Limits...
Comparative genomic analysis reveals distinct genotypic features of the emerging pathogen Haemophilus influenzae type f.

Su YC, Resman F, Hörhold F, Riesbeck K - BMC Genomics (2014)

Bottom Line: We confirmed the histidine auxotrophy and kanamycin resistance in Hif by functional experiments.Moreover, the pattern of unique or missing genes of Hif KR494 was similar in 20 Hif clinical isolates obtained from different years and geographical areas.The genomic comparative analyses facilitated identification of genotypic characteristics that may be related to the specific virulence of Hif.

View Article: PubMed Central - PubMed

Affiliation: Medical Microbiology, Department of Laboratory Medicine Malmö, Lund University, Jan Waldenströms gata 59, SE-205 02 Malmö, Sweden. kristian.riesbeck@med.lu.se.

ABSTRACT

Background: The incidence of invasive disease caused by encapsulated Haemophilus influenzae type f (Hif) has increased in the post-H. influenzae type b (Hib) vaccine era. We previously annotated the first complete Hif genome from a clinical isolate (KR494) that caused septic shock and necrotizing myositis. Here, the full genome of Hif KR494 was compared to sequenced reference strains Hib 10810, capsule type d (Hid) Rd Kw20, and finally nontypeable H. influenzae 3655. The goal was to identify possible genomic characteristics that may shed light upon the pathogenesis of Hif.

Results: The Hif KR494 genome exhibited large regions of synteny with other H. influenzae, but also distinct genome rearrangements. A predicted Hif core genome of 1390 genes was shared with the reference strains, and 6 unique genomic regions comprising half of the 191 unique coding sequences were revealed. The majority of these regions were inserted genetic fragments, most likely derived from the closely-related Haemophilus spp. including H. aegyptius, H. haemolyticus and H. parainfluenzae. Importantly, the KR494 genome possessed several putative virulence genes that were distinct from non-type f strains. These included the sap2 operon, aef3 fimbriae, and genes for kanamycin nucleotidyltranserase, iron-utilization proteins, and putative YadA-like trimeric autotransporters that may increase the bacterial virulence. Furthermore, Hif KR494 lacked a hisABCDEFGH operon for de novo histidine biosynthesis, hmg locus for lipooligosaccharide biosynthesis and biofilm formation, the Haemophilus antibiotic resistance island and a Haemophilus secondary molybdate transport system. We confirmed the histidine auxotrophy and kanamycin resistance in Hif by functional experiments. Moreover, the pattern of unique or missing genes of Hif KR494 was similar in 20 Hif clinical isolates obtained from different years and geographical areas. A cross-species comparison revealed that the Hif genome shared more characteristics with H. aegyptius than Hid and NTHi.

Conclusions: The genomic comparative analyses facilitated identification of genotypic characteristics that may be related to the specific virulence of Hif. In relation to non-type f H. influenzae strains, the Hif genome contains differences in components involved in metabolism and survival that may contribute to its invasiveness.

Show MeSH

Related in: MedlinePlus

Map of region of differences (RgDF) of theH. influenzaetype f KR494 genome. Circular representation of protein conservation between Hif KR494 and reference strains was visualized using DNA plotter. From the outside in, the outer circle shows the genome length of Hif KR494 with position markers. The second circle shows the total ORFs of KR494 genome predicted on both forward and reverse strands. Common and unique ORFs relative to the reference strains are colored in blue and magenta, respectively. Phage-related ORFs are marked in yellow and orange. The third to fifth circles represent the distribution of individual ORF with high homology (≥85% similarity) (in red) to the corresponding ORF of reference strains, Hib 10810, Hid Rd Kw20 and NTHi 3655, respectively. Gaps between the conserved ORFs represent region of difference in the Hif KR494 genome, and were denoted as RgDF1 to 6 (marked with green lines). The GC plot and GC skew of the Hif KR494 genome are shown in the sixth and seventh circle, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC3928620&req=5

