Molecular Characterization of Carbapenem/Colistin-Resistant Acinetobacter baumannii Clinical Isolates from Egypt by Whole-Genome Sequencing

Figures & data

Figure 1 Minimum spanning tree generated by cgMLST coloured by ST (Pasteur) based on 3487 targets. Numbers between the nodes indicate the number of alleles that are different.

Table 1 Resistomes in Seven Colistin-Resistant A. Baumannii Isolates by WGS

Isolate	Beta-Lactam	Aminoglycoside	Trimethoprim	Sulphonamide	Tetracycline	Macrolide	Phenicol	Fluoroquinolone/Aminoglycoside
R14	blaADC-117 blaGES-35 blaOXA-23 blaOXA-65	aph(3ʹ)-VIa-like aacA4-like	dfrA7	sul1		mph(E) msr(E)	-	aac(6ʹ)Ib-cr-like
R13	blaADC-30 blaNDM-1 blaOXA-66 blaTEM-1D	aac(6ʹ)-Il-like aph(3ʹ)-Ic aph(3ʹ)-VIa-like strA strB	-	sul sul2	tet(B)-like	-	-	-
R18	blaADC-30 blaNDM-1 blaOXA-66 blaTEM-1D	aac(6ʹ)-Il-like aph(3ʹ)-Ic aph(3ʹ)-VIa-like strA strB	-	sul1 sul2	tet(B)-like	-	-	-
R45	blaADC-82 blaGES-35 blaOXA-23 blaOXA-66	aadA1 aph(3ʹ)-Ic like aph(3ʹ)-VIa-like armA strA strB aacA4-like	dfrA7	sul1	tet(B)-like	mph(E)	catB8	aac(6ʹ)Ib-cr-like
R11	blaADC-73 blaOXA-23 blaOXA-66 blaTEM-1D	aadA1 aph(3ʹ)-Ic-like armA strA strB aacA4-like	-	sul1-like	tet(B)-like	msr(E)	catB8	aac(6ʹ)Ib-cr-like
R41	blaADC-30 blaOXA-23 blaNDM-1 blaOXA-66 blaTEM-1D	aac(6ʹ)-Il-like aph(3ʹ)-Ic aph(3ʹ)-VIa-like	-	-	-	-	-	-
R2	blaADC-73 blaOXA-23 blaOXA-66 blaTEM-1D	aadA1 aph(3ʹ)-Ic-like armA strA strB aacA4-like	-	sul1	tet(B)-like	mph(E) msr(E)	catB8	aac(6ʹ)Ib-cr-like

Table 2 Amino Acids Substitution in PmrCAB System in Seven Sequenced Isolates in Comparison to ACICU Strain

Isolate	Substitutions Compared to ACICU
	PmrA	PmrB	PmrC*
R2	Identical to ACICU	Ala138-Thr	Ala354-Ser substitution
R11
R13		Identical to ACICU
R18
R41
R45
R14	Ile18-Thr substitution	Val444-Ala	Ile42-Val, Ile115-Val, Leu150-Phe, and Thr515-Lys.

Note: *ACICU has a 25 amino acid deletion in PmrC (YQIPENLKKKWCKDGECYDDILIDS) at position 324 when compared to the seven investigated isolates.

Figure 2 Alignment of the PmrC amino acid sequences based on whole-genome sequencing. ST2 isolates are represented by isolate R11.

Data availability

Repositories:

Raw reads generated were submitted to the Sequencing Read Archive (https://www.ncbi.nlm.nih.gov/sra/) of the National Center for Biotechnology Information (NCBI) under the SRA accession number SRP131448 and BioProject PRJNA431710.