Re-Emergence of Salmonellosis in Hog Farms: Outbreak and Bacteriological Characterization.
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ABSTRACT:
SUBMITTER: Meneguzzi M
PROVIDER: S-EPMC8146755 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Antimicrobial resistance caused by the overuse of antimicrobials by farmers is an essential health issue. Currently, signing contracts between farmers and cooperatives has become crucial for small farmers to integrate into the modern agricultural industry chain. Unlike vertical government governance, which aims to intervene in the overuse of antimicrobials by farmers through many mandatory or incentive measures, contract governance refers to the social governance model that clarifies rights and obligations between farmers and cooperatives to ensure the adequate performance of contracts, which is especially beneficial to regulate farmers' safe production behavior such as the standard use of antimicrobials. However, there is a research gap concerning the effectiveness of contract governance in inhibiting farmers' overuse of animal antimicrobials. This study applies propensity score matching and mediation analysis method to assess how contract governance affects the overuse of antimicrobials by hog farmers. The paper uses data from 498 hog farmers of China's Hebei, Henan, and Hubei provinces to explore the impact and underlying mechanisms of contract governance on antimicrobial overuse in agriculture. The results showed that contract governance was found to inhibit the overuse of antimicrobials, with the amount paid for antimicrobials reduced by 118 yuan/household. We found evidence that this effect is exerted through three mechanisms: cooperative supervision (CS), technical guidance (TG), and product premium perception (PP). The CS, TG, and PP mediation effects accounted for 19.94%, 27.90%, and 26.93% of the total impact, respectively. Therefore, policy implications of these results include strengthening the standard of contract signing procedures and the integrity of executing contracts, increasing the market premium for products that meet the antimicrobial residue standards, and enhancing farmers' knowledge and contracting ability.
| S-EPMC11327576 | biostudies-literature
Project description:A 2018 publication reported that communities living near hog Concentrated Animal Feeding Operations (CAFO) in North Carolina, USA have increased negative health outcomes and mortalities. While the authors stated that the associations do not imply causation, speculative interpretation of their results by media and subsequent use as evidence in lawsuits caused detrimental effects on the swine industry. We repeated their study using updated data to evaluate the strength of conclusions and appropriateness of methods used with the ultimate goal of alerting on the impact that study limitations may have when used as evidence. As done in the 2018 study, logistic regression was conducted at the individual level using 2007-2018 data, while presumably correcting for six confounders drawn from zip code or county-level databases. Exposure to CAFOs was defined by categorizing zip codes into three by swine density; where, >1 hogs/km2 (G1), > 232 hogs/km2 (G2), and no hogs (Control). Association with CAFO exposure resulting in mortality, hospital admissions, and emergency department visits were analyzed related to eight conditions (six from the previous study: anemia, kidney disease, infectious diseases, tuberculosis, low birth weight, and we added HIV and diabetes). Re-evaluation identified shortcomings including ecological fallacy, residual confounding, inconsistency of associations, and overestimation of exposure. HIV and diabetes, which are not causally relatable to CAFOs, were also prominent in these neighborhoods likely reflecting underlying systemic health disparities. Hence, we emphasize the need for improved exposure analysis and the importance of responsible interpretation of ecological studies that affect both public health and agriculture.
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Project description:Background & objectivesEpidemiological interventions and mosquito control are the available measures for dengue control. The former approach uses serotype and genetic information on the circulating virus strains. Dengue has been frequently reported from Nepal, but this information is mostly lacking. The present study was done to generate a comprehensive clinical and virological picture of a dengue outbreak in Nepal during 2013.MethodsA hospital-based study involving patients from five districts of Nepal was carried out. Demographic information, clinical details and dengue serological status were obtained. Viral RNA was characterized at the molecular level by reverse-transcription polymerase chain reaction (RT-PCR), nucleotide sequencing and phylogenetic analysis.ResultsFrom among the 2340 laboratory-confirmed dengue cases during the study period, 198 patients consented for the study. Clinically they had fever (100%), headache (59.1%), rashes (18.2%), retro-orbital pain (30.3%), vomiting (15.1%), joint pain (28.8%) and thrombocytopenia (74.3%). Fifteen (7.5%) of them had mucosal bleeding manifestations, and the rest were uncomplicated dengue fever. The patients were mostly adults with a mean age of 45.75 ± 38.61 yr. Of the 52 acute serum samples tested, 15 were positive in RT-PCR. The causative virus was identified as DENV serotype 2 belonging to the Cosmopolitan genotype.Interpretations & conclusionsWe report here the involvement of DENV serotype 2 in an outbreak in Nepal in 2013. Earlier outbreaks in the region in 2010 were attributed to serotype 1 virus. As serotype shifts are frequently associated with secondary infections and severe disease, there is a need for enhancing surveillance especially in the monsoon and post-monsoon periods to prevent large-scale, severe dengue outbreaks in the region.
