Epidemiological Information Research Articles

Optimal Protocols and Management of Clinical and Genomic Data Collection to Assist in the Early Diagnosis and Treatment of Multiple Congenital Anomalies.

Standardized protocols have been designed and developed specifically for clinical information collection and obtaining trio genomic information from infants affected with congenital anomalies (CA) and their parents, as well as securing human biological resources. The protocols include clinical and genomic information collection on multiple CA that were difficult to diagnose using pre-existing screening methods. We obtained human-derived resources and genomic information from 138 cases, including 45 families of infants with CA and their parent trios. For the clinical information collection protocol, criteria for target patient selection and a consent system for collecting and utilizing research resources are crucial. Whole genome sequencing data were generated for all participants, and standardized protocols were developed for resource collection and manufacturing. We recorded the phenotype information according to the Human Phenotype Ontology term, and epidemiological information was collected through an environmental factor questionnaire. Updating and recording of clinical symptoms and genetic information that have been newly added or changed over time are significant. The protocols enabled long-term tracking by including the growth and development status that reflect the important characteristics of newborns. Using these clinical and genetic information collection protocols for CA, an essential platform for early genetic diagnosis and diagnostic research can be established, and new genetic diagnostic guidelines can be presented in the near future.

Molecular Detection and Typing of Treponema pallidum in Non-Ocular Samples from Patients with Ocular Syphilis

ABSTRACT Introduction Ocular syphilis is a rare but potentially sight-threatening manifestation of infection with the spirochete Treponema pallidum subspecies pallidum. Molecular strain typing of clinical specimens obtained from patients with syphilis can provide useful epidemiological and clinical information. In this study, we assess the utility of non-ocular clinical samples in strain typing for patients with diagnosed ocular syphilis. Methods We collected samples of excess blood, serum, and cerebrospinal fluid (CSF) from 6 patients with ocular syphilis treated in 2013–2016. DNA was extracted, purified, and then analyzed using an enhanced molecular typing method including sequence analysis of tp0548, number of repeats in the arp gene, and restriction fragment length polymorphism of the tpr gene. Results Molecular strain typing based on tp0548 gene sequence analysis revealed two cases of type F and two cases of type G in 3 of 6 (50%) cases with CSF samples, 1 of which was obtained after starting antibiotics. In a patient with 2 distinct episodes, the same tp0548 type (type G) was identified in both episodes using different sample types (CSF, whole blood). Serum samples were available in 6 cases, but none were successfully typed with any of the methods. Amplification of the tpr and arp genes was unsuccessful in all cases. Overall, strain types were identified in 4 of the 7 episodes. Conclusion Treponema pallidum strain types F and G were detected in CSF or whole blood in 4 of 7 episodes in this series. We demonstrate moderate sensitivity of strain typing in ocular syphilis using non-ocular clinical specimens.

Leptospirosis in horses: Sentinels for a neglected zoonosis? A systematic review.

Leptospirosis is considered a neglected tropical zoonosis in low-income countries due to surveillance system limitations and non-specificity of symptoms. Humans become infected through direct contact with carrier animals or indirectly through Leptospira-contaminated environments. Conventionally, equines have been considered an uncommon source of leptospirosis, but recent publications in Latin America suggest that their role in the maintenance and dispersion of the bacteria could be more relevant than expected, as horses are susceptible to a wide variety of zoonotic Leptospira spp. from domestic and wild animals with which they share the environment. A systematic review of the published literature was conducted to compile the available information on Leptospira spp. in Ecuador, with a special focus on equine leptospirosis, to better understand the epidemiology of the bacterium and identify possible knowledge gaps. A systematic review of the published literature was conducted in PubMed, SciELO and Web of Science databases to compile the available information on Leptospira spp. in Ecuador, with a special focus on equine leptospirosis, to better understand the epidemiology of the bacterium. We used a combination of the terms (Leptospira OR Leptospirosis) AND Ecuador, without restrictions on language or publication date. Our literature review reveals that published scientific information is very scarce. Eighteen full-text original scientific articles related to Leptospira or leptospirosis cases in Ecuador were included in the systematic review. Most of the studies reported data obtained from one of the four regions (Coast), and specifically from only one of the 24 Provinces of Ecuador (Manabí), which evidence a large information bias at the geographical level. Furthermore, only the studies focused on humans included clinical signs of leptospirosis and there is only one study that analyzes the presence of Leptospira spp. in water or soil as a risk factor for pathogen transmission. Finally, only one study investigated Leptospira in horses. Since sentinel species can provide useful data on infectious diseases when epidemiologic al information is lacking, and horses could be considered excellent sentinel species to reveal circulating serovars, we propose developing a nationwide surveillance system using horses. This cost-effective epidemiological survey method provides a baseline for implementing specific prevention and control programs in Ecuador and neighboring developing countries.

