Complete Genome Sequence of WM99c, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 2 (GC2) Strain Representing an Australian GC2 Lineage

Genomics unveils country-to-country transmission between animal hospitals of a multidrug-resistant and sequence type 2 Acinetobacter baumannii clone

Acinetobacter baumannii is a globally distributed opportunistic pathogen in human health settings, including in intensive care units (ICUs). We investigated the contamination of a French small animal ICU with A. baumannii. We discovered repeated animal contamination by A. baumannii, and phylogenetic analysis traced contamination back to a potential foreign animal origin. Genomic analysis combined with antibiotic susceptibility testing revealed heteroresistance to penicillin and aminoglycoside mediated by insertion sequence dynamics and also suggest a potential cross-resistance to human-restricted piperacillin-tazobactam combination. The A. baumannii isolates of the animal ICU belong to the International Clone 2 commonly found in human health settings. Our results suggest a high adaptation of this lineage to healthcare settings and provide questions on the requirements for genetic determinants enabling adaptation to host and abiotic conditions.

The extensively antibiotic resistant ST111 Acinetobacter baumannii isolate RBH2 carries an extensive mobile element complement of plasmids, transposons and insertion sequences

The complete genome of RBH2, a sporadic, carbapenem resistant ST111 Acinetobacter baumannii isolate from Brisbane, Australia was determined and analysed. RBH2 is extensively resistant and the chromosome includes two transposons carrying antibiotic resistance genes, AbaR4 (oxa23 in Tn2006) and Tn7::Tn2006 (dfrA1, sat2, aadA1, oxa23). The chromosome also includes two copies of Tn6175, a transposon carrying putative copper resistance genes, and 1-17 copies of six different insertion sequences. RBH2 has six plasmids ranging in size from 6 kb - 141 kb, four carrying antibiotic resistance genes. Plasmids pRBH2-1 (aadB) and pRBH2-2 (aphA6 in TnaphA6) were found to be essentially identical to known plasmids pRAY*-v1 and pS21-1, respectively. The largest plasmids, pRBH2-5 (oxa23 in AbaR4) and pRBH2-6 (oxa23 in AbaR4::ISAba11 and sul2, tet(B), strA and strB in Tn6172) have known transfer-proficient relatives. pRBH2-5, an RP-T1 (RepAci6) plasmid, also carries a different putative copper resistance transposon related to Tn6177 found in pS21-2. The backbone of pRBH2-5 is related to those of previously described RepAci6 plasmids pAb-G7-2 and pA85-3 but has some distinctive features. Three different RepAci6 backbone types were distinguished, Type 1 (pAb-G7-2), Type 2 (pA85-3) and Type 3 (pRBH2-5 and pS21-2). pRBH2-6 is closely related to pAB3 and their backbones differ by only 5 SNPs. Plasmids pRBH2-3 and pRBH2-4 do not carry antibiotic resistance genes. pRBH2-3 does not include an identifiable rep gene and is a novel plasmid type. pRBH2-4 is of the R3-T3 type and includes segments of the larger pABTJ2 that heads this group. Other ST111 genomes carry different plasmids.

Acinetobacter baumannii GC2 Sublineage Carrying the aac(6')-Im Amikacin, Netilmicin, and Tobramycin Resistance Gene Cassette

The aminoglycoside antibiotics amikacin, gentamicin, and tobramycin are important therapeutic options for Acinetobacter iinfections. Several genes that confer resistance to one or more of these antibiotics are prevalent in the globally distributed resistant clones of Acinetobacter baumannii, but the aac(6')-Im (aacA16) gene (amikacin, netilmicin, and tobramycin resistance), first reported in isolates from South Korea, has rarely been reported since. In this study, GC2 isolates (1999 to 2002) from Brisbane, Australia, carrying aac(6')-Im and belonging to the ST2:ST423:KL6:OCL1 type were identified and sequenced. The aac(6')-Im gene and surrounds have been incorporated into one end of the IS26-bounded AbGRI2 antibiotic resistance island and are accompanied by a characteristic 70.3-kbp deletion of adjacent chromosome. The compete genome of the 1999 isolate F46 (RBH46) includes only two copies of ISAba1 (in AbGRI1-3 and upstream of ampC) but later isolates, which differ from one another by <10 single nucleotide differences (SND), carry two to seven additional shared copies. Several complete GC2 genomes with aac(6')-Im in an AbGRI2 island (2004 to 2017; several countries) found in GenBank and two additional Australian A. baumannii isolates (2006) carry different gene sets, KL2, KL9, KL40, or KL52, at the capsule locus. These genomes include ISAba1 copies in a different set of shared locations. The distribution of SND between F46 and AYP-A2, a 2013 ST2:ST208:KL2:OCL1 isolate from Victoria, Australia, revealed that a 640-kbp segment that includes KL2 and the AbGRI1 resistance island replaces the corresponding region in F46. Over 1,000 A. baumannii draft genomes also include aac(6')-Im, indicating that it is currently globally disseminated and significantly underreported. IMPORTANCE Aminoglycosides are important therapeutic options for treatment of Acinetobacter infections. Here, we show that a little-known aminoglycoside resistance gene, aac(6')-Im (aacA16), that confers amikacin, netilmicin, and tobramycin resistance has been circulating undetected for many years in a sublineage of A. baumannii global clone 2 (GC2), generally with a second aminoglycoside resistance gene, aacC1, which confers resistance to gentamicin. These two genes are commonly found together in GC2 complete and draft genomes and globally distributed. One isolate appears to be ancestral, as its genome contains few ISAba1 copies, providing insight into the original source of this insertion sequence (IS), which is abundant in most GC2 isolates. Tracking ISAba1 spread can provide a simple means to track the development and ongoing evolution as well as the dissemination of specific lineages and detect the formation of many sublineages. The complete ancestral genome will provide an essential base point for tracking this process.

