Molecular characterisation of Acinetobacter baumannii isolates from bloodstream infections in a tertiary-level hospital in South Africa

Abstract

Acinetobacter baumannii is an opportunistic pathogen and causes various infections in patients. This study aimed to describe the clinical, epidemiological and molecular characteristics of A. baumannii isolated from BCs in patients at a tertiary-level hospital in South Africa. Ninety-six isolates from bloodstream infections were collected. Clinical characteristics of patients were recorded from patient files. Organism identification and AST was performed using automated systems. PCR screening for the mcr-1 to mcr-5 genes was done. To infer genetic relatedness, a dendrogram was constructed using MALDI-TOF MS. All colistin-resistant isolates (n = 9) were selected for WGS. The patients were divided into three groups, infants (<1 year; n = 54), paediatrics (1–18 years; n = 6) and adults (≥19 years; n = 36) with a median age of 13 days, 1 and 41 years respectively. Of the 96 A. baumannii bacteraemia cases, 96.9% (93/96) were healthcare-associated. The crude mortality rate at 30 days was 52.2% (48/92). The majority of the isolates were multidrug-resistant (MDR). All isolates were PCR-negative for the mcr-1 to mcr-5 genes. The majority of the isolates belonged to cluster 1 (62/96) according to the MALDI-TOF MS dendrogram. Colistin resistance was confirmed in nine A. baumannii isolates (9.4%). The colistin-resistant isolates belonged to sequence type (ST) 1 (5/6) and ST2 (1/6). The majority of ST1 isolates showed low SNP diversity (≤4 SNPs). All the colistin-resistant isolates were resistant to carbapenems, exhibited an XDR phenotype and harboured the blaOXA–23 gene. The blaNDM gene was only detected in ST1 colistin-resistant isolates (n = 5). The lpsB gene was detected in all colistin-resistant isolates as well as various efflux pump genes belonging to the RND, the MFS and the SMR families. The lipooligosaccharide OCL1 was detected in all colistin-resistant ST1 and ST2 isolates and the capsular polysaccharide KL3 and KL17 were detected in ST2 and ST1 respectively. This study demonstrated a 9.4% prevalence of colistin-resistant ST1 and ST2 A. baumannii in BC isolates. The detection of the lpsB gene indicates a potential threat and requires close prospective monitoring.

Colistin Resistance in Acinetobacter baumannii: Molecular Mechanisms and Epidemiology

“…Data providing information on the epidemiology of colistin-resistant A. baumannii are generally shown by MLST categorization (Oxford and Pasteur) of these isolates [ 151 , 152 ]. According to the less discriminating Pasteur scheme, colistin-resistant A. baumannii sequence type (ST) 2 isolates are found to be most prevalent ST associated with colistin resistance in A. baumannii and occur in all continents for which data are available (Europe, Asia, Africa, and North and South America) [ 73 , 74 , 75 , 76 , 86 , 88 , 89 , 90 , 91 , 97 , 107 , 153 , 154 , 155 ] ( Figure 2 ). In addition, ST1 was detected in Europe and Africa [ 90 , 95 , 97 , 154 , 156 ], whereas other Pasteur STs occurred exclusively in specific continents (Europe—ST195, ST345, ST490, ST492, ST537, ST632, ST636, ST745, ST1421, and ST1816; Asia—ST1303; Africa—ST158 and ST570; North America—ST46 and ST94; South America—ST15, ST25, ST79, and ST730) [ 74 , 76 , 86 , 88 , 89 , 92 , 97 , 116 , 128 , 129 , 130 , 157 ] ( Figure 2 ).…”

“…MLST typing according to the Oxford scheme revealed that some STs of A. baumannii resistant to colistin are distributed across different continents: ST92 (Asia and North America) [ 101 , 158 ], ST195 (Europe and Africa) [ 76 , 154 ], ST208 [ 76 , 86 , 90 , 97 ] and ST281 [ 75 , 86 , 97 ] (Europe and North America), and ST451 (Europe, Asia, and North America) [ 86 , 90 , 97 , 139 , 158 ] ( Figure 2 ). Interestingly, ST208 has been suggested to be identical to ST92, with the typing result depending on the sequencing performed (high-throughput or Sanger, respectively) [ 86 ].…”

“…However, in North America and South America, only a single ST, ST451 [ 86 , 158 ] and ST233 [ 96 , 157 ] were detected, respectively. Additionally, some STs were detected only in single studies (ST113, ST141, ST191, ST218, ST227, ST231, ST233, ST236, ST282, ST369, ST375, ST387, ST502, ST747, ST944, ST1114, ST1557, ST1566, ST1633, ST1752, ST1809, ST1812, ST1837, ST1929, ST1962, and ST2571) [ 76 , 86 , 96 , 97 , 102 , 117 , 127 , 128 , 129 , 139 , 154 , 157 , 158 , 159 , 160 ] ( Figure 2 ).…”

NDM-1- and OXA-23-producing Acinetobacter baumannii in wastewater of a Nigerian hospital

“…Acinetobacter baumannii therapy is typically problematic ( 11 ) and is further worsened by the increasing rates of resistance to carbapenems, with high resistance rates of up to 100% reported globally ( 12 – 15 ). Carbapenem resistance in A. baumannii is encoded primarily by bla OXA-23 genes, which are more common among the globally disseminated clones and are frequently mobilized and spread between different strains via plasmids ( 3 , 8 , 16 ).…”