This study identifies the sRNA B11 as a regulator of gene expression and virulence in Mycobacterium abscessus, showing it affects colony morphology, inflammation, antibiotic resistance, and secretion system activity.

bioRxiv · Oct 27, 2022 · PreprintMicrobiology

Hypervariable-Locus Melting Typing (HLMT): a novel, fast and inexpensive sequencing-free approach to pathogen typing based on High Resolution Melting (HRM) analysis

M. Perini, A. Piazza, S. Panelli, S. Papaleo, A. Alvaro, F. Vailati, M. Corbella, F. Saluzzo, F. Gona, D. Castelli, C. Farina, P. Marone, D. M. Cirillo, A. Cavallero, G. V. Zuccotti, F. Comandatore

HLMT provides a fast, inexpensive, sequencing-free pathogen typing method using HRM analysis, comparable to PFGE, MLST, and WGS for detecting high-risk clones in hospitals.

bioRxiv · Jul 1, 2021 · PreprintMicrobiology

Deciphering Bedaquiline and Clofazimine Resistance in Tuberculosis: An Evolutionary Medicine Approach

L. Sonnenkalb, J. Carter, A. Spitaleri, Z. Iqbal, M. Hunt, K. Malone, C. Utpatel, D. M. Cirillo, C. Rodrigues, K. S. Nilgiriwala, the CRyPTIC Consortium, P. W. Fowler, M. Merker, S. Niemann

This study identifies 230 genomic variants associated with resistance to bedaquiline and clofazimine in tuberculosis using experimental evolution, genome sequencing, and structural modeling.

bioRxiv · Mar 19, 2021Microbiology

Population structure, biogeography and transmissibility of Mycobacterium tuberculosis

L. Freschi, R. Vargas, A. Hussain, S. M. Mostofa Kamal, A. Skrahina, S. Tahseen, N. Ismail, A. Barbova, S. Niemann, D. M. Cirillo, A. S. Dean, M. Zignol, M. R. Farhat

This study analyzes the population structure, biogeography, and transmissibility of Mycobacterium tuberculosis using genomic data from thousands of strains, identifying new clades and sub-lineages.

bioRxiv · Sep 29, 2020Microbiology

Xpert MTB/XDR: A ten-color reflex assay suitable for point of care settings to detect isoniazid-, fluoroquinolone-, and second line injectable drug-resistance directly from Mycobacterium tuberculosis positive sputum.

Y. Cao, H. Parmar, R. Gaur, S. Raghunath, D. Lieu, N. Via, S. Battagalia, D. M. Cirillo, C. Denkinger, S. B. Georghiou, R. Kwiatkowski, D. Persing, D. Alland, S. Chakravorty

The paper describes the development and evaluation of a 10-color Xpert MTB/XDR assay for rapid detection of drug resistance in tuberculosis directly from sputum samples.

bioRxiv · Sep 8, 2020Microbiology

A new model of chronic Mycobacterium abscessus lung infection in immunocompetent mice

C. Riva, E. Tortoli, F. Cugnata, F. Sanvito, A. Esposito, M. Rossi, A. Colarieti, T. Canu, C. Cigana, A. Bragonzi, N. I. Lore', P. Miotto, D. M. Cirillo

This study develops a new murine model of chronic Mycobacterium abscessus lung infection and demonstrates its ability to sustain infection and be monitored with MRI.

bioRxiv · Jul 30, 2020Microbiology

The persistence of Nontypeable Haemophilus influenzae fuels airway inflammation

F. Saliu, G. Rizzo, A. Bragonzi, L. Cariani, D. M. Cirillo, C. Colombo, V. Dacco', D. Girelli, S. Rizzetto, S. Barbara, C. Cigana, N. I. Lore'

This study shows that persistent Nontypeable Haemophilus influenzae (NTHi) in CF patients and mice increases inflammation by boosting IL-8, CXCL1, and cytokine levels, and recruiting immune cells.

bioRxiv · May 25, 2020Microbiology

Acquisition of cross-resistance to bedaquiline and clofazimine following treatment for tuberculosis in Pakistan

A. Ghodousi, A. H. Rizvi, A. Q. Baloch, A. Ghafoor, F. M. Khanzada, M. Qadir, E. Borroni, A. Trovato, S. Tahseen, D. M. Cirillo

The paper reports six cases of acquired resistance to bedaquiline and clofazimine in Pakistan, documenting mutations and MIC increases in tuberculosis patients on bedaquiline-containing regimens.

bioRxiv · May 7, 2019Microbiology

Isoniazid resistance in Mycobacterium tuberculosis is a heterogeneous phenotype comprised of overlapping MIC distributions with different underlying resistance mechanisms

A. Ghodousi, E. Tagliani, E. Karunaratne, S. Niemann, J. Perera, C. U. Köser, D. M. Cirillo

The paper analyzes isoniazid resistance in M. tuberculosis strains, finding overlapping MIC distributions and showing that whole-genome sequencing can explain most resistance levels.

bioRxiv · Jan 20, 2019Microbiology

Validating a 14-drug microtitre plate containing bedaquiline and delamanid for large-scale research susceptibility testing of Mycobacterium tuberculosis

P. M. Rancoita, F. Cugnata, A. L. Gibertoni Cruz, E. Borroni, S. J. Hoosdally, T. M. Walker, C. Grazian, T. J. Davies, T. E. Peto, D. W. Crook, P. W. Fowler, D. M. Cirillo, the CRyPTIC Consortium

The paper validates a 14-drug microtitre plate for measuring MICs of anti-TB compounds in M. tuberculosis isolates, finding optimal reading with the Vizion system after 14 days incubation.

bioRxiv · Jun 15, 2018Microbiology

Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of Mycobacterium tuberculosis

P. W. Fowler, A. L. Gibertoni Cruz, S. J. Hoosdally, L. Jarrett, E. Borroni, M. Chiacchiaretta, P. Rathod, T. M. Walker, E. Robinson, T. E. Peto, D. M. Cirillo, E. G. Smith, D. W. Crook

This paper introduces AMyGDA, a software tool for automated detection of M. tuberculosis growth on 96-well plates to determine drug susceptibility.

bioRxiv · Jun 15, 2018Microbiology