A single-center analysis of clonal transmission of carbapenem-resistant Acinetobacter baumannii among intensive care unit patients during the COVID-19 pandemic

Abstract

Carbapenem-Resistant Acinetobacter baumannii (CRAB) outbreak in intensive care units (ICUs) is a significant problem for healthcare facilities. In this study, we aimed to investigate the occurrence of CRAB isolates among ICU-admitted patients during the three waves of the COVID-19 pandemic in Iran using Multiple-Locus Variable Number Tandem-Repeat Analysis (MLVA). We obtained 50 (A) baumannii isolates from tracheal aspirate and blood culture samples. In the disc diffusion method, all isolates were cefotaxime, ceftriaxone, and cefepime-resistant, while 98% (49/50) of isolates were resistant to piperacillin, piperacillin-tazobactam, ceftazidime, and ciprofloxacin. Levofloxacin and tobramycin resistance was found in 76% (38/50) of isolates. In the microbroth dilution test all isolates were resistant to imipenem, 98% (49/50) to meropenem, 68% (34/50) to colistin, and 20% (10/50) to polymyxin (B) Based on the PCR findings, all isolates harbored bla_OXA-40, ISAba-1, and int-2 genes. There were no isolates found that have the bla_OXA-58, bla_OXA-143, bla_VEB-1, bla_VIM, and int-3 genes. Among Extended-spectrum beta-lactamases (ESBL) genes, bla_CTX-M, bla_TEM, bla_SHV, bla_GES, and bla_PER-1 have a prevalence of 42% (21/50), 84% (42/50), 58% (29/50), 78% (39/50), and 54% (27/50), respectively. 74% (37/50) of the isolates had the bla_OXA-23 gene, while all of the isolates carried the bla_OXA-40 gene. Among MBL genes, bla_IPM, bla_GIM, bla_SIM, and bla_NDM-1 have a prevalence of 20% (10/50), 8% (4/50), 22% (11/50), and 60% (30/50), respectively. The prevalence of int-1 was documented as 74% (37/50). Accordingly, all isolates were identified as CRAB. The co-existence of bla_OXA-23/int-2 and bla_OXA-23/isaba-1 was 74% (37/50). The co-existence of bla_NDM-1/ISAba-1 was observed in 30 (60%) isolates. Using an 80% similarity threshold on the dendrogram constructed through MLVA typing, all isolates were grouped into two clusters: cluster A with 9 isolates from wave 3, and cluster B with 41 isolates from waves 3, 4, and 5. Our study confirms a clonal transmission of CRAB during the study period and suggests using molecular typing methods like MLVA in healthcare settings to identify dominant clones, antibiotic resistance patterns, and transmission routes. This will help to better manage the emergence and spread of antibiotic-resistant strains in future outbreaks.

Keywords: COVID-19; Carbapenem-Resistant Acinetobacter baumannii; Dendrogram; ESBL; MBL; MLVA; Minimum spanning tree.

Fig. 1

Disc diffusion susceptibility pattern of the isolates. The results were interpreted based on the CLSI guidelines.

Fig. 2

MIC of the isolates generated by microbroth dilution test. The results were interpreted based on the CLSI guidelines.

Fig. 3

Clonal relationship of the isolates. The dendrogram depicts the phylogenetic relationship of the isolates. Cluster A consists of nine isolates from wave 3 with 93.2% similarity, while Cluster B consists of 41 isolates from waves 3, 4, and 5 with 83.8% similarity. The bla_{OXA−51−like} gene, specific to A. baumannii species, was present in all isolates but is not displayed on the dendrogram. The bla_OXA−58, bla_OXA−143, bla_VEB−1, bla_VIM, and int-3 genes, which were absent in all isolates, are also not shown.

Fig. 4

Distribution routes of the isolates. The tree analysis indicates that there is a strong likelihood of isolates spreading through the two paths shown in the figure. Pathway one: The sources of the isolates collected in wave 4 were the isolates 6 and 49 from wave 3. The sources of the isolates collected in wave 5 were the isolates 113, 115, 108, 125, 139, and 150 from wave 4. Pathway two: The sources of the isolates collected in wave 4 were the isolates number 5 and 58 from wave 3. The sources of the isolates collected in wave 5 were the isolates 131, 110, 120, 138, 152, and 98 from wave 4. The A. baumannii isolates ID is represented by numbers on the nodes. 100% identical isolates are represented by numbers on a single node. The size of each node corresponds to the number of connected isolates. Nodes that differ by 1 locus are connected with a short, thick line, while nodes that differ by 2, 3, or 4 loci are connected with longer, thin lines. Nodes that differ by 4 loci are connected by a dotted line.