNA V3-V4 region was targeted to decipher the diversity and dynamics of bacterial symbionts across different life stages [eggs, larvae, pupae, and adult (male and female)] and reproductive organs (ovaries and testis) of O. nipae. Clustering analysis at ≥97% similarity threshold produced 3,959 operational taxonomic units (OTUs) that belonged to nine different phyla. Proteobacteria, Actinobacteria, and Firmicutes represented the bulk of taxa that underwent notable changes during metamorphosis. Enterobacteriaceae and Dermabacteraceae were the most abundant families in immature stages (eggs, larvae, and pupae), while Anaplasmataceae family was dominated in adults (male and female) and reproductive organs (ovaries and testis). The genus Serratia and Lactococcus were most abundant in eggs, whereas Pantoea and Brachybacterium represented the bulk of larvae and pupae microbiota. Interestingly the genus Wolbachia found positive to all tested samples and was recorded extremely high (>64%) in the adults and reproductive organs. The bacteria varied across the developmental stages and responsible for various metabolic activities. Selection choice exerted by the insect host as a result of its age or developmental stage could be the main reason to ascertain the shift in the bacteria populations. Maternally inherited Wolbachia was found to be an obligate endosymbiont infecting all tested life stages, body parts, and tissues. These outcomes foster our understanding of the intricate associations between bacteria and O. nipae and will incorporate in devising novel pest control strategies against this palm pest.

Structure and role for active site lid of lactate monooxygenase from Mycobacterium smegmatis

Lactate monooxygenase (LMO) catalyzes the FMN-dependent "coupled" oxidation of lactate and O₂ to acetate, carbon dioxide, and water, involving pyruvate and hydrogen peroxide as enzyme-bound intermediates. Other α-hydroxy acid oxidase family members follow an "uncoupled pathway," wherein the α-keto acid product quickly dissociates before the reduced flavin reacts with oxygen. Here, we report the structures of Mycobacterium smegmatis wild-type LMO and a wild-type-like C203A variant at 2.1 Å and 1.7 Å resolution, respectively. The overall LMO fold and active site organization, including a bound sulfate mimicking substrate, resemble those of other α-hydroxy acid oxidases. Based on structural similarity, LMO is similarly distant from lactate oxidase, glycolate oxidase, mandelate dehydrogenase, and flavocytochrome b₂ and is the first representative enzyme of its type. Comparisons with other α-hydroxy acid oxidases reveal that LMO has a longer and more compact folded active site loop (Loop 4), which is known in related flavoenzymes to undergo order/disorder transitions to allow substrate/product binding and release. We propose that LMO's Loop 4 has an enhanced stability that is responsible for the slow product release requisite for the coupled pathway. We also note electrostatic features of the LMO active site that promote substrate binding. Whereas the physiological role of LMO remains unknown, we document what can currently be assessed of LMO's distribution in nature, including its unexpected occurrence, presumably through horizontal gene transfer, in halophilic archaea and in a limited group of fungi of the genus Beauveria. BROAD STATEMENT OF IMPACT: This first crystal structure of the FMN-dependent α-hydroxy acid oxidase family member lactate monooxygenase (LMO) reveals it has a uniquely large active site lid that we hypothesize is stable enough to explain the slow dissociation of pyruvate that leads to its "coupled" oxidation of lactate and O₂ to produce acetate, carbon dioxide, and water. Also, the relatively widespread distribution of putative LMOs supports their importance and provides new motivation for their further study.