Characterisation of an early South African multiply antibiotic-resistant global clone 1 Acinetobacter baumannii isolate

Boucher, 2009, Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America, Clin Infect Dis, 48, 1, 10.1086/595011 Wong, 2017, Clinical and pathophysiological overview of Acinetobacter infections: a century of challenges, Clin Microbiol Rev, 30, 409, 10.1128/CMR.00058-16 Adams, 2010, Genomewide analysis of divergence of antibiotic resistance determinants in closely related isolates of Acinetobacter baumannii, Antimicrob Agents Chemother, 54, 3569, 10.1128/AAC.00057-10 Blackwell, 2016, IncM plasmid R1215 is the source of chromosomally located regions containing multiple antibiotic resistance genes in the globally disseminated Acinetobacter baumannii GC1 and GC2 clones, mSphere, 1, e00117, 10.1128/mSphere.00117-16 Blackwell, 2017, Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore, J Antimicrob Chemother, 72, 1031 Blackwell, 2015, Evolution of AbGRI2-0, the progenitor of the AbGRI2 resistance island in global clone 2 of Acinetobacter baumannii, Antimicrob Agents Chemother, 60, 1421, 10.1128/AAC.02662-15 Hamidian, 2021, An outbreak of multiply antibiotic-resistant ST49:ST128:KL11:OCL8 Acinetobacter baumannii isolates at a Sydney hospital, J Antimicrob Chemother, 76, 893, 10.1093/jac/dkaa553 Hamidian, 2017, Origin of the AbGRI1 antibiotic resistance island found in the comM gene of Acinetobacter baumannii GC2 isolates, J Antimicrob Chemother, 72, 2944, 10.1093/jac/dkx206 Hamidian, 2018, The AbaR multiple antibiotic resistance islands found in Acinetobacter baumannii global clone 1 - origin and evolution, Drug Resist Updates, 41, 26, 10.1016/j.drup.2018.10.003 Hamidian, 2019, Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem and aminoglycoside resistance genes and dispersion of ISAba1, Microb Genom, 5 Holt, 2016, Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1, Microb Genom, 2 Post, 2009, AbaR5, a large multiple antibiotic resistance region found in Acinetobacter baumannii, Antimicrob Agents Chemother, 53, 2667, 10.1128/AAC.01407-08 Wright, 2016, Genome dynamics of multidrug-resistant Acinetobacter baumannii during infection and treatment, Genome Med, 8, 26, 10.1186/s13073-016-0279-y Koong, 2021, Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1, Microb Genom, 7 Post, 2010, Evolution of AbaR-type genomic resistance islands in multiply antibiotic-resistant Acinetobacter baumannii, J Antimicrob Chemother, 16, 1162, 10.1093/jac/dkq095 Hamidian, 2019, Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii, Microb Genom, 5 Hamidian, 2021, Dissemination of novel Tn7 family transposons carrying genes for synthesis and uptake of fimsbactin siderophores among Acinetobacter baumannii isolates, Microb Genom, 7 Hamidian, 2014, Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii, J Antimicrob Chemother, 69, 557, 10.1093/jac/dkt379 Álvarez, 2020, Crucial role of the accessory genome in the evolutionary trajectory of Acinetobacter baumannii global clone 1, Front Microbiol, 11, 342, 10.3389/fmicb.2020.00342 Eze, 2022, El Zowalaty ME Draft genome sequences of extensively drug resistant and pandrug resistant Acinetobacter baumannii strains isolated from hospital wastewater in South Africa, J Glob Antimicrob Resist, 31, 286, 10.1016/j.jgar.2022.08.024 Kumburu, 2019, Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania, J Antimicrob Chemother, 74, 1484, 10.1093/jac/dkz055 Eze, 2021, Antibiotic resistance and biofilm formation of Acinetobacter baumannii isolated from high-risk effluent water in tertiary hospitals in South Africa, J Glob Antimicrob Resist, 27, 82, 10.1016/j.jgar.2021.08.004 Diancourt, 2010, The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool, PLoS One, 5, 10.1371/journal.pone.0010034 