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Project description:Infectious disease outbreaks transcend the medical and public health realms, triggering widespread panic and impeding socio-economic development. Considering that self-limiting diarrhoea of sporadic cases is usually underreported, the Salmonella outbreak (SO) study offers a unique opportunity for source tracing, spatiotemporal correlation, and outbreak prediction. To summarize the pattern of SO and estimate observational epidemiological indicators, 1,134 qualitative reports screened from 1949 to 2023 were included in the systematic review dataset, which contained a 506-study meta-analysis dataset. In addition to the dataset comprising over 50 columns with a total of 46,494 entries eligible for inclusion in systematic reviews or input into prediction models, we also provide initial literature collection datasets and datasets containing socio-economic and climate information for relevant regions. This study has a broad impact on advancing knowledge regarding epidemic trends and prevention priorities in diverse salmonellosis outbreaks and guiding rational policy-making or predictive modeling to mitigate the infringement upon the right to life imposed by significant epidemics.
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Project description:Incubation period for non-typhoidal Salmonella (NTS) infections is generally reported as 6-72 h despite numerous reports of foodborne NTS outbreaks with median incubation periods >3 days. We summarised 16 years of Minnesota foodborne NTS outbreaks to better estimate the expected range of incubation periods for NTS infections. Of the 1517 NTS outbreak cases, 725 had enough data to calculate a precise incubation period. The median incubation period was 45 h; 77 (11%) cases had incubations ⩽12 h and 211 (29%) cases had incubations >72 h. Incubation period length varied by outbreak vehicle type, Salmonella serotype and outbreak setting. Based on our data, a more accurate description would be that the incubation of NTS infection is usually from 12 to 96 h, that incubations in >96 to 144 h (>4 to 6-day) range are not unusual and that incubations from 7 to 9 days and occasionally longer also occur.
| S-EPMC9134522 | biostudies-literature
Project description:ObjectiveTo perform a molecular screening to detect infections by the mayaro virus and possible coinfections with Chikungunya during an outbreak in the state of Tocantins/Brazil in 2017.ResultsOf a total 102 samples analyzed in this study, 6 cases were identified with simultaneous infection between mayaro and chikungunya viruses (5.88%). In these 6 samples, the mean Cycle threshold (Ct) for CHIKV was 26.87 (SD ± 10.54) and for MAYV was 29.58 (SD ± 6.34). The mayaro sequences generated showed 95-100% identity to other Brazilian sequences of this virus and with other MAYV isolates obtained from human and arthropods in different regions of the world. The remaining samples were detected with CHIKV monoinfection (41 cases), DENV monoinfection (50 cases) and coinfection between CHIKV/DENV (5 cases). We did not detect MAYV monoinfections.