Origin, Phylogeny, and Transmission of the Epidemic Clone ST208 of Carbapenem-Resistant Acinetobacter baumannii on a Global Scale

Carbapenem-resistant Acinetobacter baumannii (CRAB) is an opportunistic pathogen that has become a global threat. The dissemination of global clone 2 (GC2) CRAB has been well documented. Oxford sequence type (ST) 208 is one of the most prevalent lineages of A. baumannii GC2; however, its evolution and phylogeny are unclear. We collected 45 representative ST208 isolates from 14 cities in China between 1999 and 2018. Moreover, 411 ST208 genome sequences were downloaded from the GenBank database for comparison. The global ST208 phylogeny showed that ST208 might have originated from North America and subsequently evolved into two clades. Notably, the widespread OXA-23-producing ST208 A. baumannii was correlated with the transposon structure and dynamics of replicative transposition, and the Tn2009 tandem structure of five copies of blaOXA-23 and potential circular intermediate of Tn2009 were first detected. Furthermore, 15 Chinese ST208 isolates carried GR25 pABTJ1-like plasmids, which contained blaOXA-23 and have only been found in China in the last decade. In conclusion, our work suggests that replicative transposition contributes to the evolution and transmission of OXA-23-producing ST208 A. baumannii and highlights the new challenges posed by the epidemiological surveillance of globally distributed clonal groups via whole genome sequencing. IMPORTANCE ST208 as one of the most prevalent lineages of CRAB has caused several difficult-to-treat infections and outbreaks around the world. However, few studies have focused on evaluating the genetic background differences of ST208 A. baumannii isolated from very distant geographic regions. A comprehensive genomic analysis of 456 clinical strains of ST208 A. baumannii from a wide temporal and geographic range was performed in this study. Moreover, the mechanisms leading to the horizontal transfer of blaOXA-23 in ST208 A. baumannii are poorly understood. We first describe experimental evidence of the potential circular intermediate of Tn2009, and the Tn2009 tandem structure of five copies of blaOXA-23 was first detected. The interbacterial transfer of genetic elements carrying resistance to last-line antibiotic carbapenems highlights the essential need to enhance epidemiologic surveillance.

An outbreak of multiply antibiotic-resistant ST49:ST128:KL11:OCL8 Acinetobacter baumannii isolates at a Sydney hospital

OBJECTIVES

To understand the acquisition of resistance genes by a non-GC1, non-GC2 Acinetobacter baumannii strain responsible for a 4 year outbreak at a Sydney hospital.

METHODS

Representative isolates were screened for resistance to antibiotics. Three were subjected to WGS using Illumina HiSeq. One genome was completed with MinION long reads. Resistance regions were compared with known sequences using bioinformatics.

RESULTS

Isolates were resistant to third-generation cephalosporins, gentamicin and tobramycin, sulfamethoxazole and erythromycin. Sequenced isolates were ST49 (Institut Pasteur scheme) and ST128 (Oxford scheme) and carried KL11 at the capsule locus and OCL8 at the lipooligosaccharide outer core locus. The complete genome of isolate J9 revealed that the resistance genes were all in plasmids; pRAY* contained aadB, and a large plasmid, pJ9-3, contained sul2 and floR genes and a dif module containing the mph(E)-msr(E) macrolide resistance genes. Transposon Tn6168, consisting of a second copy of the chromosomal ampC gene region flanked by ISAba1s, confers resistance to third-generation cephalosporins. Tn6168 is located inside the mph(E)-msr(E) dif module. pJ9-3 includes a set of four dif modules and the orientation of the pdif sites, XerC-XerD or XerD-XerC, alternates. A large transposon, Tn6175, containing tniCABDE transposition genes and genes annotated as being involved in heavy metal metabolism, uptake or export was found in the comM gene. Other ST49:ST128:KL11:OCL8 genomes found in the GenBank WGS database carried Tn6175 but neither of the plasmids carrying the resistance genes.

CONCLUSIONS

An early carbapenem-susceptible A. baumannii outbreak recorded in Australia was caused by an unusual clone that had acquired plasmids carrying antibiotic resistance genes.

Complete Genome Sequence of A388, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 1 Isolate from Greece

Acinetobacter baumannii isolate A388, recovered in Greece in 2002, represents a distinct antibiotic-resistant lineage of global clone 1 (GC1) producing the OXA-58 carbapenemase. We present the complete 4.332-Mbp genome sequence (chromosome plus 1 plasmid), generated by combining long (MinION) and short (Illumina HiSeq) read sequencing data.

Acinetobacter baumannii isolate A388, recovered in Greece in 2002, represents a distinct antibiotic-resistant lineage of global clone 1 (GC1) producing the OXA-58 carbapenemase. We present the complete 4.332-Mbp genome sequence (chromosome plus 1 plasmid), generated by combining long (MinION) and short (Illumina HiSeq) read sequencing data.