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Resolution of a Protracted Serogroup B Meningococcal Outbreak with Whole-Genome Sequencing Shows Interspecies Genetic Transfer

View Article: PubMed Central - PubMed

ABSTRACT

A carriage study was undertaken (n = 112) to ascertain the prevalence of Neisseria spp. following the eighth case of invasive meningococcal disease in young children (5 to 46 months) and members of a large extended indigenous ethnic minority Traveller family (n = 123), typically associated with high-occupancy living conditions. Nested multilocus sequence typing (MLST) was employed for case specimen extracts. Isolates were genome sequenced and then were assembled de novo and deposited into the Bacterial Isolate Genome Sequencing Database (BIGSdb). This facilitated an expanded MLST approach utilizing large numbers of loci for isolate characterization and discrimination. A rare sequence type, ST-6697, predominated in disease specimens and isolates that were carried (n = 8/14), persisting for at least 44 months, likely driven by the high population density of houses (n = 67/112) and trailers (n = 45/112). Carriage for Neisseria meningitidis (P < 0.05) and Neisseria lactamica (P < 0.002) (2-sided Fisher's exact test) was more likely in the smaller, more densely populated trailers. Meningococcal carriage was highest in 24- to 39-year-olds (45%, n = 9/20). Evidence of horizontal gene transfer (HGT) was observed in four individuals cocolonized by Neisseria lactamica and Neisseria meningitidis. One HGT event resulted in the acquisition of 26 consecutive N. lactamica alleles. This study demonstrates how housing density can drive meningococcal transmission and carriage, which likely facilitated the persistence of ST-6697 and prolonged the outbreak. Whole-genome MLST effectively distinguished between highly similar outbreak strain isolates, including those isolated from person-to-person transmission, and also highlighted how a few HGT events can distort the true phylogenetic relationship between highly similar clonal isolates.

No MeSH data available.


Venn diagram of a whole-genome MLST comparison (loci, 1,887) showing shared alleles for N. meningitidis (M46.3 and M45.2) and N. lactamica (M45.1 and M46.2) isolates from nasopharyngeal carriage in two individuals. Cocolonizing isolates M45.1 and M45.2 shared 34 alleles while cocolonizing isolates M46.3 and M46.2 shared 61 alleles.
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Figure 5: Venn diagram of a whole-genome MLST comparison (loci, 1,887) showing shared alleles for N. meningitidis (M46.3 and M45.2) and N. lactamica (M45.1 and M46.2) isolates from nasopharyngeal carriage in two individuals. Cocolonizing isolates M45.1 and M45.2 shared 34 alleles while cocolonizing isolates M46.3 and M46.2 shared 61 alleles.

Mentions: A whole-genome comparison (1,887 loci) of two N. lactamica isolates (ST10984) and two meningococcal isolates (ST6697) cultured from their respective pharyngeal swabs was undertaken (Fig. 5). The two N. lactamica isolates shared alleles at 1,856 of 1,887 loci (98.36%). Similarly, the meningococcal isolates shared alleles at 1,759 of 1,887 loci (93.2%). All four isolates shared identical alleles at 15 loci. Meningococcal isolate M45.2 contained 34 and 33 alleles that were identical to those in N. lactamica isolates M45.1 and M46.2, respectively. Meningococcal isolate M46.3 shared 61 identical alleles each with N. lactamica isolates M45.1 and M46.2. For comparison, the next most closely related ST6697 isolate to M46.2, the carried isolate M35.1, shared seven alleles with it. Shared alleles among M45.1, M45.2, M46.2, and M46.3 included the iron acquisition gene, fetA (F5-43), a transferrin binding protein, tbpB, and a prepilin peptidase, pilD. Many of these shared alleles were observed adjacent to each other in the meningococcal genomes, suggesting acquisition via HGT. Short-read mapping-based sequence assembly tools Bowtie and SRST2 verified that neither contamination nor misassembly was the cause of this higher than usual sharing of alleles among the species.


