Mycobacterium thermoresistibile: a new pathogen for humans

Temporal dynamics of microbial composition and antibiotic resistome in fermentation bed culture pig farms across various ages

The discharge from pig farms presents significant challenges to the environment and human health, specifically regarding the dissemination of antimicrobial resistance (AMR). Fermentation bed culture has emerged as an increasingly popular and environmentally friendly pig farming model in China, as it minimizes the release of harmful substances into the environment. However, there remains a limited understanding of the occurrence and dynamics of microbiome and antibiotic resistome in fermentation bed culture. Herein, we collected fermentation bed materials (FBM) from four fermentation bed culture pig farms with varying service ages and investigated their bacterial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metal resistance genes (MRGs) and potential antibiotic-resistant bacterial hosts through metagenomics. Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota were identified as the dominant phyla present in the FBM. In total, we detected 258 unique ARGs in the FBM samples, with 79 core ARGs shared by all FBM samples, accounting for 95 % of the total ARG abundance. Our results revealed significant variations in microbial communities and ARG profiles across varying service ages of FBM. Compared to long-term FBW, short-term FBM exhibited higher numbers and abundances of ARGs, MRGs and MGEs, along with higher levels of potential bacterial pathogens and high-risk ARGs. Further analysis of metagenome-assembled genome (MAG) indicated that the putative hosts of ARGs primarily belonged to Pseudomonadota, Actinomycetota and Bacillota. Alarmingly, among the 80 recovered ARG-carrying MAGs, 23 MAGs encoded multi-resistance, including clinically significant species that require urgent attention. Overall, this study provided valuable insights into the temporal patterns of antibiotic resistome and bacterial communities within FBM, enhancing our understanding of FBM in pig farming. The findings could potentially contribute to the development of effective strategies for evaluating and regulating fermentation bed culture practices in pig farming.

Disseminated Mycobacterium thermoresistibile Infection presented with Lymphadenectasis in an AIDS patient: case report and review of literature

BACKGROUND

Nontuberculous mycobacteria disease is a common invasive infectious disease in patients with HIV. However, Mycobacterium thermoresistibile association with lymphadenectasis is unusual in AIDS patients.

CASE PRESENTATION

This report covers the case of a 25-year-old male AIDS patient infected with Mycobacterium thermoresistibile. The case was identified via pathogen-targeted next-generation sequencing (ptNGS).

CONCLUSION

This is the first report of disseminated M. thermoresistibile infection presented with lymphadenectasis in an AIDS patient. Prompt diagnosis and antimicrobial treatment are crucial.

A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland

BACKGROUND

In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case.

RESULTS

Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy's bone lesion and high mercury concentrations.

CONCLUSIONS

The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly.

A genuine mycobacterial thermophile: Mycobacterium hassiacum growth, survival and GpgS stability at near-pasteurization temperatures

Mycobacterium hassiacum is so far the most thermophilic among mycobacteria as it grows optimally at 50 °C and up to 65 °C in a glycerol-based medium, as verified in this study. Since this and other nontuberculous mycobacteria (NTM) thrive in diverse natural and artificial environments, from where they may access and infect humans, we deemed essential to probe M. hassiacum resistance to heat, a strategy routinely used to control microbial growth in water-supply systems, as well as in the food and drink industries. In addition to possibly being a threat in its own right in rare occasions, M. hassiacum is also a good surrogate for studying other NTM species more often associated with opportunistic infection, namely Mycobacterium avium and Mycobacterium abscessus as well as their strictly pathogenic counterparts Mycobacterium tuberculosis and Mycobacterium leprae. In this regard, this thermophilic species is likely to be useful as a source of stable proteins that may provide more detailed structures of potential drug targets. Here, we investigate M. hassiacum growth at near-pasteurization temperatures and at different pHs and also characterize its thermostable glucosyl-3-phosphoglycerate synthase (GpgS), an enzyme considered essential for M. tuberculosis growth and associated with both nitrogen starvation and thermal stress in different NTM species.