Fig2: Map of region of differences (RgDF) of theH. influenzaetype f KR494 genome. Circular representation of protein conservation between Hif KR494 and reference strains was visualized using DNA plotter. From the outside in, the outer circle shows the genome length of Hif KR494 with position markers. The second circle shows the total ORFs of KR494 genome predicted on both forward and reverse strands. Common and unique ORFs relative to the reference strains are colored in blue and magenta, respectively. Phage-related ORFs are marked in yellow and orange. The third to fifth circles represent the distribution of individual ORF with high homology (≥85% similarity) (in red) to the corresponding ORF of reference strains, Hib 10810, Hid Rd Kw20 and NTHi 3655, respectively. Gaps between the conserved ORFs represent region of difference in the Hif KR494 genome, and were denoted as RgDF1 to 6 (marked with green lines). The GC plot and GC skew of the Hif KR494 genome are shown in the sixth and seventh circle, respectively.

Mentions: In the Hif KR494 genome, 6 unique regions of difference (RgD) (i.e. relative to the reference strains) were identified and hereafter referred to as RgDF. The RgDFs were defined as regions in the Hif genome with a low level of conservation at the protein level relative to the reference strains (Hib 10810, Rd Kw20 and NTHi 3655), and containing a minimum of 5 neighboring CDSs with <85% sequence similarity. The RgDFs comprised a total of 144893 bp or 7.8% of the full genome (Figure 2). With the exception of RgDF3 and 6, the G + C contents of the remaining RgDFs (range 35.03-39.28%) were distinct from the remaining part of the genome (38.05%) (Additional file3). This clearly indicated that the RgDFs were acquired from foreign source(s). The RgDFs contained several traits common to mobile genetic elements, including tRNA and rRNA genes, integrases (catalyze unidirectional DNA recombination), and transposases (catalyze movement of transposons). The majority of phage-related genes were found at RgDF1, 3 and 4, which were considered as prophage islands. The RgDF1, 4, 5 and 6 included the predicted Hif KR494 genomic islands (GifKR494) 11, 13, 16 and 21, respectively (Additional file4).Figure 2


Comparative genomic analysis reveals distinct genotypic features of the emerging pathogen Haemophilus influenzae type f.

Su YC, Resman F, Hörhold F, Riesbeck K - BMC Genomics (2014)

Map of region of differences (RgDF) of theH. influenzaetype f KR494 genome. Circular representation of protein conservation between Hif KR494 and reference strains was visualized using DNA plotter. From the outside in, the outer circle shows the genome length of Hif KR494 with position markers. The second circle shows the total ORFs of KR494 genome predicted on both forward and reverse strands. Common and unique ORFs relative to the reference strains are colored in blue and magenta, respectively. Phage-related ORFs are marked in yellow and orange. The third to fifth circles represent the distribution of individual ORF with high homology (≥85% similarity) (in red) to the corresponding ORF of reference strains, Hib 10810, Hid Rd Kw20 and NTHi 3655, respectively. Gaps between the conserved ORFs represent region of difference in the Hif KR494 genome, and were denoted as RgDF1 to 6 (marked with green lines). The GC plot and GC skew of the Hif KR494 genome are shown in the sixth and seventh circle, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3928620&req=5

