MALDI-TOF MS for identification of Tsukamurella species: Tsukamurella tyrosinosolvens as the predominant species associated with ocular infections

Mycolyltransferase is important for biofilm formation and pathogenesis of Tsukamurella keratitis

Tsukamurella, a group of multi-drug resistant, Gram-positive, aerobic, and partially acid-fast bacteria, are emerging causes of bacterial conjunctivitis and keratitis. However, the pathogenesis of Tsukamurella keratitis is largely unknown. To address this, we used New Zealand White rabbits to develop the first eye infection model and conducted in vitro tests to study the pathogenesis mechanisms of Tsukamurella. There is increasing evidence that biofilms play a significant role in ocular infections, leading us to hypothesize that biofilm formation is crucial for effective Tsukamurella infection. In order to look for potential candidate genes which are important in biofilm formation and Tsukamurella keratitis. We performed genome sequencing of two ocular isolates, T. pulmonis-PW1004 and T. tyrosinosolvens-PW899, to identify potential virulence factors. Through in vitro and in vivo studies, we characterized their biological roles in mediating Tsukamurella keratitis. Our findings confirmed that Tsukamurella is an ocular pathogen by fulfilling Koch's postulates, and using genome sequence data, we identified tmytC, encoding a mycolyltransferase, as a crucial gene in biofilm formation and causing Tsukamurella keratitis in the rabbit model. This is the first report demonstrating the novel role of mycolyltransferase in causing ocular infections. Overall, our findings contribute to a better understanding of Tsukamurella pathogenesis and provide a potential target for treatment. Specific inhibitors targeting TmytC could serve as an effective treatment option for Tsukamurella infections.

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.

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.

Epidemiology and in vitro antimicrobial susceptibility of aerobic Actinomycetales in a clinical setting

INTRODUCTION

The incidence of infections caused by aerobic actinomycetes is increasing. Recent changes in taxonomy and the variability in susceptibility patterns among species make necessary a proper identification and antibiotic susceptibility testing.

MATERIAL AND METHODS

Fifty-three strains of aerobic actinomycetes were identified by MALDI-TOF MS using the VITEK MS Mycobacterium/Nocardia kit (bioMérieux, France) in a tertiary hospital in Spain during a six-year period. Antimicrobial susceptibility testing of the isolates was performed using the Sensititre Rapmycoi microdilution panel (Thermo Fisher Scientific, Massachusetts, USA).

RESULTS

Forty strains of Nocardia spp. were identified in the study, being N. farcinica and N. cyriacigeorgica the most prevalent ones. All isolates were susceptible to linezolid and the resistance to amikacin was only observed in one isolate of Gordonia sputi. Resistance to cotrimoxazole was only found in five isolates.

CONCLUSIONS

Routine identification and antimicrobial susceptibility testing of aerobic actinomycetes is advisable for an efficient identification of species and effective treatment.

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.

Chronic Pulmonary Disease Caused by Tsukamurella toyonakaense

Unidentified Mycobacterium species are sometimes detected in respiratory specimens. We identified a novel Tsukamurella species (Tsukamurella sp. TY48, RIMD 2001001, CIP 111916^T), Tsukamurella toyonakaense, from a patient given a misdiagnosis of nontuberculous mycobacterial pulmonary disease caused by unidentified mycobacteria. Genomic identification of this Tsukamurella species helped clarify its clinical characteristics and epidemiology.