Draft Genome Sequences of Five Rapidly Growing Mycobacterium Species, M. thermoresistibile, M. fortuitum subsp. acetamidolyticum, M. canariasense, M. brisbanense, and M. novocastrense

We report here the draft genome sequences of five rapidly growing Mycobacterium (RGM) species potentially pathogenic to humans, M. thermoresistibile, M. fortuitum subsp. acetamidolyticum, M. canariasense, M. brisbanense, and M. novocastrense. As the clinical importance of RGMs is increasingly being recognized worldwide, these sequences would contribute to further advances in RGM research.

Infection due to Mycobacterium thermoresistibile: a case associated with an orthopedic device

Mycobacterium thermoresistibile is a rapidly growing environmental nontuberculous mycobacterium, seldom reported in human infections. Here, we describe a rare case of tibial-nail-related osteomyelitis due to Mycobacterium thermoresistibile. We also review the literature about the infections caused by this pathogen.

Mycobacterium thermoresistibile as a source of thermostable orthologs of Mycobacterium tuberculosis proteins

The genus Mycobacterium comprises major human pathogens such as the causative agent of tuberculosis, Mycobacterium tuberculosis (Mtb), and many environmental species. Tuberculosis claims ~1.5 million lives every year, and drug resistant strains of Mtb are rapidly emerging. To aid the development of new tuberculosis drugs, major efforts are currently under way to determine crystal structures of Mtb drug targets and proteins involved in pathogenicity. However, a major obstacle to obtaining crystal structures is the generation of well-diffracting crystals. Proteins from thermophiles can have better crystallization and diffraction properties than proteins from mesophiles, but their sequences and structures are often divergent. Here, we establish a thermophilic mycobacterial model organism, Mycobacterium thermoresistibile (Mth), for the study of Mtb proteins. Mth tolerates higher temperatures than Mtb or other environmental mycobacteria such as M. smegmatis. Mth proteins are on average more soluble than Mtb proteins, and comparison of the crystal structures of two pairs of orthologous proteins reveals nearly identical folds, indicating that Mth structures provide good surrogates for Mtb structures. This study introduces a thermophile as a source of protein for the study of a closely related human pathogen and marks a new approach to solving challenging mycobacterial protein structures.

Structure of nitrilotriacetate monooxygenase component B from Mycobacterium thermoresistibile

Mycobacterium tuberculosis belongs to a large family of soil bacteria which can degrade a remarkably broad range of organic compounds and utilize them as carbon, nitrogen and energy sources. It has been proposed that a variety of mycobacteria can subsist on alternative carbon sources during latency within an infected human host, with the help of enzymes such as nitrilotriacetate monooxygenase (NTA-Mo). NTA-Mo is a member of a class of enzymes which consist of two components: A and B. While component A has monooxygenase activity and is responsible for the oxidation of the substrate, component B consumes cofactor to generate reduced flavin mononucleotide, which is required for component A activity. NTA-MoB from M. thermoresistibile, a rare but infectious close relative of M. tuberculosis which can thrive at elevated temperatures, has been expressed, purified and crystallized. The 1.6 Å resolution crystal structure of component B of NTA-Mo presented here is one of the first crystal structures determined from the organism M. thermoresistibile. The NTA-MoB crystal structure reveals a homodimer with the characteristic split-barrel motif typical of flavin reductases. Surprisingly, NTA-MoB from M. thermoresistibile contains a C-terminal tail that is highly conserved among mycobacterial orthologs and resides in the active site of the other protomer. Based on the structure, the C-terminal tail may modulate NTA-MoB activity in mycobacteria by blocking the binding of flavins and NADH.

Mycobacterium thermoresistibile: case report of a rarely isolated mycobacterium from Europe and review of literature

Mycobacterium thermoresistibile is a non-tuberculous mycobacterium strongly associated with human infections. Since 1966, there have only been six reports of its isolation from clinical samples. We report on the first case from Europe and review all the previous cases. Identification was achieved with sequencing of the 16S rRNA and hsp65 genes. This study presents its phenotypic and biochemical profile, susceptibilities to selected antibiotics and hsp65 polymerase chain reaction-restriction fragment length polymorphism profile with BsteII and Hae III .

Mycobacterium thermoresistibile infection following knee-replacement surgery

We report a case of Mycobacterium thermoresistibile as a cause of infection following total knee replacement. This infection was masked by the prior isolation of a vancomycin-resistant enterococcus. The infection was resolved with long-term therapy using moxifloxacin and doxycycline.