Severe viral lower respiratory tract infections in Brazilian children: Clinical features of a national cohort

BackgroundThe accurate etiological diagnosis of lower respiratory tract infections (LRTI) is essential for their effective clinical management. The extensive use of molecular methods during the COVID-19 pandemic has enabled massive data acquisition on viral lower respiratory tract infections. The current study aims to identify clinical features associated with eight viral agents among children presenting severe LRTI. Methodsretrospective cohort study of data from the Brazilian Influenza Epidemiological Surveillance Information System. Patients under 20 years-old who had severe LRTI with etiological confirmation through RT-PCR between 2020 and 2022 were included. Binary logistic regressions were used to examine associations between pathogens and symptoms. Results60,657 cases were assessed. The main viral agents detected were Sars-CoV-2 (COV2) (41.2%), Respiratory Syncytial Virus (29.1%), Human Rhinovirus (HRV) (12.1%), and Influenza (FLU) (5.5%). A general mortality rate of 4.3% was observed. The multivariate analysis evidenced that COV2 less likely presented with cough (OR: 0.34; 95%CI: 0.32–0.36), respiratory discomfort (Adjusted Odds Ratio (aOR): 0.61; 95%Confidence Interval (CI): 0.59–0.64), and desaturation (aOR: 0.71; 95%CI: 0.69–0.75). RSV strongly associated with cough (aOR: 2.59; 95%CI: 2.45–2.75) and respiratory discomfort (aOR: 1.54; 95%CI: 1.46–1.62), whereas FLU was linked to fever (aOR: 2.27; 95%CI: 2.06–2.50) and sore throat (aOR: 1.48; 95%CI: 1.34–1.64). ConclusionsThe viral agents responsible for severe LRTI have distinct associations with clinical features in children.

Neutralizing Antibody Levels and Epidemiological Characteristics of Patients with Breakthrough COVID-19 Infection in Toyama, Japan.

Breakthrough infection (BI) after coronavirus disease 2019 (COVID-19) vaccination has increased owing to the emergence of novel SARS-CoV-2 variants. In this study, we analyzed the epidemiological information and possession status of neutralizing antibodies in patients with BI using SARS-CoV-2 pseudotyped viruses. Analysis of 44 specimens from patients diagnosed with COVID-19 after two or more vaccinations showed high inhibition of infection by 90% or more against the Wuhan strain and the Alpha and Delta variants of pseudotyped viruses in 40 specimens. In contrast, almost no neutralizing activity was observed against the Omicron BA.1 variant. Many patients without neutralizing activity or BI were immunosuppressed. The results of this study show that contact with an infected person can result in BI, even when there are sufficient neutralizing antibodies in the blood. Thus, sufficient precautions must be taken to prevent infection even after vaccination.

Epidemiological Identification of Maternal Mortality Rates in Tuban Regency in 2021

The maternal mortality rate is an important indicator in determining the level of public health. Identifying the maternal mortality rate will make it easier for regional governments and the Health Service to determine policies to reduce the mortality rate in the coming year and make it easier to plan programs and activities that focus on reducing the maternal mortality rate in an integrated manner. This epidemiological identification is useful for providing epidemiological information and advice for decision makers at the central and regional levels in order to identify, prioritize and plan programs to overcome public health problems and assess the success of existing health programs.

Subcutaneous mycoses: Endemic but neglected among the Neglected Tropical Diseases in Ethiopia.

Subcutaneous (deep) mycoses are a chronic infectious disease of the skin and underlying structures endemic in tropical countries. The disease has serious medical and socioeconomic consequences for patients, communities and health services in endemic areas. The inclusion of mycetoma and other subcutaneous mycoses in the list of Neglected Tropical Diseases by WHO highlights the need to assess the burden of these diseases and establish control programs where necessary. In Ethiopia no strategies can be devised because of a lack of epidemiologic information. To address this evidence gap, we performed a national rapid assessment of the geographic distribution of subcutaneous mycoses. We conducted a rapid retrospective assessment using hospital records to identify all suspected and confirmed cases of subcutaneous mycoses in 13 referral hospitals across the country between 2015 and 2022. In each hospital the logbooks were reviewed for diagnoses of subcutaneous mycosess, as diagnosed per routine practice. Descriptive analysis was done. From 13 hospitals we extracted 143 cases of subcutaneous mycoses, registered from July 2018 to September 2022. 118 (82.5%) patients were diagnosed as mycetoma, 21 (14.7%) as chromoblastomycosis and the remaining 4 (2.8%) as sporotrichosis. The mean age of patients was 35.8 years (SD = 14.5). 101 (70.6%) patients were male and 96 (67.1%) patients were farmers. 64 (44.8%) cases were from the Tigray regional state. 56 (65.9%) patients had information on diagnostic microscopic evaluation: for mycetoma histopathologic evaluation and fine needle aspiration cytology had a higher positivity rate while for chromoblastomycosis potassium hydroxide (KOH) staining had a better yield. The main clinical presentations were nodules, sinuses and infiltrative plaques on the skin. Radiologic findings of bone involvement was present in some. Mycetoma and other subcutaneous mycoses are endemic in Ethiopia, with cases reported from almost all regions with the highest cases numbers reported from the northern part of the country. A routine program and systems should be developed to identify and document the burden of subcutaneous fungal infections in the country. Diagnosis and treatment guidelines should be developed.