Streptococcus oriscaviae sp. nov. Infection Associated with Guinea Pigs

Pet bite-related infections are commonly caused by the pet's oral flora transmitted to the animal handlers through the bite wounds. In this study, we isolated a streptococcus, HKU75T, in pure culture from the purulent discharge collected from a guinea pig bite wound in a previously healthy young patient. HKU75T was alpha-hemolytic on sheep blood agar and agglutinated with Lancefield group D and group G antisera. API 20 STREP showed that the most likely identity for HKU75T was S. suis I with 85.4% confidence while Vitek 2 showed that HKU75T was unidentifiable. MALDI-TOF MS identified HKU75T as Streptococcus suis (score of 1.86 only). 16S rRNA gene sequencing showed that HKU75T was most closely related to S. parasuis (98.3% nucleotide identity), whereas partial groEL and rpoB gene sequencing showed that it was most closely related to S. suis (81.8% and 89.8% nucleotide identity respectively). Whole genome sequencing and intergenomic distance determined by ANI revealed that there was <85% identity between the genome of HKU75T and those of all other known Streptococcus species. Genome classification using concatenated sequences of 92 bacterial core genes showed that HKU75T belonged to the Suis group. groEL gene sequences identical to that of HKU75T could be directly amplified from the oral cavities of the two guinea pigs owned by the patient. HKU75T is a novel Streptococcus species, which we propose to be named S. oriscaviae. The oral cavity of guinea pigs is presumably a reservoir of S. oriscaviae. Some of the reported S. suis strains isolated from clinical specimens may be S. oriscaviae. IMPORTANCE We reported the discovery of a novel Streptococcus species, propose to be named Streptococcus oriscaviae, from the pus collected from a guinea pig bite wound in a healthy young patient. The bacterium was initially misidentified as S. suis/S. parasuis by biochemical tests, mass spectrometry. and housekeeping genes sequencing. Its novelty was confirmed by whole genome sequencing. Comparative genomic studies showed that S. oriscaviae belongs to the Suis group. S. oriscaviae sequences were detected in the oral cavities of the two guinea pigs owned by the patient, suggesting that the oral cavity of guinea pigs could be a reservoir of S. oriscaviae. Some of the reported S. suis strains may be S. oriscaviae. Further studies are warranted to refine our knowledge on this novel Streptococcus species.

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.

Cocaine esterase occurrence in global wastewater microbiomes and potential for biotransformation of novel psychoactive substances

The analysis of drugs in wastewater for forensic purposes has been constantly increasing and the investigation of the potential interaction between drugs or metabolites and sewage microbiota is important. The results demonstrated that cocaine esterase genes were widely distributed in 1142 global wastewater samples collected from 64 countries and linked to several bacterial species. In addition, in silico predictions indicated that carfentanil, 4F-MDMB-BINACA, 5F-MDMB-PICA, MDMB-4en-PINACA and mitragynine might also undergo microbial hydrolysis, in a similar fashion of cocaine degradation by cocaine esterase. In conclusion, it was demonstrated the microbial potential to hydrolyze drugs of abuse in wastewater environments, contributing to the critical evaluation of potential metabolites as biomarkers for microbial and human transformation of drugs in wastewater.

Epidemiology and in vitro antimicrobial susceptibility of aerobic Actinomycetales in a clinical setting

INTRODUCTION

The incidence of infections caused by aerobic actinomycetes is increasing. Recent changes in taxonomy and the variability in susceptibility patterns among species make necessary a proper identification and antibiotic susceptibility testing.

MATERIAL AND METHODS

Fifty-three strains of aerobic actinomycetes were identified by MALDI-TOF MS using the VITEK MS Mycobacterium/Nocardia kit (bioMérieux, France) in a tertiary hospital in Spain during a six-year period. Antimicrobial susceptibility testing of the isolates was performed using the Sensititre Rapmycoi microdilution panel (Thermo Fisher Scientific, Massachusetts, USA).

RESULTS

Forty strains of Nocardia spp. were identified in the study, being N. farcinica and N. cyriacigeorgica the most prevalent ones. All isolates were susceptible to linezolid and the resistance to amikacin was only observed in one isolate of Gordonia sputi. Resistance to cotrimoxazole was only found in five isolates.

CONCLUSIONS

Routine identification and antimicrobial susceptibility testing of aerobic actinomycetes is advisable for an efficient identification of species and effective treatment.

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.

Catheter-related bloodstream infection due to Tsukamurella pulmonis identified by MALDI-TOF spectrometry, 16S rRNA gene sequencing, and secA1 gene sequencing in an immunocompromised child: a case report and literature review

Tsukamurella species are Gram-positive bacilli related to aerobic Actinomyces. Originally reported from the environment, Tsukamurella species have also been described in human infections, especially in bacteremia. A literature review analysis revealed that Tsukamurella spp. are often initially considered as contaminant microorganisms, especially due to bacterial identification issues. Here, we report a catheter-related bloodstream infection in an immunocompromised child caused by Tsukamurella pulmonis. Matrix-Assisted Laser Desorption/Ionization-Time Of Flight (MALDI-TOF) mass spectrometry allowed rapid genus-level identification and contributed to better patient care. However, accurate species-level identification required 16S rRNA gene sequencing and secA1 gene sequencing. Considering the increased number of Tsukamurella infections, the implementation of new Tsukamurella species in MALDI-TOF databases is required to be more discriminant.

