Background Improved genetic understanding of Mycobacterium tuberculosis (MTB) resistance to novel and repurposed anti-tubercular agents can aid the development of rapid molecular diagnostics. Methods Adhering to PRISMA guidelines, in March 2018, we performed a systematic review of studies implicating mutations in resistance through sequencing and phenotyping before and/or after spontaneous resistance evolution, as well as allelic exchange experiments. We focused on the novel drugs bedaquiline, delamanid, pretomanid and the repurposed drugs clofazimine and linezolid. A database of 1373 diverse control MTB whole genomes, isolated from patients not exposed to these drugs, was used to further assess genotype–phenotype associations. Results Of 2112 papers, 54 met the inclusion criteria. These studies characterized 277 mutations in the genes atpE, mmpR, pepQ, Rv1979c, fgd1, fbiABC and ddn and their association with resistance to one or more of the five drugs. The most frequent mutations for bedaquiline, clofazimine, linezolid, delamanid and pretomanid resistance were atpE A63P, mmpR frameshifts at nucleotides 192–198, rplC C154R, ddn W88* and ddn S11*, respectively. Frameshifts in the mmpR homopolymer region nucleotides 192–198 were identified in 52/1373 (4%) of the control isolates without prior exposure to bedaquiline or clofazimine. Of isolates resistant to one or more of the five drugs, 59/519 (11%) lacked a mutation explaining phenotypic resistance. Conclusions This systematic review supports the use of molecular methods for linezolid resistance detection. Resistance mechanisms involving non-essential genes show a diversity of mutations that will challenge molecular diagnosis of bedaquiline and nitroimidazole resistance. Combined phenotypic and genotypic surveillance is needed for these drugs in the short term.

Rheumatoid arthritis (RA) is a systemic inflammatory disorder, with the most common extra-articular manifestation of RA being lung involvement. While essentially any of the lung compartments can be affected and manifest as interstitial lung disease (ILD), pleural effusion, cricoarytenoiditis, constrictive or follicular bronchiolitis, bronchiectasis, pulmonary vasculitis, and pulmonary hypertension, RA-ILD is a leading cause of death in patients with RA and is associated with significant morbidity and mortality. In this review, we focus on the common pulmonary manifestations of RA, RA-ILD and airway disease, and discuss evolving concepts in the pathogenesis of RA-associated pulmonary fibrosis, as well as therapeutic strategies, and have revised our previous review on the topic. A rational clinical approach for the diagnosis and management of RA-ILD, as well as an approach to patients with clinical worsening in the setting of treatment with disease-modifying agents, is included. Future directions for research and areas of unmet need in the realm of RA-associated lung disease are raised.

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Over the past three decades, an increasing number of publications have reported the association between interstitial lung disease (ILD) and anti-neutrophil cytoplasmic antibody (ANCA) or ANCA-associated vasculitis (AAV). With this increased awareness, we have reviewed the literature to date and provide an update in this narrative review. The vast majority of cases of ILD have been shown to be in the setting of positive anti-myeloperoxidase antibody and can be present in up to 45% of patients of microscopic polyangiitis, though cases of ILD associated with proteinase 3 ANCA have rarely been reported. Pulmonary fibrosis and ANCA positivity can occur with or without systemic involvement. The pathogenetic mechanisms establishing the relationship between ANCA and the development of pulmonary fibrosis remain unclear. Histologic and radiographic features of ANCA-ILD most commonly reveal usual interstitial pneumonia or non-specific interstitial pneumonia patterns, though other atypical features such as bronchiolitis have been described. ILD in the setting of AAV has been associated with worse outcomes, and thus early identification and treatment in these patients is appropriate. We advocate that ANCA antibody testing be performed as a baseline evaluation in patients presenting with idiopathic interstitial pneumonia. Suggested treatment of ANCA-ILD includes immunosuppression and/or antifibrotic agents, though supporting data and clinical trials to substantiate use of these therapies are needed.