| S-EPMC9351195 | biostudies-literature
Project description:BackgroundWe report a genomic surveillance of SARS-CoV-2 lineages circulating in Paraná, southern Brazil, from March 2020 to April 2021. Our analysis, based on 333 genomes, revealed that the first variants detected in the state of Paraná in March 2020 were the B.1.1.33 and B.1.1.28 variants. The variants B.1.1.28 and B.1.1.33 were predominant throughout 2020 until the introduction of the variant P.2 in August 2020 and a variant of concern (VOC), Gamma (P.1), in January 2021. The VOC Gamma, a ramification of the B.1.1.28 lineage first detected in Manaus (northern Brazil), has grown rapidly since December 2020 and was thought to be responsible for the deadly second wave of COVID-19 throughout Brazil.MethodsThe 333 genomic sequences of SARS-CoV-2 from March 2020 to April 2021 were generated as part of the genomic surveillance carried out by Fiocruz in Brazil Genomahcov Fiocruz. SARS-CoV-2 sequencing was performed using representative samples from all geographic areas of Paraná. Phylogenetic analyses were performed using the 333 genomes also included other SARS-CoV-2 genomes from the state of Paraná and other states in Brazil that were deposited in the GISAID. In addition, the time-scaled phylogenetic tree was constructed with up to 3 random sequences of the Gamma variant from each state in Brazil in each month of 2021. In this analysis we also added the sequences identified as the B.1.1.28 lineage of the Amazonas state and and the Gamma-like-II (P.1-like-II) lineage identified in different regions of Brazil.ResultsPhylogenetic analyses of the SARS-CoV-2 genomes that were previously classified as the VOC Gamma lineage by WHO/PANGO showed that some genomes from February to April 2021 branched in a monophyletic clade and that these samples grouped together with genomes recently described with the lineage Gamma-like-II. Additionally, a new mutation (E661D) in the spike (S) protein has been identified in nearly 10% of the genomes classified as the VOC Gamma from Paraná in March and April 2021.Finally, we analyzed the correlation between the lineage and the Gamma variant frequency, age group (patients younger or older than 60 years old) and the clinical data of 86 cases from the state of Paraná.ConclusionsOur results provided a reliable picture of the evolution of the SARS-CoV-2 pandemic in the state of Paraná characterized by the dominance of the Gamma strain, as well as a high frequencies of the Gamma-like-II lineage and the S:E661D mutation. Epidemiological and genomic surveillance efforts should be continued to unveil the biological relevance of the novel mutations detected in the VOC Gamma in Paraná.
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Project description:The rapid emergence of multidrug resistant Salmonella is a global public-health concern as outbreaks in recent years have mostly been caused by multidrug resistant strains. Here, we evaluated an outbreak in China caused by multidrug resistant Salmonella enterica serovar Typhimurium (S. Typhimurium) by employing an epidemiological and laboratory investigation using conventional methods and whole genome sequencing (WGS). Eleven of the 12 people who participated in a banquet showed gastrointestinal symptoms, and 8S. Typhimurium strains were recovered. Isolated outbreak strains showed multidrug resistance (MDR), and decreased susceptibility to ciprofloxacin, a first-line drug recommended by WHO for clinical treatment of intestinal infections. Antimicrobial resistance (AMR) gene analysis indicated that the MDR phenotype of these outbreak strains may be due to the presence of a number of AMR genes, including the blaOXA-1 and blaTEM-1 β-lactamase genes, which are often plasmid-borne and easily transferred. Further virulence gene analysis indicated that these outbreak strains also carried a large number of virulence genes, including 2 types of Salmonella pathogenicity islands (SPI-1 and SPI-2) and many adhesion-related virulence genes. Cluster analysis based on pulse-field gel electrophoresis data and phylogenetic analysis based on WGS revealed that the outbreak clone was closely related to and thus probably derived from local strains. This outbreak caused by multidrug resistant S. Typhimurium highlights the need for government improved strategies for the prevention and control of Salmonella infections.
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Project description:A multi-provincial outbreak of Salmonella enterica serovar Enteritidis was linked to newly hatched chicks and poults from a single hatchery during the spring of 2015. In total, there were 61 human cases that were epidemiologically confirmed to be linked to the chicks and poults and the outbreak was deemed to have ended in the summer of 2015. PulseNet Canada, in coordination with the affected provinces, used genome sequencing of human and agricultural Salmonella Enteritidis isolates to aid in the epidemiological investigation, while also using traditional typing methods such as phagetyping and pulsed-field gel electrophoresis (PFGE). All human outbreak cases, except one, were Phage Type (PT) 13a. Single nucleotide variant analysis (SNV) was able to provide a level of resolution commensurate with the results of the epidemiological investigation. SNV analysis was also able to separate PT13a outbreak-related isolates from isolates not linked to chicks or poults, while clustering some non-PT13a agricultural strains with the outbreak cluster. Based on conventional typing methods (phagetyping or PFGE), clinical and agricultural PT13a SE isolates would have been considered as part of a related cluster. In contrast, phagetyping would have led to the exclusion of several non- PT13a strains that clustered with the outbreak isolates using the genome sequence data. This study demonstrates the improved resolution of genome sequence analysis for coordinated surveillance and source attribution of both human and agricultural SE isolates.
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