Emergence of Staphylococcus lugdunensis as a Cause of Urinary Tract Infection: Results of the Routine Use of MALDI-TOF MS

We analyzed the incidence and the clinical and laboratory characteristics of Staphylococcus lugdunensis urinary tract infections (UTIs) during a 10-year period (2009–2018) and compared them with those of Staphylococcus saprophyticus UTIs. A total of 38 and 162 episodes of S. lugdunensis and S. saprophyticus UTIs were observed. The number of S. saprophyticus UTIs was stable throughout the 10 years, whereas there was an obvious surge in the apparent number of S. lugdunensis UTIs since 2014, coinciding with the commencement of a routine use of MALDI-TOF MS. Univariate analysis showed that male sex (p < 0.001), advanced age (p < 0.001), hospital-acquired infections, (p < 0.001), upper UTI (p < 0.005), polymicrobial infections (p < 0.05), hypertension (p < 0.001), solid-organ malignancies (p < 0.001), renal stones (p < 0.001), urinary stricture (p < 0.05), vesicoureteral reflux (p < 0.001), and presence of a urinary catheter (p < 0.001) were significantly associated with S. lugdunensis UTI. Multivariable analysis revealed that S. lugdunensis UTI was associated with male sex (OR = 6.08, p < 0.05), solid-organ malignancies (OR = 12.27, p < 0.01), and urological system abnormalities (OR = 7.44, p < 0.05). There were significant differences in the patient population affected and predisposing factors between S. lugdunensis and S. saprophyticus UTIs.

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 application of proteomic methods (MALDI-toff MS) for studying protein profiles of some nematodes (dirofilaria and ascaris) for differentiating species

INTRODUCTION

Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-toff MS) is a reliable method for diagnosing a number of bacterial and fungal infections. It is also effective as a method of rapid diagnosis of several parasitic agents. We used MALDI-toff MS to study the protein profiles of four nematodes: Dirofilaria repens, Dirofilaria. immitis, Ascaris suum and Ascaris lumbricoides.

METHODS

We studied the protein profiles of dirofilaria (five of each species: D. repens and D. immitis) and ascaris (five of each species: A. suum and A. lumbricoides), using a proteomic analysis based on MALDI-toff MS.

RESULTS

Analysis of protein extracts of dirofilaria and ascaris showed spectra with high-intensity peaks in the range of 2-20 kDa. The quality of the spectra (clear graphical reflection of mass/charge to luminous intensity, consistent in repeated analyzes) and the intensity of the spectral peaks were consistent in all samples of the same species. The spectra profiles of D. repens and D. immitis differed in eight major peaks which makes it possible to differentiate species according to the protein profile. The spectra profiles obtained from A. suum and A. lumbricoides proteins differed slightly in 3 major peaks in both species and were discovered in m/z 13000; 13400 and 14400. The protein peaks in diapason 3000 kD-7300 kD specific for all genus ascaris are constant.

CONCLUSIONS

MALDI-toff MS-based proteomic analysis can serve as an effective taxonomic tool for parasitological studies.

Clinical Mass Spectrometry in the Bioinformatics Era: A Hitchhiker's Guide

Mass spectrometry (MS) is a sensitive, specific and versatile analytical technique in the clinical laboratory that has recently undergone rapid development. From initial use in metabolic profiling, it has matured into applications including clinical toxicology assays, target hormone and metabolite quantitation, and more recently, rapid microbial identification and antimicrobial resistance detection by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In this mini-review, we first succinctly outline the basics of clinical mass spectrometry. Examples of hard ionization (electron ionization) and soft ionization (electrospray ionization, MALDI) are presented to demonstrate their clinical applications. Next, a conceptual discourse on mass selection and determination is presented: quadrupole mass filter, time-of-flight mass spectrometer and the Orbitrap; and MS/MS (tandem-in-space, tandem-in-time and data acquisition), illustrated with clinical examples. Current applications in (1) bacterial and fungal identification, antimicrobial susceptibility testing and phylogenetic classification, (2) general unknown urine toxicology screening and expanded new-born metabolic screening and (3) clinical metabolic profiling by gas chromatography are outlined. Finally, major limitations of MS-based techniques, including the technical challenges of matrix effect and isobaric interference; and novel challenges in the post-genomic era, such as protein molecular variants, are critically discussed from the perspective of service laboratories. Computer technology and structural biology have played important roles in the maturation of this field. MS-based techniques have the potential to replace current analytical techniques, and existing expertise and instrument will undergo rapid evolution. Significant automation and adaptation to regulatory requirements are underway. Mass spectrometry is unleashing its potentials in clinical laboratories.