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Interdisciplinary Sciences,... Jun 2021The identification of clinically relevant bacterial amino acid changes can be performed using different methods aimed at the identification of genes showing positively...
The identification of clinically relevant bacterial amino acid changes can be performed using different methods aimed at the identification of genes showing positively selected amino acid sites (PSS). Nevertheless, such analyses are time consuming, and the frequency of genes showing evidence for PSS can be low. Therefore, the development of a pipeline that allows the quick and efficient identification of the set of genes that show PSS is of interest. Here, we present Auto-PSS-Genome, a Compi-based pipeline distributed as a Docker image, that automates the process of identifying genes that show PSS using three different methods, namely codeML, FUBAR, and omegaMap. Auto-PSS-Genome accepts as input a set of FASTA files, one per genome, containing all coding sequences, thus minimizing the work needed to conduct positively selected sites analyses. The Auto-PSS-Genome pipeline identifies orthologous gene sets and corrects for multiple possible problems in input FASTA files that may prevent the automated identification of genes showing PSS. A FASTA file containing all coding sequences can also be given as an external global reference, thus easing the comparison of results across species, when gene names are different. In this work, we use Auto-PSS-Genome to analyse Mycobacterium leprae (that causes leprosy), and the closely related species M. haemophilum, that mainly causes ulcerating skin infections and arthritis in persons who are severely immunocompromised, and in children causes cervical and perihilar lymphadenitis. The genes identified in these two species as showing PSS may be those that are partially responsible for virulence and resistance to drugs.
Topics: Amino Acids; Bacteria; Child; Genome, Bacterial; Humans; Mycobacterium leprae; Virulence
PubMed: 34009546
DOI: 10.1007/s12539-021-00439-2 -
BMJ Case Reports Jan 2022is a rarely encountered pathogen that is difficult to identify given its unique growth requirements. It is most often seen in adult patients who are immunosuppressed...
is a rarely encountered pathogen that is difficult to identify given its unique growth requirements. It is most often seen in adult patients who are immunosuppressed due to advanced HIV or haematological malignancy. Our case highlights a typical presentation of an atypical pathogen in a patient with rheumatoid arthritis receiving anti-tumour necrosis factor therapy. This case represents an important patient population in whom this previously rare infection is increasingly common.
Topics: Adult; Arthritis, Rheumatoid; Cellulitis; Humans; Infliximab; Mycobacterium Infections; Mycobacterium haemophilum
PubMed: 35039354
DOI: 10.1136/bcr-2021-245853 -
Dermatology Online Journal Sep 2017A 61-year-old immunosuppressed renal transplant patient with inflammatory bowel disease presented with tender pink nodules on the trunk and extremities. An initial...
A 61-year-old immunosuppressed renal transplant patient with inflammatory bowel disease presented with tender pink nodules on the trunk and extremities. An initial biopsy was suggestive of metastatic Crohn disease, but after disease persistence, a second biopsy revealed disseminated Mycobacterium haemophilum. Atypical mycobacterial infections should be considered in immunosuppressed patients. This case highlights the complexities of diagnosing such infections in patients with an underlying granulomatous condition and the particular growth requirements of M. haemophilum.
Topics: Crohn Disease; Diagnosis, Differential; Female; Humans; Immunocompromised Host; Immunosuppressive Agents; Kidney Failure, Chronic; Kidney Transplantation; Middle Aged; Mycobacterium Infections; Mycobacterium haemophilum; Opportunistic Infections
PubMed: 29469723
DOI: No ID Found -
Digestive and Liver Disease : Official... Sep 2020
Topics: Aged; Crohn Disease; Female; Humans; Immunocompromised Host; Mycobacterium Infections; Mycobacterium haemophilum; Skin Diseases, Bacterial
PubMed: 32340886
DOI: 10.1016/j.dld.2020.03.018 -
Annals of Dermatology May 2023A 38-year-old female with systemic lupus erythematosus (SLE) initiated belimumab treatment. One month later, she presented with a reddish painful swelling on her right...
A 38-year-old female with systemic lupus erythematosus (SLE) initiated belimumab treatment. One month later, she presented with a reddish painful swelling on her right lower leg. She was treated with ceftriaxone and vancomycin. However, novel erythematous papules and indurated nodules appeared on both her lower legs. Skin biopsy revealed microabscess formation with mixed cell granuloma surrounded by inflammatory cell infiltration within the dermis with subcutaneous fat tissue. A large number of acid-fast bacilli were observed with Ziehl-Neelsen staining. DNA sequencing of both the hsp65 and the 16S rRNA sequences showed a 100% match with the corresponding region of . Mycobacterial culture revealed satellite growth enhancement on Middlebrook 7H11 agar plates around a paper strip containing hemin. She was treated with levofloxacin, rifabutin, and ethambutol. Within 13 months, her cutaneous lesions improved markedly without any side effects. The B cell-targeted biologic belimumab, a fully humanized IgG1γ monoclonal antibody that inactivates B lymphocyte stimulator, has been considered to be beneficial for active SLE. However, this therapy could increase the risk for the development of biologic therapy-associated mycobacterial infections, both tuberculosis and nontuberculous mycobacteria infections.
