Klebsiella pneumoniae is a nosocomial pathogen, pointed out by the World Helth Organisation (WHO) as 'critical' regarding the highly limited options of treatment. Lipopolysaccharide (LPS, O-antigen) and capsular polysaccharide (K-antigen) are its virulence factors and surface antigens, determining O- and K-serotypes and encoded by O- or K-loci. They are promising targets for antibody-based therapies (vaccines and passive immunization) as an alternative to antibiotics. To make such immunotherapy effective, knowledge about O/K-antigen structures, drift, and distribution among clinical isolates is needed. At present, the structural analysis of O-antigens is efficiently supported by bioinformatics. O- and K-loci-based genotyping by polymerase chain reaction (PCR) or whole genome sequencing WGS has been proposed as a diagnostic tool, including the Kaptive tool available in the public domain. We analyzed discrepancies for O2 serotyping between Kaptive-based predictions (O2 variant 2 serotype) and the actual phenotype (O2 variant 1) for two K. pneumoniae clinical isolates. Identified length discrepancies from the reference O-locus resulted from insertion sequences (ISs) within rfb regions of the O-loci. In silico analysis of 8130 O1 and O2 genomes available in public databases indicated a broader distribution of ISs in rfbs that may influence the actual O-antigen structure. Our results show that current high-throughput genotyping algorithms need to be further refined to consider the effects of ISs on the LPS O-serotype.

Lipopolysaccharide, NMR, LPS, O-antigen, Klebsiella, O-serotype, Kaptive, WGS

There is only one chemically distinct structure:

SVGMWSMILES3D molIonize

 

*O[C@H]1[C@H]([C@H](O)CO)O[C@@H](O[C@@H]2[C@@H](O)[C@@H](*)O[C@H](CO)[C@@H]2O[C@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)[C@@H]1O

486.423 g/mol (C₁₈H₃₀R₂O₁₅, R = next and previous repeats, not counted in mol weight)

Klebsiella pneumoniae is a nosocomial pathogen, pointed out by the World Helth Organisation (WHO) as 'critical' regarding the highly limited options of treatment. Lipopolysaccharide (LPS, O-antigen) and capsular polysaccharide (K-antigen) are its virulence factors and surface antigens, determining O- and K-serotypes and encoded by O- or K-loci. They are promising targets for antibody-based therapies (vaccines and passive immunization) as an alternative to antibiotics. To make such immunotherapy effective, knowledge about O/K-antigen structures, drift, and distribution among clinical isolates is needed. At present, the structural analysis of O-antigens is efficiently supported by bioinformatics. O- and K-loci-based genotyping by polymerase chain reaction (PCR) or whole genome sequencing WGS has been proposed as a diagnostic tool, including the Kaptive tool available in the public domain. We analyzed discrepancies for O2 serotyping between Kaptive-based predictions (O2 variant 2 serotype) and the actual phenotype (O2 variant 1) for two K. pneumoniae clinical isolates. Identified length discrepancies from the reference O-locus resulted from insertion sequences (ISs) within rfb regions of the O-loci. In silico analysis of 8130 O1 and O2 genomes available in public databases indicated a broader distribution of ISs in rfbs that may influence the actual O-antigen structure. Our results show that current high-throughput genotyping algorithms need to be further refined to consider the effects of ISs on the LPS O-serotype.

Lipopolysaccharide, NMR, LPS, O-antigen, Klebsiella, O-serotype, Kaptive, WGS

There is only one chemically distinct structure:

SVGMWSMILES3D molIonize

 

*O[C@H]1[C@H]([C@H](O)CO)O[C@@H](O[C@@H]2[C@@H](O[C@H]3O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)[C@@H](*)O[C@H](CO)[C@@H]2O)[C@@H]1O

486.423 g/mol (C₁₈H₃₀R₂O₁₅, R = next and previous repeats, not counted in mol weight)

