Genomic Epidemiology of Corynebacterium diphtheriae in New Caledonia

Abstract

An increasing number of isolations of Corynebacterium diphtheriae has been observed in recent years in the archipelago of New Caledonia. We aimed to analyze the clinical and microbiological features of samples with C. diphtheriae. All C. diphtheriae isolates identified in New Caledonia from May 2015 to May 2019 were included. For each case, a retrospective consultation of the patient files was conducted. Antimicrobial susceptibility phenotypes, tox gene and diphtheria toxin expression, biovar, and the genomic sequence were determined. Core genome multilocus sequence typing (cgMLST), 7-gene MLST, and search of genes of interest were performed from genomic assemblies. Fifty-eight isolates were included, with a median age of patients of 28 years (range: 9 days to 78 years). Cutaneous origin accounted for 51 of 58 (87.9%) isolates, and C. diphtheriae was associated with Staphylococcus aureus and/or Streptococcus pyogenes in three-quarters of cases. Half of cases came either from the main city Noumea (24%, 14/58) or from the sparsely populated island of Lifou (26%, 15/58). Six tox-positive isolates were identified, associated with recent travel to Vanuatu; 5 of these cases were linked and cgMLST confirmed recent transmission. Two cases of endocarditis in young female patients with a history of rheumatic fever involved tox-negative isolates. The 58 isolates were mostly susceptible to commonly used antibiotics. In particular, no isolate was resistant to the first-line molecules amoxicillin or erythromycin. Resistance to tetracycline was found in a genomic cluster of 17 (29%) isolates, 16 of which carried the tetO gene. There were 13 cgMLST sublineages, most of which were also observed in the neighboring country Australia. Cutaneous infections may harbor nontoxigenic C. diphtheriae isolates, which circulate largely silently in nonspecific wounds. The possible introduction of tox-positive strains from a neighboring island illustrates that diphtheria surveillance should be maintained in New Caledonia, and that immunization in neighboring islands must be improved. Genomic sequencing uncovers how genotypes circulate locally and across neighboring countries. IMPORTANCE The analysis of C. diphtheriae from the tropical archipelago of New Caledonia revealed a high genetic diversity with sublineages that may be linked to Polynesia, Australia, or metropolitan France. Genomic typing allowed confirming or excluding suspected transmission events among cases and contacts. A highly prevalent tetracycline-resistant sublineage harboring the tetO gene was uncovered. Toxigenic isolates were observed from patients returning from Vanuatu, showing the importance of improving vaccination coverage in settings where it is insufficient. This study also illustrates the importance for diphtheria surveillance of the inclusion of isolates from cutaneous sources in addition to respiratory cases, in order to provide a more complete epidemiological picture of the diversity and transmission of C. diphtheriae.

Keywords: Corynebacterium diphtheriae; New Caledonia; clinical presentation; diphtheria; genomic epidemiology; tropical island; whole-genome sequencing.

FIG 1

Geographic distribution of Corynebacterium diphtheriae cases in New Caledonia. The number of patients whose living place is in each district, is indicated as a heatmap (see key). The arrow indicates the direction of the North.

FIG 2

Diversity of Corynebacterium diphtheriae isolates from New Caledonia. The first column after the isolate identifier represents the locations of origin of the isolates (see color key). After the year of isolation column, the tox-negative isolates are represented by an empty star, and tox-positive ones by a full red star. The biovar is represented next: green for Gravis, purple for Mitis, brown for Belfanti. The following columns represent the presence of genes spuA (likely involved in glycogen metabolism; positive in biovar Gravis) and narG (involved in nitrate metabolism; positive in biovars Gravis and Mitis). On the four next columns, alternating dark and light colors indicate each sequence type (ST), sublineage (SL), genetic cluster (GC) or cgST change. Sublineages are given as: internal number = alias number (inherited, where possible, from 7-gene MLST numbers). The next column represents the tetracycline resistance phenotype: red for resistant (with R letter), gray for susceptible. The presence of the tetO gene is symbolized in orange on the next column, its absence in gray. The last two columns indicate in the same way, the penicillin phenotype and presence of gene pbp2m (I: intermediate).