Brisse, 2000, Molecular surveillance of European quinolone-resistant clinical isolates of Pseudomonas aeruginosa and Acinetobacter spp. using automated ribotyping, J Clin Microbiol, 38, 3636, 10.1128/JCM.38.10.3636-3645.2000 van Dessel, 2004, Identification of a new geographically widespread multiresistant Acinetobacter baumannii clone from European hospitals, Res Microbiol, 155, 105, 10.1016/j.resmic.2003.10.003 Wiegand, 2008, Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances, Nature Protocols, 3, 163, 10.1038/nprot.2007.521 Wick, 2017, Unicycler: resolving bacterial genome assemblies from short and long sequencing reads, PLoS Comput Biol, 13, 10.1371/journal.pcbi.1005595 Nigro, 2011, Aminoglycoside resistance in multiply antibiotic-resistant Acinetobacter baumannii belonging to global clone 2 from Australian hospitals, J Antimicrob Chemother, 66, 1504, 10.1093/jac/dkr163 Hamidian, 2019, Complete genome sequence of A388, an antibiotic-resistant Acinetobacter baumannii global clone 1 isolate from Greece, Microbiol Resour Announc, 8, e00971, 10.1128/MRA.00971-19 Lam, 2022, Detection and typing of plasmids in Acinetobacter baumannii using rep genes encoding replication initiation proteins, Microbiol Spectrum, 11 Wyres, 2020, Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive, Microb Genom, 6 Blackwell, 2017, The tet39 determinant and the msrE-mphE genes in Acinetobacter plasmids are each part of discrete modules flanked by inversely oriented pdif (XerC-XerD) sites, Antimicrob Agents Chemother, 61, e00780, 10.1128/AAC.00780-17 Sambrook, 1989 Moran, 2019, An improved plasmid size standard, 39R861, Plasmid, 102, 6, 10.1016/j.plasmid.2019.01.002 Pong, 2021, An X1α plasmid from a Salmonella enterica serovar Ohio isolate carrying a novel IS26-bounded tet(C) pseudo-compound transposon, Plasmid, 114, 102561, 10.1016/j.plasmid.2021.102561 Hamidian, 2019, Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2, Microb Genom, 5 Harmer, 2022, Complete genome of the extensively antibiotic-resistant GC1 Acinetobacter baumannii isolate MRSN 56 reveals a novel route to fluoroquinolone resistance, J Antimicrob Chemother, 77, 1851, 10.1093/jac/dkac115 Hamidian, 2012, Variants of the gentamicin and tobramycin resistance plasmid pRAY are widely distributed in Acinetobacter, J Antimicrob Chemother, 67, 2833, 10.1093/jac/dks318 Holt, 2015, Genome sequence of Acinetobacter baumannii strain A1, an early example of antibiotic-resistant Global Clone 1, Genome Announc, 3, e00032, 10.1128/genomeA.00032-15 Amidian, 2014, Tn6168, a transposon carrying an ISAba1-activated ampC gene and conferring cephalosporin resistance in Acinetobacter baumannii, J Antimicrob Chemother, 69, 77, 10.1093/jac/dkt312 Ambrose, 2021, Origin of the dfrA44 trimethoprim resistance gene, J Antimicrob Chemother, 76, 930 Blackwell, 2019, Mobilisation of a small Acinetobacter plasmid carrying an oriT transfer origin by conjugative RepAci6 plasmids, Plasmid, 103, 36, 10.1016/j.plasmid.2019.04.002 Hamidian, 2014, Resistance to third-generation cephalosporins in Acinetobacter baumannii due to horizontal transfer of a chromosomal segment containing ISAba1-ampC, J Antimicrob Chemother, 69, 2865, 10.1093/jac/dku202 Hawkey, 2015, ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data, BMC Genomics, 16, 667, 10.1186/s12864-015-1860-2 Hamidian, 2020, Analysis of complete genome sequence of Acinetobacter baumannii strain ATCC 19606 reveals novel mobile genetic elements and novel prophage, Microorganisms, 8, 1851, 10.3390/microorganisms8121851 Jones, 2022, Evolution of Acinetobacter baumannii plasmids carrying the oxa58 carbapenemase resistance gene via plasmid fusion, IS26-mediated events and dif module shuffling, Plasmid, 121, 102628, 10.1016/j.plasmid.2022.102628