title: Paradoxical Hypersusceptibility of Drug-resistant Mycobacteriumtuberculosis to β-lactam Antibiotics.
abstract: Mycobacterium tuberculosis (M. tuberculosis) is considered innately resistant to β-lactam antibiotics. However, there is evidence that susceptibility to β-lactam antibiotics in combination with β-lactamase inhibitors is variable among clinical isolates, and these may present therapeutic options for drug-resistant cases. Here we report our investigation of susceptibility to β-lactam/β-lactamase inhibitor combinations among clinical isolates of M. tuberculosis, and the use of comparative genomics to understand the observed heterogeneity in susceptibility. Eighty-nine South African clinical isolates of varying first and second-line drug susceptibility patterns and two reference strains of M. tuberculosis underwent minimum inhibitory concentration (MIC) determination to two β-lactams: amoxicillin and meropenem, both alone and in combination with clavulanate, a β-lactamase inhibitor. 41/91 (45%) of tested isolates were found to be hypersusceptible to amoxicillin/clavulanate relative to reference strains, including 14/24 (58%) of multiple drug-resistant (MDR) and 22/38 (58%) of extensively drug-resistant (XDR) isolates. Genome-wide polymorphisms identified using whole-genome sequencing were used in a phylogenetically-aware linear mixed model to identify polymorphisms associated with amoxicillin/clavulanate susceptibility. Susceptibility to amoxicillin/clavulanate was over-represented among isolates within a specific clade (LAM4), in particular among XDR strains. Twelve sets of polymorphisms were identified as putative markers of amoxicillin/clavulanate susceptibility, five of which were confined solely to LAM4. Within the LAM4 clade, 'paradoxical hypersusceptibility' to amoxicillin/clavulanate has evolved in parallel to first and second-line drug resistance. Given the high prevalence of LAM4 among XDR TB in South Africa, our data support an expanded role for β-lactam/β-lactamase inhibitor combinations for treatment of drug-resistant M. tuberculosis.
authors.affiliation: Pulmonary and Critical Care Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban, South Africa. Electronic address: kacohen@partners.org.
authors.forename: Keira A
authors.initials: KA
authors.lastname: Cohen
authors.affiliation: IBM Research-Haifa, Haifa, Israel.
authors.forename: Tal
authors.initials: T
authors.lastname: El-Hay
authors.affiliation: IBM Research - Australia, Carlton, Victoria, Australia; Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia.
authors.forename: Kelly L
authors.initials: KL
authors.lastname: Wyres
authors.affiliation: IBM Research-Haifa, Haifa, Israel.
authors.forename: Omer
authors.initials: O
authors.lastname: Weissbrod
authors.affiliation: KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban, South Africa.
authors.forename: Vanisha
authors.initials: V
authors.lastname: Munsamy
authors.affiliation: IBM Research-Haifa, Haifa, Israel.
authors.forename: Chen
authors.initials: C
authors.lastname: Yanover
authors.affiliation: IBM Research-Haifa, Haifa, Israel.
authors.forename: Ranit
authors.initials: R
authors.lastname: Aharonov
authors.affiliation: IBM Research-Haifa, Haifa, Israel.
authors.forename: Oded
authors.initials: O
authors.lastname: Shaham
authors.affiliation: IBM Research - Australia, Carlton, Victoria, Australia.
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Conway
authors.affiliation: IBM Research-Haifa, Haifa, Israel.
authors.forename: Yaara
authors.initials: Y
authors.lastname: Goldschmidt
authors.affiliation: Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, MD, USA.
authors.forename: William R
authors.initials: WR
authors.lastname: Bishai
authors.affiliation: KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban, South Africa. Electronic address: alex.pym@k-rith.org.
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Pym
mesh_terms: D000658:Amoxicillin / Q000494:pharmacology; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001499:Bayes Theorem; D019818:Clavulanic Acid / Q000494:pharmacology; D024901:Drug Resistance, Multiple, Bacterial / Q000187:drug effects / Q000235:genetics; D005798:Genes, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D000077731:Meropenem; D008826:Microbial Sensitivity Tests; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000187:drug effects* / Q000201:enzymology / Q000235:genetics / Q000302:isolation & purification; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013845:Thienamycins / Q000494:pharmacology; D014376:Tuberculosis / Q000175:diagnosis / Q000382:microbiology; D001618:beta-Lactamases / Q000737:chemistry / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D013845:Thienamycins; D019818:Clavulanic Acid; D000658:Amoxicillin; D001618:beta-Lactamases; D000077731:Meropenem
keywords: Antimicrobial chemotherapy; Beta-lactam antibiotics; Extensively drug resistant (XDR); Multi-drug resistant (MDR); Recombination; pks12; tuberculosis