Fig2: Map of region of differences (RgDF) of theH. influenzaetype f KR494 genome. Circular representation of protein conservation between Hif KR494 and reference strains was visualized using DNA plotter. From the outside in, the outer circle shows the genome length of Hif KR494 with position markers. The second circle shows the total ORFs of KR494 genome predicted on both forward and reverse strands. Common and unique ORFs relative to the reference strains are colored in blue and magenta, respectively. Phage-related ORFs are marked in yellow and orange. The third to fifth circles represent the distribution of individual ORF with high homology (≥85% similarity) (in red) to the corresponding ORF of reference strains, Hib 10810, Hid Rd Kw20 and NTHi 3655, respectively. Gaps between the conserved ORFs represent region of difference in the Hif KR494 genome, and were denoted as RgDF1 to 6 (marked with green lines). The GC plot and GC skew of the Hif KR494 genome are shown in the sixth and seventh circle, respectively.
Mentions: In the Hif KR494 genome, 6 unique regions of difference (RgD) (i.e. relative to the reference strains) were identified and hereafter referred to as RgDF. The RgDFs were defined as regions in the Hif genome with a low level of conservation at the protein level relative to the reference strains (Hib 10810, Rd Kw20 and NTHi 3655), and containing a minimum of 5 neighboring CDSs with <85% sequence similarity. The RgDFs comprised a total of 144893 bp or 7.8% of the full genome (Figure 2). With the exception of RgDF3 and 6, the G + C contents of the remaining RgDFs (range 35.03-39.28%) were distinct from the remaining part of the genome (38.05%) (Additional file3). This clearly indicated that the RgDFs were acquired from foreign source(s). The RgDFs contained several traits common to mobile genetic elements, including tRNA and rRNA genes, integrases (catalyze unidirectional DNA recombination), and transposases (catalyze movement of transposons). The majority of phage-related genes were found at RgDF1, 3 and 4, which were considered as prophage islands. The RgDF1, 4, 5 and 6 included the predicted Hif KR494 genomic islands (GifKR494) 11, 13, 16 and 21, respectively (Additional file4).Figure 2

Bottom Line: We confirmed the histidine auxotrophy and kanamycin resistance in Hif by functional experiments.Moreover, the pattern of unique or missing genes of Hif KR494 was similar in 20 Hif clinical isolates obtained from different years and geographical areas.The genomic comparative analyses facilitated identification of genotypic characteristics that may be related to the specific virulence of Hif.

View Article: PubMed Central - PubMed

Affiliation: Medical Microbiology, Department of Laboratory Medicine Malmö, Lund University, Jan Waldenströms gata 59, SE-205 02 Malmö, Sweden. kristian.riesbeck@med.lu.se.

ABSTRACT

Background: The incidence of invasive disease caused by encapsulated Haemophilus influenzae type f (Hif) has increased in the post-H. influenzae type b (Hib) vaccine era. We previously annotated the first complete Hif genome from a clinical isolate (KR494) that caused septic shock and necrotizing myositis. Here, the full genome of Hif KR494 was compared to sequenced reference strains Hib 10810, capsule type d (Hid) Rd Kw20, and finally nontypeable H. influenzae 3655. The goal was to identify possible genomic characteristics that may shed light upon the pathogenesis of Hif.

Results: The Hif KR494 genome exhibited large regions of synteny with other H. influenzae, but also distinct genome rearrangements. A predicted Hif core genome of 1390 genes was shared with the reference strains, and 6 unique genomic regions comprising half of the 191 unique coding sequences were revealed. The majority of these regions were inserted genetic fragments, most likely derived from the closely-related Haemophilus spp. including H. aegyptius, H. haemolyticus and H. parainfluenzae. Importantly, the KR494 genome possessed several putative virulence genes that were distinct from non-type f strains. These included the sap2 operon, aef3 fimbriae, and genes for kanamycin nucleotidyltranserase, iron-utilization proteins, and putative YadA-like trimeric autotransporters that may increase the bacterial virulence. Furthermore, Hif KR494 lacked a hisABCDEFGH operon for de novo histidine biosynthesis, hmg locus for lipooligosaccharide biosynthesis and biofilm formation, the Haemophilus antibiotic resistance island and a Haemophilus secondary molybdate transport system. We confirmed the histidine auxotrophy and kanamycin resistance in Hif by functional experiments. Moreover, the pattern of unique or missing genes of Hif KR494 was similar in 20 Hif clinical isolates obtained from different years and geographical areas. A cross-species comparison revealed that the Hif genome shared more characteristics with H. aegyptius than Hid and NTHi.

Conclusions: The genomic comparative analyses facilitated identification of genotypic characteristics that may be related to the specific virulence of Hif. In relation to non-type f H. influenzae strains, the Hif genome contains differences in components involved in metabolism and survival that may contribute to its invasiveness.

Show MeSH
Related in: MedlinePlus