Genotypic and Phenotypic Modifications of Neisseria meningitidis after an Accidental Human Passage

Abstract

A scientist in our laboratory was accidentally infected while working with Z5463, a Neisseria meningitidis serogroup A strain. She developed severe symptoms (fever, meningism, purpuric lesions) that fortunately evolved with antibiotic treatment to complete recovery. Pulse-field gel electrophoresis confirmed that the isolate obtained from the blood culture (Z5463BC) was identical to Z5463, more precisely to a fourth subculture of this strain used the week before the contamination (Z5463PI). In order to get some insights into genomic modifications that can occur in vivo, we sequenced these three isolates. All the strains contained a mutated mutS allele and therefore displayed an hypermutator phenotype, consistent with the high number of mutations (SNP, Single Nucleotide Polymorphism) detected in the three strains. By comparing the number of SNP in all three isolates and knowing the number of passages between Z5463 and Z5463PI, we concluded that around 25 bacterial divisions occurred in the human body. As expected, the in vivo passage is responsible for several modifications of phase variable genes. This genomic study has been completed by transcriptomic and phenotypic studies, showing that the blood strain used a different haemoglobin-linked iron receptor (HpuA/B) than the parental strains (HmbR). Different pilin variants were found after the in vivo passage, which expressed different properties of adhesion. Furthermore the deletion of one gene involved in LOS biosynthesis (lgtB) results in Z5463BC expressing a different LOS than the L9 immunotype of Z2491. The in vivo passage, despite the small numbers of divisions, permits the selection of numerous genomic modifications that may account for the high capacity of the strain to disseminate.

Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease

“…These genomic differences can most parsimoniously be explained by 11 mutational events affecting eight different loci, resulting on average in three mutational events per strain pair (95%-CI = [1, 5]). In contrast to a previous case report of a laboratory infection with a mutS deficient mutator strain [18], we could not detect any mutations in mismatch repair genes in any of the four strains pairs. Considering that mutator strains with defects in the mismatch repair pathway display 10–100-fold higher phase variation rates compared to non-mutator strains [66], the number of mutations reported here is therefore in good agreement with the 30 mutations described in the aforementioned work [18].…”

“…In contrast to a previous case report of a laboratory infection with a mutS deficient mutator strain [18], we could not detect any mutations in mismatch repair genes in any of the four strains pairs. Considering that mutator strains with defects in the mismatch repair pathway display 10–100-fold higher phase variation rates compared to non-mutator strains [66], the number of mutations reported here is therefore in good agreement with the 30 mutations described in the aforementioned work [18]. Together, these 11 mutational events comprised eight SSM and three recombination events due to gene conversion.…”

“…influenzae bacteremia [15], the recent development of powerful next-generation sequencing (NGS) technologies has opened new avenues for the experimental study of bacterial within-host genomic changes even during acute infections [16–18]. Obtaining reliable sequencing results particularly at SSR loci is paramount, but analysis remains challenging due to high error rates inherent to certain types of NGS data [16, 19].…”

Type IV Pilin Proteins: Versatile Molecular Modules

“…This recombination event can cause a hyperpiliated phenotype or, more commonly, a nonpiliated strain, where a frameshift in the pilE sequence creates a premature stop codon (116). A more recent study of isolates recovered from a scientist accidentally infected with a single N. meningitidis strain (302) showed that even with the limited number of in vivo cell divisions (ϳ25) estimated to have occurred before resolution of the infection by antibiotic therapy, at least 7 different pilin variants with different adhesive capacities arose, showing rapid diversification. Neisseria is naturally competent for DNA uptake, in a T4P-dependent manner, and can undergo intergenic recombination with DNA scavenged from its environment.…”

Meningococcal Disease: Shifting Epidemiology and Genetic Mechanisms That May Contribute to Serogroup C Virulence

“…An example of the rapid genetic variation that occurs in N. meningitidis was detailed in a recent report describing the accidental in vivo passage of N. meningitidis in a laboratory worker: an estimated 25 bacterial generations occurred in vivo, resulting in 11 sequence differences between the last passage of the laboratory strain before infection and the blood culture isolate. These genetic changes could affect phenotypes including iron acquisition, adhesion, and lipooligosaccharide structure [23].…”