The K5 capsular polysaccharide of the bacterium Acinetobacter baumannii SDF with the same K unit containing Leg5Ac7Ac as the K7 capsular polysaccharide but a different linkage between the K units

Structure of the K141 capsular polysaccharide produced by Acinetobacter baumannii isolate KZ1106 that carries KL141 at the chromosomal K locus

The structure of the K141 type capsular polysaccharide (CPS) produced by Acinetobacter baumannii KZ1106, a clinical isolate recovered from Kazakhstan in 2016, was established by sugar analyses and one- and two-dimensional 1H and 13C NMR spectroscopy. The CPS was shown to consist of branched tetrasaccharide repeating units (K-units) with the following structure: This structure was found to be consistent with the genetic content of the KL141 CPS biosynthesis gene cluster at the chromosomal K locus in the KZ1106 whole genome sequence. Assignment of the encoded enzymes allowed the first sugar of the K unit to be identified, which revealed that the β-d-GlcpNAc-(1→3)-d-GlcpNAc bond is the linkage between K-units formed by the WzyKL141 polymerase.

The Acinetobacter baumannii K239 capsular polysaccharide includes heptasaccharide units that are structurally related to K86 but joined by different linkages formed by different Wzy polymerases

The K239 type capsular polysaccharide (CPS) isolated from Acinetobacter baumannii isolate MAR19-4435 was studied by sugar analysis, one- and two-dimensional 1H and 13C NMR spectroscopy. K239 consists of branched heptasaccharide repeats (K-units) comprised of five residues of l-rhamnose (l-Rhap), and one residue each of d-glucuronic acid (d-GlcpA) and N-acetyl-d-glucosamine (d-GlcpNAc). The structure of K239 is closely related to that of the A. baumannii K86 CPS type, though the two differ in the 2,3-substitution patterns on the l-Rhap residue that is involved in the linkage between K-units in the CPS polymer. This structural difference was attributed to the presence of a gtr221 glycosyltransferase gene and a wzyKL239 polymerase gene in KL239 that replaces the gtr80 and wzyKL86 genes in the KL86 CPS biosynthesis gene cluster. Comparison of the two structures established the role of a novel WzyKL239 polymerase encoded by KL239 that forms the β-d-GlcpNAc-(1→2)-l-Rhap linkage between K239 units. A. baumannii MAR19-4435 was found to be non-susceptible to infection by the APK86 bacteriophage, which encodes a depolymerase that specifically cleaves the linkage between K-units in the K86 CPS, indicating that the difference in 2,3-substitution of l-Rhap influences the susceptibility of this isolate to bacteriophage activity.

5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic Acids in the Capsular Polysaccharides of Acinetobacter baumannii

The polysaccharide capsule surrounding bacterial cell plays an important role in pathogenesis of infections caused by the opportunistic pathogen Acinetobacter baumannii by providing protection from external factors. The structures of the capsular polysaccharide (CPS) produced by A. baumannii isolates and the corresponding CPS biosynthesis gene clusters are highly diverse, although many of them are related. Many types of A. baumannii CPSs contain isomers of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acid (DTNA). Three of these isomers, namely acinetaminic acid (l-glycero-l-altro isomer), 8-epiacinetaminic acid (d-glycero-l-altro isomer), and 8-epipseudaminic acid (d-glycero-l-manno isomer), have not been found so far in naturally occurring carbohydrates from other species. In A. baumannii CPSs, DTNAs carry N-acyl substituents at positions 5 and 7; in some CPSs, both N-acetyl and N-(3-hydroxybutanoyl) groups are present. Remarkably, pseudaminic acid carries the (R)-isomer and legionaminic acid carries the (S)-isomer of the 3-hydroxybutanoyl group. The review addresses the structure and genetics of biosynthesis of A. baumannii CPSs containing di-N-acyl derivatives of DTNA.

