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  1. AU="Chiacchiaretta, Matteo"
  2. AU="Woo, Jennifer"
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  1. Article ; Online: Updating the WHO target product profile for next-generation Mycobacterium tuberculosis drug susceptibility testing at peripheral centres.

    MacLean, Emily Lai-Ho / Miotto, Paolo / González Angulo, Lice / Chiacchiaretta, Matteo / Walker, Timothy M / Casenghi, Martina / Rodrigues, Camilla / Rodwell, Timothy C / Supply, Philip / André, Emmanuel / Kohli, Mikashmi / Ruhwald, Morten / Cirillo, Daniela Maria / Ismail, Nazir / Zignol, Matteo

    PLOS global public health

    2023  Volume 3, Issue 3, Page(s) e0001754

    Abstract: There were approximately 10 million tuberculosis (TB) cases in 2020, of which 500,000 were drug-resistant. Only one third of drug-resistant TB cases were diagnosed and enrolled on appropriate treatment, an issue partly driven by a lack of rapid, accurate ...

    Abstract There were approximately 10 million tuberculosis (TB) cases in 2020, of which 500,000 were drug-resistant. Only one third of drug-resistant TB cases were diagnosed and enrolled on appropriate treatment, an issue partly driven by a lack of rapid, accurate drug-susceptibility testing (DST) tools deployable in peripheral settings. In 2014, World Health Organization (WHO) published target product profiles (TPPs) which detailed minimal and optimal criteria to address high-priority TB diagnostic needs, including DST. Since then, the TB community's needs have evolved; new treatment regimens, changes in TB definitions, further emergence of drug resistance, technological advances, and changing end-users requirements have necessitated an update. The DST TPP's revision was therefore undertaken by WHO with the Stop TB Partnership New Diagnostics Working Group. We describe the process of updating the TPP for next-generation TB DST for use at peripheral centres, highlight key updates, and discuss guidance regarding technical and operational specifications.
    Language English
    Publishing date 2023-03-31
    Publishing country United States
    Document type Journal Article
    ISSN 2767-3375
    ISSN (online) 2767-3375
    DOI 10.1371/journal.pgph.0001754
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex.

    Yenew, Bazezew / Ghodousi, Arash / Diriba, Getu / Tesfaye, Ephrem / Cabibbe, Andrea Maurizio / Amare, Misikir / Moga, Shewki / Alemu, Ayinalem / Dagne, Binyam / Sinshaw, Waganeh / Mollalign, Hilina / Meaza, Abyot / Tadesse, Mengistu / Gamtesa, Dinka Fikadu / Abebaw, Yeshiwork / Seid, Getachew / Zerihun, Betselot / Getu, Melak / Chiacchiaretta, Matteo /
    Gaudin, Cyril / Marceau, Michael / Didelot, Xavier / Tolera, Getachew / Abdella, Saro / Kebede, Abebaw / Getahun, Muluwork / Mehammed, Zemedu / Supply, Philip / Cirillo, Daniela Maria

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 7519

    Abstract: The Mycobacterium tuberculosis complex (MTBC) includes several human- and animal-adapted pathogens. It is thought to have originated in East Africa from a recombinogenic Mycobacterium canettii-like ancestral pool. Here, we describe the discovery of a ... ...

    Abstract The Mycobacterium tuberculosis complex (MTBC) includes several human- and animal-adapted pathogens. It is thought to have originated in East Africa from a recombinogenic Mycobacterium canettii-like ancestral pool. Here, we describe the discovery of a clinical tuberculosis strain isolated in Ethiopia that shares archetypal phenotypic and genomic features of M. canettii strains, but represents a phylogenetic branch much closer to the MTBC clade than to the M. canettii strains. Analysis of genomic traces of horizontal gene transfer in this isolate and previously identified M. canettii strains indicates a persistent albeit decreased recombinogenic lifestyle near the emergence of the MTBC. Our findings support that the MTBC emergence from its putative free-living M. canettii-like progenitor is evolutionarily very recent, and suggest the existence of a continuum of further extant derivatives from ancestral stages, close to the root of the MTBC, along the Great Rift Valley.
    MeSH term(s) Animals ; Humans ; Mycobacterium tuberculosis ; Phylogeny ; Ethiopia ; Tuberculosis/microbiology ; Africa, Eastern
    Language English
    Publishing date 2023-11-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-42755-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Emergence of two novel sequence types (3366 and 3367) NDM-1- and OXA-48-co-producing K. pneumoniae in Italy.

    Gona, Floriana / Bongiorno, Dafne / Aprile, Ausilia / Corazza, Erika / Pasqua, Betta / Scuderi, Maria Grazia / Chiacchiaretta, Matteo / Cirillo, Daniela Maria / Stefani, Stefania / Mezzatesta, Maria Lina

    European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology

    2019  Volume 38, Issue 9, Page(s) 1687–1691

    Abstract: The aim of this study was to analyze the alarming spread of NDM-1- and OXA-48-co-producing Klebsiella pneumoniae clinical isolates, collected between October 2016 and January 2018 in a neonatal intensive care unit of the University Hospital, Catania, ... ...