PubMed: 37853868
DOI: 10.5021/ad.21.077 -
BMJ Case Reports Oct 2016Opportunistic infections are a major concern in renal and transplant medicine. We present the case of a renal transplant recipient with a generalised Mycobacterium...
Opportunistic infections are a major concern in renal and transplant medicine. We present the case of a renal transplant recipient with a generalised Mycobacterium haemophilum infection after an increase in immunosuppressive therapy and treatment with a tumour necrosis factor-α (TNF-α) inhibitor. Infection involved skin and soft tissue, joints and bones, as well as the renal transplant with an interstitial nephritis. Rapid diagnosis using PCR and DNA sequencing allowed early appropriate treatment. Triple antibiotic therapy and reduction in immunosuppression resulted in a slow but sustained recovery. Immunosuppression causes severe opportunistic infections. TNF-α inhibitors are very effective and well tolerated but have an increased susceptibility to infections with mycobacteria. Mycobacterial infections represent a significant clinical risk to transplant recipients because of their aggressive clinical course and the need for complex toxic antibiotic treatments. In these patients, M. haemophilum is a cause of skin infections.
Topics: Adult; Antitubercular Agents; Biopsy; Humans; Immunocompromised Host; Immunosuppressive Agents; Kidney Function Tests; Kidney Transplantation; Male; Mycobacterium Infections; Mycobacterium haemophilum; Opportunistic Infections
PubMed: 27799227
DOI: 10.1136/bcr-2016-216042 -
Dermatology Online Journal Jun 2021Nontuberculous mycobacteria are pathogens with diverse manifestations in immunocompromised hosts. The lesser-known Mycobacterium haemophilum usually causes cutaneous...
Nontuberculous mycobacteria are pathogens with diverse manifestations in immunocompromised hosts. The lesser-known Mycobacterium haemophilum usually causes cutaneous infection. Diagnosis is challenging but is aided by molecular testing and multidisciplinary communication. We present an immunocompromised patient with disseminated cutaneous mycobacterial infection with digital tenosynovitis.
Topics: Female; Hematopoietic Stem Cell Transplantation; Humans; Middle Aged; Mycobacterium Infections, Nontuberculous; Postoperative Complications
PubMed: 34387060
DOI: 10.5070/D327654059 -
The American Journal of Tropical... Jul 2021Mycobacterium tuberculosis (MTB) stands out as the main causative agent of pulmonary tuberculosis (TB). However, nontuberculous mycobacteria (NTM) species also have the...
Mycobacterium tuberculosis (MTB) stands out as the main causative agent of pulmonary tuberculosis (TB). However, nontuberculous mycobacteria (NTM) species also have the potential to infect and cause TB in susceptible individuals. The objective of this study was to identify NTM species that cause public health problems in remote areas. The study was carried out using 105 sputum smears obtained from patients from the Guna Yala Region of Panama with clinical signs suggestive of TB. DNA was extracted from sputum smears. Nontuberculous mycobacteria and MTB were characterized using polymerase chain reaction restriction analysis (hsp65, rpob) and an evaluation of 24-mycobacterial interspersed repetitive units-variable number of tandem repeats loci. Twenty-six Mycobacterium species were characterized; 19 (18%) were identified as MTB, and 7 (6.7%) were identified as NTM (four M. avium complex, two M. haemophilum, one M. tusciae). These results suggest that at least one in five cases of pulmonary TB among this population is caused by an NTM. Thus, identifying the bacteria causing pulmonary disease is key even in remote regions of the world where standard diagnosis and culture are not available. Strengthening the laboratory capacity within the Guna Yala Region is needed to identify NTM infections promptly.
Topics: DNA, Bacterial; Genotyping Techniques; Humans; Nontuberculous Mycobacteria; Panama; Polymerase Chain Reaction; Sputum; Tuberculosis, Pulmonary
PubMed: 34237018
DOI: 10.4269/ajtmh.21-0096 -
Indian Journal of Dermatology,... 2020
Topics: Female; Humans; Immunocompromised Host; Middle Aged; Mycobacterium Infections; Mycobacterium haemophilum; Skin Diseases, Bacterial
PubMed: 31898640
DOI: 10.4103/ijdvl.IJDVL_736_17 -
Open Forum Infectious Diseases 2017
PubMed: 28959701
DOI: 10.1093/ofid/ofx165