The K218 capsular polysaccharide produced by Acinetobacter baumannii isolate 52-249 includes 5,7-di-N-acetylpseudaminic acid linked by a KpsS3 glycosyltransferase

Two acylated forms of the higher sugar, 5,7-diamino-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid called pseudaminic acid, Pse5Ac7Ac and Pse5Ac7RHb where R indicates (R)-3-hydroxybutanoyl, have been found to occur in many capsular polysaccharide (CPS) types produced by isolates of an important human pathogen, Acinetobacter baumannii. The presence of either a psaABCEDF or psaABCGHF gene module at the K locus (KL) for CPS biosynthesis determines the type of the variant produced. Here, an A. baumannii clinical isolate 52-249, recovered in 2015 in Moscow, Russia, was found to include a novel psaABCIJF gene module in the KL218 sequence at the K locus. The CPS from 52-249 was extracted and studied by sugar analysis and partial acid hydrolysis along with one- and two-dimensional ¹H and ¹³C NMR spectroscopy. A branched tetrasaccharide repeating unit was identified, which included a →3)-α-d-Galp-(1→6)-α-d-GlcpNAc-(1→3)-β-d-GalpNAc-(1→ main chain and Pse5Ac7Ac attached as a side branch, indicating that the psaABCIJF gene module is associated with synthesis of this variant. The K218 CPS was found to be structurally related to the K46 CPS of A. baumannii, and a comparison of the two structures enabled the assignment of glycosyltransferases. A KpsS3 protein for the α-(2→6) linkage of the Pse5Ac7Ac residue to D-Galp in K218 was identified.

Structure of the K98 capsular polysaccharide from Acinetobacter baumannii REV-1184 containing a cyclic pyruvic acid acetal

The K98 capsular polysaccharide (CPS) from the Acinetobacter baumannii clinical isolate, REV-1184, was studied by sugar analysis and Smith degradation along with one- and two-dimensional ¹H and ¹³C NMR spectroscopy and high-resolution electrospray ionization mass spectrometry. The CPS was found to consist of linear tetrasaccharide repeats (K-units) that include one residue each of d-GlcpNAc, d-GalpNAc, 2-acetamido-2-deoxy-d-galacturonic acid (d-GalpNAcA), and 2-acetamido-2,6-dideoxy-d-glucose (N-acetylquinovosamine, d-QuipNAc), with the GalpNAc residue decorated with a (R)-configurated 4,6-pyruvic acid acetal group. The CPS has a similar composition to that of A. baumannii K4 but the topology of the tetrasaccharide K-unit is different (linear in K98 versus branched in K4). This was due to a difference in sequence for the Wzy polymerases encoded by the CPS biosynthesis gene clusters KL98 and KL4, with the Wzy_K98 polymerase forming a β-d-QuipNAc-(1→3)-d-GalpNAc linkage between the K98 units.

Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive

Multiply antibiotic-resistant Acinetobacter baumannii infections are a global public health concern and accurate tracking of the spread of specific lineages is needed. Variation in the composition and structure of capsular polysaccharide (CPS), a critical determinant of virulence and phage susceptibility, makes it an attractive epidemiological marker. The outer core (OC) of lipooligosaccharide also exhibits variation. To take better advantage of the untapped information available in whole genome sequences, we have created a curated reference database of 92 publicly available gene clusters at the locus encoding proteins responsible for biosynthesis and export of CPS (K locus), and a second database for 12 gene clusters at the locus for outer core biosynthesis (OC locus). Each entry has been assigned a unique KL or OCL number, and is fully annotated using a simple, transparent and standardized nomenclature. These databases are compatible with Kaptive, a tool for in silico typing of bacterial surface polysaccharide loci, and their utility was validated using (a) >630 assembled A. baumannii draft genomes for which the KL and OCL regions had been previously typed manually, and (b) 3386 A. baumannii genome assemblies downloaded from NCBI. Among the previously typed genomes, Kaptive was able to confidently assign KL and OCL types with 100 % accuracy. Among the genomes retrieved from NCBI, Kaptive detected known KL and OCL in 87 and 90 % of genomes, respectively, indicating that the majority of common KL and OCL types are captured within the databases; 13 of the 92 KL in the database were not detected in any publicly available whole genome assembly. The failure to assign a KL or OCL type may indicate incomplete or poor-quality genomes. However, further novel variants may remain to be documented. Combining outputs with multilocus sequence typing (Institut Pasteur scheme) revealed multiple KL and OCL types in collections of a single sequence type (ST) representing each of the two predominant globally distributed clones, ST1 of GC1 and ST2 of GC2, and in collections of other clones comprising >20 isolates each (ST10, ST25, and ST140), indicating extensive within-clone replacement of these loci. The databases are available at https://github.com/katholt/Kaptive and will be updated as further locus types become available.