    Abstract The aim of this study was to analyze the alarming spread of NDM-1- and OXA-48-co-producing Klebsiella pneumoniae clinical isolates, collected between October 2016 and January 2018 in a neonatal intensive care unit of the University Hospital, Catania, Italy, through whole genome sequencing. All confirmed carbapenem-resistant K. pneumoniae (CRKp) isolates were characterized pheno- and geno-typically, as well as by whole genome sequencing (WGS). A total of 13 CRKp isolates were identified from 13 patients. Pulsed-field gel electrophoresis (PFGE) was performed, and the multilocus sequence typing (MLST) scheme used was based on the gene sequence as published on the MLST Pasteur website. Core genome MLST (cgMLST) was also performed. All isolates co-carried bla
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Bacterial Typing Techniques ; Carbapenems/pharmacology ; Disease Outbreaks ; Electrophoresis, Gel, Pulsed-Field ; Humans ; Infant, Newborn ; Intensive Care, Neonatal ; Italy ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/drug effects ; Klebsiella pneumoniae/enzymology ; Klebsiella pneumoniae/genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Whole Genome Sequencing ; beta-Lactamases/genetics
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Carbapenems ; beta-Lactamases (EC 3.5.2.6) ; beta-lactamase NDM-1 (EC 3.5.2.6) ; oxacillinase (EC 3.5.2.6)
    Language English
    Publishing date 2019-06-05
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 603155-9
    ISSN 1435-4373 ; 0934-9723 ; 0722-2211
    ISSN (online) 1435-4373
    ISSN 0934-9723 ; 0722-2211
    DOI 10.1007/s10096-019-03597-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Corrigendum: Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of

    Fowler, Philip W / Gibertoni Cruz, Ana Luíza / Hoosdally, Sarah J / Jarrett, Lisa / Borroni, Emanuele / Chiacchiaretta, Matteo / Rathod, Priti / Lehmann, Sarah / Molodtsov, Nikolay / Grazian, Clara / Walker, Timothy M / Robinson, Esther / Hoffmann, Harald / Peto, Timothy E A / Cirillo, Daniela Maria / Smith, Grace E / Crook, Derrick W

    Microbiology (Reading, England)

    2019  Volume 165, Issue 5, Page(s) 585

    Language English
    Publishing date 2019-10-04
    Publishing country England
    Document type Journal Article ; Published Erratum
    ZDB-ID 1180712-x
    ISSN 1465-2080 ; 1350-0872
    ISSN (online) 1465-2080
    ISSN 1350-0872
    DOI 10.1099/mic.0.000795
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of Mycobacterium tuberculosis.

    Fowler, Philip W / Gibertoni Cruz, Ana Luíza / Hoosdally, Sarah J / Jarrett, Lisa / Borroni, Emanuele / Chiacchiaretta, Matteo / Rathod, Priti / Lehmann, Sarah / Molodtsov, Nikolay / Walker, Timothy M / Robinson, Esther / Hoffmann, Harald / Peto, Timothy E A / Cirillo, Daniela Maria / Smith, Grace E / Crook, Derrick W

    Microbiology (Reading, England)

    2018  Volume 164, Issue 12, Page(s) 1522–1530

    Abstract: M. tuberculosis grows slowly and is challenging to work with experimentally compared with many other bacteria. Although microtitre plates have the potential to enable high-throughput phenotypic testing of M. tuberculosis, they can be difficult to read ... ...

    Abstract M. tuberculosis grows slowly and is challenging to work with experimentally compared with many other bacteria. Although microtitre plates have the potential to enable high-throughput phenotypic testing of M. tuberculosis, they can be difficult to read and interpret. Here we present a software package, the Automated Mycobacterial Growth Detection Algorithm (AMyGDA), that measures how much M. tuberculosis is growing in each well of a 96-well microtitre plate. The plate used here has serial dilutions of 14 anti-tuberculosis drugs, thereby permitting the MICs to be elucidated. The three participating laboratories each inoculated 38 96-well plates with 15 known M. tuberculosis strains (including the standard H37Rv reference strain) and, after 2 weeks' incubation, measured the MICs for all 14 drugs on each plate and took a photograph. By analysing the images, we demonstrate that AMyGDA is reproducible, and that the MICs measured are comparable to those measured by a laboratory scientist. The AMyGDA software will be used by the Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) to measure the drug susceptibility profile of a large number (>30000) of samples of M. tuberculosis from patients over the next few years.
    MeSH term(s) Antitubercular Agents/pharmacology ; Automation, Laboratory ; Diagnostic Tests, Routine ; Drug Resistance, Bacterial ; Image Processing, Computer-Assisted ; Microbial Sensitivity Tests/instrumentation ; Microbial Sensitivity Tests/methods ; Mycobacterium tuberculosis/drug effects ; Mycobacterium tuberculosis/growth & development ; Reproducibility of Results ; Software
    Chemical Substances Antitubercular Agents
    Language English
    Publishing date 2018-10-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1180712-x
    ISSN 1465-2080 ; 1350-0872
    ISSN (online) 1465-2080
    ISSN 1350-0872
    DOI 10.1099/mic.0.000733
    Database MEDical Literature Analysis and Retrieval System OnLINE

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