WGS-Based Analysis of Carbapenem-Resistant Acinetobacter baumannii in Vietnam and Molecular Characterization of Antimicrobial Determinants and MLST in Southeast Asia

Abstract

Carbapenem-resistant Acinetobacter baumannii (A. baumannii, CRAb) is an emerging global threat for healthcare systems, particularly in Southeast Asia. Next-generation sequencing (NGS) technology was employed to map genes associated with antimicrobial resistance (AMR) and to identify multilocus sequence types (MLST). Eleven strains isolated from humans in Vietnam were sequenced, and their AMR genes and MLST were compared to published genomes of strains originating from Southeast Asia, i.e., Thailand (n = 49), Myanmar (n = 38), Malaysia (n = 11), Singapore (n = 4) and Taiwan (n = 1). Ten out of eleven Vietnamese strains were CRAb and were susceptible only to colistin. All strains harbored ant(3”)-IIa, armA, aph(6)-Id and aph(3”) genes conferring resistance to aminoglycosides, and blaOXA-51 variants and blaADC-25 conferring resistance to ß-lactams. More than half of the strains harbored genes that confer resistance to tetracyclines, sulfonamides and macrolides. The strains showed high diversity, where six were assigned to sequence type (ST)/2, and two were allocated to two new STs (ST/1411-1412). MLST analyses of 108 strains from Southeast Asia identified 19 sequence types (ST), and ST/2 was the most prevalent found in 62 strains. A broad range of AMR genes was identified mediating resistance to ß-lactams, including cephalosporins and carbapenems (e.g., blaOXA-51-like, blaOXA-23, blaADC-25, blaADC-73, blaTEM-1, blaNDM-1), aminoglycosides (e.g., ant(3”)-IIa, aph(3”)-Ib, aph(6)-Id, armA and aph(3’)-Ia), phenicoles (e.g., catB8), tetracyclines (e.g., tet.B and tet.39), sulfonamides (e.g., sul.1 and sul.2), macrolides and lincosamide (e.g., mph.E, msr.E and abaF). MLST and core genome MLST (cgMLST) showed an extreme diversity among the strains. Several strains isolated from different countries clustered together by cgMLST; however, different clusters shared the same ST. Developing an action plan on AMR, increasing awareness and prohibiting the selling of antibiotics without prescription must be mandatory for this region. Such efforts are critical for enforcing targeted policies on the rational use of carbapenem compounds and controlling AMR dissemination and emergence in general.

Genetic Configuration of Genomic Resistance Islands in Acinetobacter baumannii Clinical Isolates From Egypt

“…Isolates that belong to this CC were reported from Egypt (Jalal et al, 2021), Saudi Arabia (Lopes et al, 2015), and Brazil (Leal et al, 2020). Another ST identified here, ST164 Pas /1418 Oxf , was reported in the isolates from Myanmar (Tada et al, 2020), Vietnam (Wareth et al, 2021), Brazil (Coelho-Souza et al, 2013, Kenya (Musila et al, 2021), and as a major clone in Thailand (Khuntayaporn et al, 2021). SNP-based phylogenetic analysis showed that our isolates were clustered with others from different parts of the world.…”

“…Updates on the genetic background of MDR and XDR A. baumannii are continuously being published from different parts of the world (Hamidian and Nigro, 2019;Gheorghe et al, 2021;Wareth et al, 2021) and from Egypt as well (Hassan et al, 2021;Jalal et al, 2021;Wasfi et al, 2021). However, reports about the association of resistance genes with RIs are relatively scarce.…”

The Molecular Detection of Class B and Class D Carbapenemases in Clinical Strains of Acinetobacter calcoaceticus-baumannii Complex: The High Burden of Antibiotic Resistance and the Co-Existence of Carbapenemase Genes

“…Carbapenem-resistant Acinetobacter calcoaceticus - baumannii complex (CRACB) is a well-known nosocomial pathogen that causes severe public health problems, primarily in low- and middle-income countries (LMICs) [ 1 , 2 ]. Recent data indicate that antimicrobial resistance (AMR) is becoming the leading cause of death; bacterial AMR was associated with 4.95 million deaths worldwide in 2019, of which 1.27 million deaths were caused by AMR, with relatively higher mortality among LMICs due to their fragile healthcare systems [ 3 ].…”

Genetic Diversity of Antimicrobial Resistance and Key Virulence Features in Two Extensively Drug-Resistant Acinetobacter baumannii Isolates

“…Therefore, the intermediate susceptibility (increased exposure) of strain #36 carrying ADC-6 to cefepime is in agreement with the antibiogram profile of this strain, showing a low degree of cefepime resistance ( Table 2 ). Vice versa, strain #150 is resistant to cefepime (MIC ≥ 64 mg/L), possessing the ADC-25 β-lactamase, which is the most prevalent among A. baumannii strains [ 34 , 35 , 36 ]. The blaADC-25 nucleotide sequence alignment with available A. baumannii genomes revealed 100% identity with blaADC-33 .…”