Mycobacterium thermoresistible recovered from a cutaneous lesion in an otherwise healthy individual

This is the first report of coinfection by Mycobacterium thermoresistible and Mycobacterium fortuitum and only the fifth case of human infection by M. thermoresistible reported in the world literature.

Chronic pneumonia caused by Mycobacterium thermoresistibile in a cat

Mycobacterium thermoresistibile was isolated in pure culture from ultrasound-guided pulmonary aspirates taken from a young cat with severe, chronic, pyogranulomatous pneumonia. Thoracic radiography and ultrasonography before therapy demonstrated severe diffuse alveolar disease. Twelve months combination therapy with doxycycline, rifampicin and clarithromycin resolved the infection. Thoracic radiographs taken at the completion of therapy showed multifocal pulmonary mineralisation. M thermoresistibile has been infrequently reported as a human or animal pathogen. This is the first reported pulmonary infection by M thermoresistibile in a cat and documents the successful treatment of the organism in a feline patient.

Diagnosis and treatment of disease caused by nontuberculous mycobacteria. This official statement of the American Thoracic Society was approved by the Board of Directors, March 1997. Medical Section of the American Lung Association

Diagnostic criteria of nontuberculous mycobacterial lung disease in HIV-seropositive and -seronegative hosts. The following criteria apply to symptomatic patients with infiltrate, nodular or cavitary disease, or a high resolution computed tomography scan that shows multifocal bronchiectasis and/or multiple small nodules. A. If three sputum/bronchial wash results are available from the previous 12 mo: 1. three positive cultures with negative AFB smear results or 2. two positive cultures and one positive AFB smear B. If only one bronchial wash is available: 1. positive culture with a 2+, 3+, or 4+ AFB smear or 2+, 3+, or 4+ growth on solid media C. If sputum/bronchial wash evaluations are nondiagnostic or another disease cannot be excluded: 1. transbronchial or lung biopsy yielding a NTM or 2. biopsy showing mycobacterial histopathologic features (granulomatous inflammation and/or AFB) and one or more sputums or bronchial washings are positive for an NTM even in low numbers.

COMMENTS

these criteria fit best with M. avium complex, M. abscessus, and M. kansasii. Too little is known of other NTM to be certain how applicable these criteria will be. At least three respiratory samples should be evaluated from each patient. Other reasonable causes for the disease should be excluded. Expert consultation should be sought when diagnostic difficulties are encountered.

Clinical features of pulmonary disease caused by rapidly growing mycobacteria. An analysis of 154 patients

The role of rapidly growing mycobacteria (RGM) as pulmonary pathogens has been unclear. We identified 154 cases of lung disease caused by RGM using the microbiologic and radiographic criteria of the American Thoracic Society (ATS) and availability of the causative organism for study. More than one third of patients had positive lung biopsy cultures. Patients were predominantly white (83%), female (65%) nonsmokers (66%), and they had prolonged periods from onset of symptoms to diagnosis of their disease. Cough was an almost universal presenting symptom, whereas constitutional symptoms became more important with progression of disease. Upper lobe infiltrates were most common (88%), with 77% of patients developing bilateral disease. Cavitation was present in only 16% of the patients. Specific underlying diseases were infrequent, but they included previously treated mycobacterial disease (18%), coexistent Mycobacterium avium complex (8%), cystic fibrosis (6%), and gastroesophageal disorders with chronic vomiting (6%). The majority of isolates (82%) were M. abscessus (formerly M. chelonae subsp. abscessus). Effective treatment for M. fortuitum long disease was accomplished with drug therapy, whereas surgical resection of localized disease was the only effective long-term therapy for M. abscessus. Although the disease was generally slowly progressive, 21 of 154 (14%) patients died as a consequence of progressive RGM lung disease and respiratory failure. RGM should be recognized as a cause of chronic mycobacterial lung disease, and respiratory isolates should be assessed carefully.