Resolution of a Protracted Serogroup B Meningococcal Outbreak with Whole-Genome Sequencing Shows Interspecies Genetic Transfer
Venn diagram of a whole-genome MLST comparison (loci, 1,887) showing shared alleles for N. meningitidis (M46.3 and M45.2) and N. lactamica (M45.1 and M46.2) isolates from nasopharyngeal carriage in two individuals. Cocolonizing isolates M45.1 and M45.2 shared 34 alleles while cocolonizing isolates M46.3 and M46.2 shared 61 alleles.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5121376&req=5

Figure 5: Venn diagram of a whole-genome MLST comparison (loci, 1,887) showing shared alleles for N. meningitidis (M46.3 and M45.2) and N. lactamica (M45.1 and M46.2) isolates from nasopharyngeal carriage in two individuals. Cocolonizing isolates M45.1 and M45.2 shared 34 alleles while cocolonizing isolates M46.3 and M46.2 shared 61 alleles.
Mentions: A whole-genome comparison (1,887 loci) of two N. lactamica isolates (ST10984) and two meningococcal isolates (ST6697) cultured from their respective pharyngeal swabs was undertaken (Fig. 5). The two N. lactamica isolates shared alleles at 1,856 of 1,887 loci (98.36%). Similarly, the meningococcal isolates shared alleles at 1,759 of 1,887 loci (93.2%). All four isolates shared identical alleles at 15 loci. Meningococcal isolate M45.2 contained 34 and 33 alleles that were identical to those in N. lactamica isolates M45.1 and M46.2, respectively. Meningococcal isolate M46.3 shared 61 identical alleles each with N. lactamica isolates M45.1 and M46.2. For comparison, the next most closely related ST6697 isolate to M46.2, the carried isolate M35.1, shared seven alleles with it. Shared alleles among M45.1, M45.2, M46.2, and M46.3 included the iron acquisition gene, fetA (F5-43), a transferrin binding protein, tbpB, and a prepilin peptidase, pilD. Many of these shared alleles were observed adjacent to each other in the meningococcal genomes, suggesting acquisition via HGT. Short-read mapping-based sequence assembly tools Bowtie and SRST2 verified that neither contamination nor misassembly was the cause of this higher than usual sharing of alleles among the species.

View Article: PubMed Central - PubMed

ABSTRACT

A carriage study was undertaken (n = 112) to ascertain the prevalence of Neisseria spp. following the eighth case of invasive meningococcal disease in young children (5 to 46 months) and members of a large extended indigenous ethnic minority Traveller family (n = 123), typically associated with high-occupancy living conditions. Nested multilocus sequence typing (MLST) was employed for case specimen extracts. Isolates were genome sequenced and then were assembled de novo and deposited into the Bacterial Isolate Genome Sequencing Database (BIGSdb). This facilitated an expanded MLST approach utilizing large numbers of loci for isolate characterization and discrimination. A rare sequence type, ST-6697, predominated in disease specimens and isolates that were carried (n = 8/14), persisting for at least 44 months, likely driven by the high population density of houses (n = 67/112) and trailers (n = 45/112). Carriage for Neisseria meningitidis (P < 0.05) and Neisseria lactamica (P < 0.002) (2-sided Fisher's exact test) was more likely in the smaller, more densely populated trailers. Meningococcal carriage was highest in 24- to 39-year-olds (45%, n = 9/20). Evidence of horizontal gene transfer (HGT) was observed in four individuals cocolonized by Neisseria lactamica and Neisseria meningitidis. One HGT event resulted in the acquisition of 26 consecutive N. lactamica alleles. This study demonstrates how housing density can drive meningococcal transmission and carriage, which likely facilitated the persistence of ST-6697 and prolonged the outbreak. Whole-genome MLST effectively distinguished between highly similar outbreak strain isolates, including those isolated from person-to-person transmission, and also highlighted how a few HGT events can distort the true phylogenetic relationship between highly similar clonal isolates.

No MeSH data available.