Genomic landscape of prominent XDR Acinetobacter clonal complexes from Dhaka, Bangladesh

Abstract

Background: Acinetobacter calcoaceticus-A. baumannii (ACB) complex pathogens are known for their prevalence in nosocomial infections and extensive antimicrobial resistance (AMR) capabilities. While genomic studies worldwide have elucidated the genetic context of antibiotic resistance in major international clones (ICs) of clinical Acinetobacter spp., not much information is available from Bangladesh. In this study, we analysed the AMR profiles of 63 ACB complex strains collected from Dhaka, Bangladesh. Following this, we generated draft genomes of 15 of these strains to understand the prevalence and genomic environments of AMR, virulence and mobilization associated genes in different Acinetobacter clones.

Results: Around 84% (n = 53) of the strains were extensively drug resistant (XDR) with two showing pan-drug resistance. Draft genomes generated for 15 strains confirmed 14 to be A. baumannii while one was A. nosocomialis. Most A. baumannii genomes fell under three clonal complexes (CCs): the globally dominant CC1 and CC2, and CC10; one strain had a novel sequence type (ST). AMR phenotype-genotype agreement was observed and the genomes contained various beta-lactamase genes including bla_OXA-23 (n = 12), bla_OXA-66 (n = 6), and bla_NDM-1 (n = 3). All genomes displayed roughly similar virulomes, however some virulence genes such as the Acinetobactin bauA and the type IV pilus gene pilA displayed high genetic variability. CC2 strains carried highest levels of plasmidic gene content and possessed conjugative elements carrying AMR genes, virulence factors and insertion sequences.

Conclusion: This study presents the first comparative genomic analysis of XDR clinical Acinetobacter spp. from Bangladesh. It highlights the prevalence of different classes of beta-lactamases, mobilome-derived heterogeneity in genetic architecture and virulence gene variability in prominent Acinetobacter clonal complexes in the country. The findings of this study would be valuable in understanding the genomic epidemiology of A. baumannii clones and their association with closely related pathogenic species like A. nosocomialis in Bangladesh.

Keywords: Acinetobacter baumannii; Acinetobacter nosocomialis; Clonal complex; Comparative genomics; WGS.

Fig. 1

a. Antimicrobial susceptibility profile of 63 ACB complex strains against 14 antibiotics. b. Source distribution of 63 ACB complex strains c. Source-wise antimicrobial susceptibility profiles of the 63 ACB complex strains. AK = Amikacin; CN = Gentamicin; CAZ = Ceftazidime; FEP = Cefepime; CTX = Cefotaxime; CRO = Ceftriaxone; IPM = Imipenem; MEM = Meropenem; TZP = Tazobactam/Piperacillin; CIP = Ciprofloxacin; LEV = Levofloxacin; TGC = Tigecycline; CT = Colistin, PB = Polymyxin B

Fig. 2

Core-genome maximum likelihood tree of a) 14 sequenced A. baumannii strains b) the A. nosocomialis strain NGCE1007 along with other reference strains for each species obtained from NCBI. Core genome alignment was generated with Roary while the ML tree was generated using IQTree with 1000 bootstrap resampling. The trees were rooted at midpoint, visualized and annotated using iTOL. The branch thickness of the trees directly correlates to bootstrap value

Fig. 3

Antimicrobial susceptibility and resistome profiles of 15 sequenced Acinetobacter strains. The bipartite heatmap depicts the distribution of antimicrobial resistance genes at the top, and the phenotypic susceptibility status of the 15 sequenced strains against 14 tested antibiotics at the bottom. AMR genes were initially identified using ResFinder database (coverage > 60%; identity > 90%). The specific gene numbers for beta-lactamases were identified using the BLDB BLAST [43]

Fig. 4

a) Virulome profiles of 15 Acinetobacter genomes. Virulence gene distribution was determined in by BLAST against 135 A. baumannii virulence genes in the VFDB database. Only those genes with the e-value below 1e⁻⁵, coverage > 90% and identity > 60% were considered. The colours depicted in the heatmap indicate the number of hits for each gene as explained in the legend. b) Genetic variance in virulence genes of Acinetobacter spp. strains calculated over three sets. Set A contains genes associated with all 15 Acinetobacter genomes as well as the VFDB reference gene. Set B contains all genes from Set A except for those associated with A. nosocomialis genome NGCE1007. Set C contains only those genes associated with the 14 A. baumannii genomes, i.e., sans the VFDB reference gene. The genetic variance was calculated with DnaSP in terms of the ratio SNP/bp where bp stood for the length of the aligned gene. The SNP/bp ratio is represented with a colour scale as shown in the legend

Fig. 5

a) Level of shared gene content of 15 Acinetobacter strains when compared against 578 A. baumannii reference plasmids. b) Level of shared gene content of 15 Acinetobacter strains when compared against 27 A. nosocomialis reference plasmids. The numbers on the colour scale represent percentage of the genome that matched against the databases. c) Schematic diagrams showing the arrangements of nodes associated with conjugative systems and replicase genes found in common among several Acinetobacter genomes. d) Relational diagram showing association between insertion sequences (ISs) and various AMR genes. The colour of the links joining AMR genes to ISs represent the number of times the connection appeared among the 15 Acinetobacter genomes analysed. The diagram was generated using CIRCOS