Klebsiella pneumoniae is a nosocomial pathogen, pointed out by the World Helth Organisation (WHO) as 'critical' regarding the highly limited options of treatment. Lipopolysaccharide (LPS, O-antigen) and capsular polysaccharide (K-antigen) are its virulence factors and surface antigens, determining O- and K-serotypes and encoded by O- or K-loci. They are promising targets for antibody-based therapies (vaccines and passive immunization) as an alternative to antibiotics. To make such immunotherapy effective, knowledge about O/K-antigen structures, drift, and distribution among clinical isolates is needed. At present, the structural analysis of O-antigens is efficiently supported by bioinformatics. O- and K-loci-based genotyping by polymerase chain reaction (PCR) or whole genome sequencing WGS has been proposed as a diagnostic tool, including the Kaptive tool available in the public domain. We analyzed discrepancies for O2 serotyping between Kaptive-based predictions (O2 variant 2 serotype) and the actual phenotype (O2 variant 1) for two K. pneumoniae clinical isolates. Identified length discrepancies from the reference O-locus resulted from insertion sequences (ISs) within rfb regions of the O-loci. In silico analysis of 8130 O1 and O2 genomes available in public databases indicated a broader distribution of ISs in rfbs that may influence the actual O-antigen structure. Our results show that current high-throughput genotyping algorithms need to be further refined to consider the effects of ISs on the LPS O-serotype.

Lipopolysaccharide, NMR, LPS, O-antigen, Klebsiella, O-serotype, Kaptive, WGS

There is only one chemically distinct structure:

SVGMWSMILES3D molIonize

 

*O[C@H]1[C@@H](O)[C@@H](CO)O[C@H](O[C@@H]2[C@@H](O)[C@H](*)O[C@H](CO)[C@@H]2O)[C@@H]1O

324.282 g/mol (C₁₂H₂₀R₂O₁₀, R = next and previous repeats, not counted in mol weight)

Klebsiella pneumoniae is a nosocomial pathogen, pointed out by the World Helth Organisation (WHO) as 'critical' regarding the highly limited options of treatment. Lipopolysaccharide (LPS, O-antigen) and capsular polysaccharide (K-antigen) are its virulence factors and surface antigens, determining O- and K-serotypes and encoded by O- or K-loci. They are promising targets for antibody-based therapies (vaccines and passive immunization) as an alternative to antibiotics. To make such immunotherapy effective, knowledge about O/K-antigen structures, drift, and distribution among clinical isolates is needed. At present, the structural analysis of O-antigens is efficiently supported by bioinformatics. O- and K-loci-based genotyping by polymerase chain reaction (PCR) or whole genome sequencing WGS has been proposed as a diagnostic tool, including the Kaptive tool available in the public domain. We analyzed discrepancies for O2 serotyping between Kaptive-based predictions (O2 variant 2 serotype) and the actual phenotype (O2 variant 1) for two K. pneumoniae clinical isolates. Identified length discrepancies from the reference O-locus resulted from insertion sequences (ISs) within rfb regions of the O-loci. In silico analysis of 8130 O1 and O2 genomes available in public databases indicated a broader distribution of ISs in rfbs that may influence the actual O-antigen structure. Our results show that current high-throughput genotyping algorithms need to be further refined to consider the effects of ISs on the LPS O-serotype.

Lipopolysaccharide, NMR, LPS, O-antigen, Klebsiella, O-serotype, Kaptive, WGS

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6
3	bDGalf	110.1	80.5	85.2	82.6	71.5	63.5
	aDGalp	100.2	67.8	77.8	70.1	72.0	61.9


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6
3	bDGalf	5.22	4.42	4.07	4.26	3.88	3.69
	aDGalp	5.09	3.94	3.94	4.14	4.14	3.75


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6
3	bDGalf	110.1/5.22	80.5/4.42	85.2/4.07	82.6/4.26	71.5/3.88	63.5/3.69
	aDGalp	100.2/5.09	67.8/3.94	77.8/3.94	70.1/4.14	72.0/4.14	61.9/3.75

There is only one chemically distinct structure:

SVGMWSMILES3D molIonize

 

*O[C@H]1[C@H]([C@H](O)CO)O[C@@H](O[C@@H]2[C@@H](O)[C@@H](*)O[C@H](CO)[C@@H]2O)[C@@H]1O

324.282 g/mol (C₁₂H₂₀R₂O₁₀, R = next and previous repeats, not counted in mol weight)