Genomic Characterization of Yersinia enterocolitica Isolates, Costa Rica

TL;DR

This study uses genomic analysis to show that Yersinia enterocolitica spreads between animals and humans in Costa Rica, with high antibiotic resistance.

Contribution

The study provides the first genomic characterization of Yersinia enterocolitica in Costa Rica, revealing persistent transmission and resistance patterns.

Findings

Yersinia enterocolitica isolates show persistent circulation between animal reservoirs and humans.

Unusual levels of antimicrobial resistance were detected in the isolates.

Genomic surveillance is highlighted as essential for monitoring Yersinia-caused infections in the region.

Abstract

Data on enteric yersinioses in Central America are limited. Genomic characterization of 78 Yersinia
enterocolitica isolates from Costa Rica indicated persistent infection-source circulation between animal reservoirs and humans, as well as unusual antimicrobial resistance levels. Our study highlights the importance of genomic surveillance to monitor Yersinia-caused infections in Costa Rica.

Figures

Full text

The Yersinia genus encompasses 2 enteropathogenic species, Y. enterocolitica and Y. pseudotuberculosis (1,2). Those bacteria are the cause of foodborne infections that range from mild enteritis, especially in children, to systemic infections in the elderly or patients with underlying disorders (3). Enteric yersiniosis is the third most frequently reported zoonosis in Europe, mainly caused by Y. enterocolitica infections (4). Isolates can be classified into nonpathogenic genotypes (1Aa and 1Ab) and 11 other pathogenic genotypes (2).

In France, genomic surveillance based on a Y. enterocolitica core genome multilocus sequence typing (cgMLST) scheme was useful in identifying genetically closely related isolates and initiating an epidemiologic investigation with public health authorities to identify a common source of infection (5). Epidemiologic information on enteric yersinioses is scarce in the Americas. We studied Yersinia isolates from Costa Rica to evaluate their circulation in the country and to characterize them at the genomic level.

We analyzed 78 isolates collected during 2003–2023; all were of clinical origin except 1 veterinary isolate (Appendix 1). Genomic characterization based on a Yersinia 500-gene cgMLST enabled us to identify all isolates as pathogenic Y. enterocolitica: 2 isolates belonged to genotype 2/3-5a and the 76 others to genotype 4. All patients (n = 77) experienced enteric infections; we only identified pathogenic isolates. Epidemiologic records of the 77 clinical isolates showed that the sex ratio was 1:1 as expected in other countries (4). Most (76%) of the isolates were collected from patients <20 years of age; 20% were from adults 21–60 years of age. We observed a slight (4%) increase in patients >61 years of age. Most (97%) isolates came from feces, indicating that patients had a digestive form of infection, whereas 3% of the isolates were collected from blood (Appendix 2 Table). Overall, the epidemiology of Y. enterocolitica isolates circulating in Costa Rica was similar to that of other countries (4).

Geographic distribution of the isolates showed that the 78 isolates were distributed in the 7 provinces of Costa Rica; 60 (77%) isolates were from the Gran Area Metropolitana, a densely populated region around San Jose, the capital city (Figure). Phylogenetic reconstruction of the 76 genotype 4 isolates revealed 4 distinct bacterial subgroups (Figure). No geographic association was found between subgroups or provinces. We conducted a genomic comparison of isolates on the basis of a Y. enterocolitica 1,727-gene cgMLST and subsequent clustering of isolates with a 5-mismatch threshold; we found that 51/76 isolates belonged to 9 clusters of >2 isolates (Table; Appendix 1 Figure). We identified 3 clusters with isolates collected over a long period: cluster 6122 for 10 years, cluster 6127 for 13 years, and cluster 6124 for 8 years. Those periods suggest persistence of the source of contamination. We found that cluster 3151 is composed of mixed clinical and veterinary isolates, suggesting circulation between the animal reservoir and humans (Table; Appendix 2 Table). Of note, cluster 5652 is composed of 2 isolates from Costa Rica and 1 from France. Epidemiologic records of the France isolate showed that the patient was returning from Costa Rica at the time of sampling, suggesting that he was infected during his trip.

Among the 76 genotype 4 isolates, antimicrobial susceptibility testing revealed unusually high levels of resistance to cefoxitin (7.9%), nalidixic acid (23.7%), and tetracycline (9.2%) (Figure; Appendix 1 Table) (6). Nalidixic acid resistance was associated with mutations in the quinolone resistance–determining region of the gyrA gene; we identified the previously described S83R mutation (7) in 15 isolates and D87G mutation in 3 isolates. Cefoxitin resistance in 6 isolates was associated with a G751A mutation of the ampC gene, identical to the mutation present in the naturally cefoxitin-resistant genotype 2/3-5a. Those 6 isolates are in the upper part of the tree, suggesting the mutation was acquired during emergence of the branch (Figure). In 6/7 tetracycline-resistant isolates, resistance was associated with acquisition of the tetC gene located on a 13.7 kb plasmid circulating in other enterobacteria. Those 6 isolates are on the upper branch of the tree, suggesting that plasmid acquisition occurred during emergence of the branch (Figure). The other tetracycline-resistant isolate was associated with the tetA gene, together with aph(3ʹ)-Ib and aph(6)-Id, floR, and sul2, located on an 81.2 kb multidrug-resistant plasmid (Figure). The presence of those genes was phenotypically associated with resistance to tetracycline, streptomycin, chloramphenicol, and sulfonamides.

In summary, this study brings insights into the distribution of enteropathogenic Yersinia species circulating in Costa Rica. Diversity is low because most of the Y. enterocolitica isolates belonged to biotype 4. Many closely related isolates were identified within a long timeframe, sometimes between human clinical and veterinary isolates, suggesting a persistence of the source of infection and the circulation between the reservoir and humans. Implementation of routine genomic surveillance in Costa Rica could help to monitor the circulation of closely related Yersinia isolates and initiate epidemiologic investigation to implement control measures in the event of an outbreak.