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Molecular Epidemiology of Salmonellosis in Florida, USA, 2017-2018.

ABSTRACT: The state of Florida reports a high burden of non-typhoidal Salmonella enterica with approximately two times higher than the national incidence. We retrospectively analyzed the population structure and molecular epidemiology of 1,709 clinical isolates from 2017 and 2018. We found 115 different serotypes. Rarefaction suggested that the serotype richness did not differ between children under 2 years of age and older children and adults and, there are ~22 well-characterized dominant serotypes. There were distinct differences in dominant serotypes between Florida and the USA as a whole, even though S. Enteritidis and S. Newport were the dominant serotypes in Florida and nationally. S. Javiana, S. Sandiego, and S. IV 50:z4, z23:- occurred more frequently in Florida than nationally. Legacy Multi Locus Sequence Typing (MLST) was of limited use for differentiating clinical Salmonella isolates beyond the serotype level. We utilized core genome MLST (cgMLST) hierarchical clusters (HC) to identify potential outbreaks and compared them to outbreaks detected by Pulse Field Gel Electrophoresis (PFGE) surveillance for five dominant serotypes (Enteritidis, Newport, Javiana, Typhimurium, and Bareilly). Single nucleotide polymorphism (SNP) phylogenetic-analysis of cgMLST HC at allelic distance 5 or less (HC5) corroborated PFGE detected outbreaks and generated well-segregated SNP distance-based clades for all studied serotypes. We propose "combination approach" comprising "HC5 clustering," as efficient tool to trigger Salmonella outbreak investigations, and "SNP-based analysis," for higher resolution phylogeny to confirm an outbreak. We also applied this approach to identify case clusters, more distant in time and place than traditional outbreaks but may have been infected from a common source, comparing 176 Florida clinical isolates and 1,341 non-clinical isolates across USA, of most prevalent serotype Enteritidis collected during 2017-2018. Several clusters of closely related isolates (0-4 SNP apart) within HC5 clusters were detected and some included isolates from poultry from different states in the US, spanning time periods over 1 year. Two SNP-clusters within the same HC5 cluster included isolates with the same multidrug-resistant profile from both humans and poultry, supporting the epidemiological link. These clusters likely reflect the vertical transmission of Salmonella clones from higher levels in the breeding pyramid to production flocks.

SUBMITTER: Singh N

PROVIDER: S-EPMC8100233 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Non-typhoidal Salmonella enterica infections cause a high disease burden in the United States with an estimated 1.2 million illnesses annually. The state of Florida consistently has a relatively high incidence compared to other states in the United States. Nevertheless, studies regarding the epidemiology of nontyphoidal salmonellosis and its spatial and temporal patterns in Florida were rarely reported. We examined the spatial and temporal patterns of 62,947 salmonellosis cases reported to FL Health Charts between 2009 and 2018. Dominant serotypes circulating in Florida were also explored using whole genome sequencing (WGS) based serotype-prediction for 2,507 Salmonella isolates sequenced by the Florida Department of Health during 2017 and 2018. The representativeness of laboratory-sequenced isolates for reported cases was determined by regression modeling. The annual incidence rate of salmonellosis decreased from 36.0 per 100,000 population in 2009 to 27.8 per 100,000 in 2016, and gradually increased in 2017 and 2018. Increased use of culture-independent testing did not fully explain this increase. The highest incidence rate was observed in children, contributing 40.9% of total reported cases during this period. A seasonal pattern was observed with the incidence peaking in September and October, later than the national average pattern. Over these 10 years, the Northeast and Northwest regions of the state had higher reported incidence rates, while reported rates in the Southeast and South were gradually increasing over time. Serotypes were predicted based on WGS data in the EnteroBase platform. The top-five most prevalent serotypes in Florida during 2017-2018 were Enteritidis, Newport, Javiana, Sandiego and Braenderup. The highest percentage of isolates was from children under 5 years of age (41.4%), and stool (84.7%) was the major source of samples. A zero-inflated negative binomial regression model showed that the reported case number was a strong predictor for the number of lab-sequenced isolates in individual counties, and the geospatial distribution of sequenced isolates was not biased by other factors such as age group. The spatial and temporal patterns identified in this study along with the prevalence of different serotypes will be helpful for the development of efficient prevention and control strategies for salmonellosis in Florida.

Project description:BackgroundAs a consequence of war and the collapse of the health system in Yemen, which prevented many people from accessing health facilities to obtain primary health care, vaccination coverage was affected, leading to a deadly diphtheria epidemic at the end of 2017.ObjectiveThis study aimed to describe the epidemiology of diphtheria in Yemen and determine its incidence and case fatality rate.MethodsData were obtained from the diphtheria surveillance program 2017-2018, using case definitions of the World Health Organization. A probable case was defined as a case involving a person having laryngitis, pharyngitis, or tonsillitis and an adherent membrane of the tonsils, pharynx, and/or nose. A confirmed case was defined as a probable case that was laboratory confirmed or linked epidemiologically to a laboratory-confirmed case. Data from the Central Statistical Organization was used to calculate the incidence per 100,000 population. A P value <.05 was considered significant.ResultsA total of 2243 cases were reported during the period between July 2017 and August 2018. About 49% (1090/2243, 48.6%) of the cases were males. About 44% (978/2243, 43.6%) of the cases involved children aged 5 to 15 years. Respiratory tract infection was the predominant symptom (2044/2243, 91.1%), followed by pseudomembrane (1822/2243, 81.2%). Based on the vaccination status, the percentages of partially vaccinated, vaccinated, unvaccinated, and unknown status patients were 6.6% (148/2243), 30.8% (690/2243), 48.6% (10902243), and 14.0% (315/2243), respectively. The overall incidence of diphtheria was 8 per 100,000 population. The highest incidence was among the age group <15 years (11 per 100,000 population), and the lowest incidence was among the age group ≥15 years (5 per 100,000 population). The overall case fatality rate among all age groups was 5%, and it was higher (10%) in the age group <5 years. Five governorates that were difficult to access (Raymah, Abyan, Sa'ada, Lahj, and Al Jawf) had a very high case fatality rate (22%).ConclusionsDiphtheria affected a large number of people in Yemen in 2017-2018. The majority of patients were partially or not vaccinated. Children aged ≤15 years were more affected, with higher fatality among children aged <5 years. Five governorates that were difficult to access had a case fatality rate twice that of the World Health Organization estimate (5%-10%). To control the diphtheria epidemic in Yemen, it is recommended to increase routine vaccination coverage and booster immunizations, increase public health awareness toward diphtheria, and strengthen the surveillance system for early detection and immediate response.

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Molecular Epidemiology of Salmonellosis in Florida, USA, 2017-2018.

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