Isoelectric focusing patterns of beta-lactamases in the rapidly growing mycobacteria

beta-lactamases from 259 strains of rapidly growing mycobacteria that included the third biovariant complex of Mycobacterium fortuitum, M. peregrinum, M. abscessus, M. chelonae, the M. chelonae-like organisms (MCLO), and M. smegmatis were analyzed by isoelectric focusing (IEF). All isolates produced acidic beta-lactamases with major band isoelectric points (pIs) between 4.4 and 6.0. Each of the 6 taxonomic groups exhibited 1 or 2 characteristic beta-lactamase IEF patterns. Heterogeneity among IEF patterns was evident in 5 of the 6 groups, however, and was greatest among the third biovariant complex of M. fortuitum. beta-lactamase patterns correlated with previously identified taxonomic subgroups of M. smegmatis and the third biovariant complex of M. fortuitum. beta-lactamase IEF analysis of MCLO strains isolated from two outbreaks demonstrated its possible usefulness for epidemiologic evaluation.

Agents of newly recognized or infrequently encountered mycobacterial diseases

This paper reviews recent information on the systematics and clinical significance of potentially pathogenic environmental mycobacteria. A short history of these mycobacteria is given. Information on species for which clinical and systematic aspects have already been well documented, i.e., Mycobacterium kansasii, M. marinum, M. scrofulaceum, M. simiae, M. szulgai, M. ulcerans, M. xenopi, and members of the M. fortuitum complex, is updated. Although the M. avium complex was extensively reviewed in earlier literature, major new systematic and clinical information is presented in some detail. Species that have received very limited prior coverage, i.e., M. asiaticum, M. haemophilum, M. malmoense, and M. shimoidei, are the main subjects of this review and are discussed in detail. The rare infections attributed to species that are normally considered nonpathogenic, i.e., M. gastri, M. gordonae, the M. terrae complex, and most of the rapidly growing mycobacteria outside of the M. fortuitum complex, are critically reviewed. Finally, suggestions are offered for practical measures that can minimize the risk of failing to isolate or misidentifying some of the more obscure potentially pathogenic environmental mycobacteria that are only infrequently recognized.

Differentiation of Mycobacterium thermoresistibile from Mycobacterium phlei and other rapidly growing mycobacteria

Mycobacterium thermoresistibile is the only chromogenic rapidly growing mycobacterial species reported to cause infections in humans and animals. DNA-DNA hybridization (S1 nuclease method) showed that M. thermoresistibile formed a DNA relatedness group which was only 24 to 30% related to M. phlei. Alkaline phosphatase and beta-galactosidase differentiated M. thermoresistibile from M. phlei. Among the rapidly growing mycobacteria, the mycolic acid pattern of M. thermoresistibile was unique (alpha-, alpha'-, methoxy-and keto-mycolates). Fourteen other species of chromogenic rapidly growing mycobacteria, including M. phlei, produced different mycolic acid patterns which always included dicarboxylic mycolate. Nine species of non-chromogenic rapidly growing mycobacteria produced mycolic acid patterns devoid of ketomycolate.

Mycobacterium thermoresistibile: extrapulmonary infection in a cat

The first evidence of the potential pathogenicity of Mycobacterium thermoresistibile in cats is presented. This mycobacterium was isolated repeatedly from intra- and subcutaneous nodules, aspirated fluid from fluctuating skin lesions, and lymph nodes. The distinctive characteristics of the cultured organisms matched those of M. thermoresistibile.

The "atypical" mycobacteria: recognition and disease association

Although techniques based on immunologic or chromatographic analyses have been described for identifying mycobacteria in clinical laboratories, most microbiologists continue to rely on a series of specialized physiological and biochemical tests for this purpose. The recognition of additional significant species over the past decade has required the addition of more tests to the battery used for mycobacterial identification. This paper will review briefly the taxonomic status of species likely to be encountered in clinical specimens and the most useful tests for characterizing them. Strategies will be presented for using these tests in the most efficient way to provide optimal resolution of taxa without use of an unreasonably large battery of tests. A brief survey of techniques that may become more practical in the future will also be included.

Mycobacterium thermoresistibile infection in an immunocompromised host

This is the second report of Mycobacterium thermoresistibile as the etiological agent of a pulmonary granuloma and the first occurrence of this organism in a patient who has not been outside the continental United States. The organism is susceptible to rifampin, ethambutol, and streptomycin but resistant to isoniazid and p-aminosalicylic acid.