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Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 2019.

ABSTRACT: Between July 2018 and May 2019, Corynebacterium diphtheriae was isolated from eight patients with non-respiratory infections, seven of whom experienced homelessness and had stayed at shelters in King County, WA, USA. All isolates were microbiologically identified as nontoxigenic C. diphtheriae biovar mitis. Whole-genome sequencing confirmed that all case isolates were genetically related, associated with sequence type 445 and differing by fewer than 24 single-nucleotide polymorphisms (SNPs). Compared to publicly available C. diphtheriae genomic data, these WA isolates formed a discrete cluster with SNP variation consistent with previously reported outbreaks. Virulence-related gene content variation within the highly related WA cluster isolates was also observed. These results indicated that genome characterization can readily support epidemiology of nontoxigenic C. diphtheriae.

SUBMITTER: Xiaoli L

PROVIDER: S-EPMC8116682 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Determining the causes of biological impairment in urban stream settings presents unique challenges because there are many potential stressors associated with human development. A rigorous, scientifically based process is more likely to identify influential stressors that can be reduced to improve stream condition. We used the U.S. Environmental Protection Agency's (U.S. EPA) CADDIS (Causal Analysis/Decision Information System) stressor identification process to assess eight candidate causes in the urban Soos Creek Basin in Washington State. The eight candidate causes capable of negatively affecting the abundance and diversity of benthic macroinvertebrates are: flow alteration, increased fine sediments, reduced habitat complexity, elevated water temperature, low dissolved oxygen, elevated nutrients, increased ionic concentration, and toxic pollutants. We assembled multiple lines of evidence, as well as the consistency of that evidence and agreement with other assessments. We evaluated the influence of natural and cumulative anthropogenic stressors on macroinvertebrate communities by comparing various chemical, physical, and biological measures at sites in the Soos Creek Basin with regional reference sites. Of the stressors evaluated, flow alteration, increased fine sediments, and loss of habitat complexity were the most probable causes of biological impairment, with multiple biological metrics responding predictably across levels of impairment. Key findings from this study include: the use of specific community alterations as evidence in causal assessment, demonstration of links in a complete causal pathway, and the use of multiple models to show which pathway is likely stronger. In addition to the value to the specific case, the analyses increased our understanding of the responses of stream invertebrate communities in urban environments. Ultimately, demonstrating the utility of causal assessment in a practical situation provides greater confidence that mitigation efforts aimed at improving biological health of urban stream communities will have detectable desired effects while also providing a baseline from which the effectiveness of management practices can be evaluated.

Project description: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.

Dataset Information

Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 2019.

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