K units of the K8 and K54 capsular polysaccharides produced by Acinetobacter baumannii BAL 097 and RCH52 have the same structure but contain different di-N-acyl derivatives of legionaminic acid and are linked differently

The K8 and K54 capsular polysaccharides were isolated from Acinetobacter baumannii BAL 097 and RCH52, respectively, and studied by sugar analysis, partial acid hydrolysis and selective solvolysis with CF₃CO₂H in the presence of 2-methyl-1-propanol, along with 1D and 2D ¹H and ¹³C NMR spectroscopy. The following structures of related branched tetrasaccharide repeats (K units) of the polysaccharides were established: where Leg indicates 5,7-diamino-3,5,7,9-tetradeoxy-d-glycero-d-galacto-non-2-ulosonic (legionaminic) acid and R indicates (R)-3-hydroxybutanoyl or acetyl in the ratio ~2.5:1. The sequences of the KL8 and KL54 capsule gene clusters were closely related. The difference in the acyl group at O-7 on the sidechain legionaminic acid is due to differences in two genes in the legionaminic acid biosynthesis cluster. The wzy genes encoding the K unit polymerases are also different and make different linkages between the K units, allowing the first sugar of both K units to be identified as d-GlcpNAc. The shared Gtr20 glycosyltransferase, also encoded in KL63, forms the α-l-FucpNAc-(1 → 3)-d-GlcpNAc linkage, and Gtr19 was predicted to form α-d-GalpNAc-(1 → 3)-l-FucpNAc. Gtr18 from KL8 is 75% identical to Gtr108 from KL54 and both would link the Leg derivative to d-GalpNAc. Hence the genes present at the K locus were consistent with the composition and structures of the K8 and K54 capsular polysaccharides.

The K46 and K5 capsular polysaccharides produced by Acinetobacter baumannii NIPH 329 and SDF have related structures and the side-chain non-ulosonic acids are 4-O-acetylated by phage-encoded O-acetyltransferases

Acinetobacter baumannii isolate NIPH 329 carries a novel capsular polysaccharide (CPS) gene cluster, designated KL46, that is closely related to the KL5 locus in A. baumannii isolate SDF but includes genes for synthesis of 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic (di-N-acetylpseudaminic) acid (Pse5Ac7Ac) instead of the corresponding D-glycero-D-galacto isomer (di-N-acetyllegionaminic acid) (Leg5Ac7Ac). In agreement with the genetic content of KL46, chemical studies of the K46 CPS produced by NIPH 329 revealed a branched tetrasaccharide repeat (K unit) with an overall structure the same as K5 from SDF but with â-Pse5Ac7Ac replacing α-Leg5Ac7Ac. As for K5, the K46 unit begins with d-GalpNAc and includes α-d-GlcpNAc-(1→3)-d-GalpNAc and α-d-Galp-(1→6)-d-GlcpNAc linkages, formed by Gtr14 and Gtr15 glycosyltransferases, respectively. The Gtr94_K46 glycosyltransferase, which is related to Gtr13_K5, links Pse5Ac7Ac to d-Galp in the growing K unit via a â-(2→6) linkage. Nearly identical Wzy enzymes connect the K46 and K5 units via a α-D-GalpNAc-(1→3)-α-D-Galp linkage to form closely related CPSs. Both Pse5Ac7Ac in K46 and Leg5Ac7Ac in K5 are acetylated at O4 but no acetyltransferase gene is present in KL46 or KL5. Related acetyltransferases were found encoded in the NIPH 329 and SDF genomes, but not in other strains carrying an unacetylated Pse or Leg derivative in the CPS. The genes encoding the acetyltransferases were in different putative phage genomes. However, related acetyltransferases were rare among the >3000 publically available genome sequences.