The limits of conformity analysis under the Newcomb-Benford law and the COVID-19 pandemic in Brazil

This research investigated the possible divergences in results due to the use of the Newcomb-Benford Law to assess the conformity of information regarding infections and deaths caused by the SARS-CoV-2 coronavirus, from transversal clippings made two years after the arrival of the COVID-19 pandemic in Brazil, through the comparative analysis of the results of statistics related to the Z test, the Chi-square test (X2), the Kolmogorov-Smirnov test (KS), and also the mean absolute deviation (MAD). For this, two distinct samples were analyzed: one referring to data accumulated over two years of the pandemic in Brazil, from 02/25/2020 to 02/25/2022; and another exclusively to data from the day the pandemic was completed two years of its arrival in Brazil, therefore exclusively on 02/25/2022. Thus, it was possible to observe that the Brazilian epidemiological information system, governed by the health policies adopted by the Government, did not function properly during the COVID-19 pandemic, and still, there was no improvement in quality, even after two years of the pandemic. Additionally, evidence was observed that the data series relating to the contaminations and deaths caused by the SARS-CoV-2 coronavirus present behavior distinct from the expected frequency distributions according to the Newcomb-Benford Law, either as a result of a natural process or due to particular issues of the Brazilian information system itself, for example, logistics, data distortions, forms of geographic aggregation, errors and/or negligence, among other factors.

Prevalence of gastrointestinal parasites in endangered captive Asian Elephants (Elephas maximus) of Chitwan National Park in Nepal

In order to ascertain the comprehensive prevalence of gastrointestinal parasites among captive Asian elephants in Chitwan National Park, a cross-sectional investigation was conducted. A total of 103 samples was purposefully collected. Demographic details encompassing age and gender, along with epidemiological information concerning deworming status, timing intervals, and nutritional condition for both government-owned and privately-owned elephants, were procured through a structured questionnaire survey. The process involved microscopic identification and quantification of gastrointestinal parasites through sedimentation, centrifugal floatation, and MacMaster Egg Per Gram (EPG) count methods. The resultant data indicated an overall prevalence of gastrointestinal parasites at 47.57% (49 out of 103 samples). The dominant class of parasites observed was Nematodes (n=30, 61.22%), followed by Trematodes (n=14, 28.57%) and Cestodes (n=5, 10.20%). Six distinct parasite genera were identified with positive results: Strongylus (26.53%), Trichostrongylus (24.48%), Fasciola (16.35%), Paramphistomum (12.24%), Anoplocephala (10.20%), and Ascaris (10.20%). Notably, the prevalence was markedly higher in females (39.80%) in comparison to males (7.76%), with the disparity being statistically significant (p>0.05). Additionally, a noteworthy correlation was observed between parasite prevalence, age groups, and deworming history, with statistical significance (p<0.05). The Egg Per Gram (EPG) count analysis demonstrated that the majority (87.75%) of the positively identified samples exhibited mild infection (100-500 eggs), while a relatively low percentage (6.12%) displayed heavy infection (1000-1500 eggs). The mean EPG was calculated as (248.39 ± 54.25). Consequently, the heightened prevalence of gastrointestinal parasites in captive elephants within Chitwan National Park underscores the necessity for targeted interventions to mitigate the risk of parasitic infestations.

Clinical characteristics and prognostic models of gonadal and extra-gonadal yolk sac tumors: a population-based analysis in children and adolescents.

Yolk sac tumors (YST) are a rare and aggressive germ cell tumor. We aimed to conduct a population-based cohort study and develop a nomogram to predict overall survival (OS) in pediatric patients with YST. The Surveillance, Epidemiology, and End Results (SEER) database was used to identify all pediatric patients with YST diagnosed between 2000 and 2018. The log-rank test was used to compare survival curves. To examine the impact of each factor on overall survival, a multivariate Cox proportional hazards model was created. Based on the results of the Cox regression model, a nomogram was constructed. A total of 520 YST patients were identified. Overall survival rates for all patients were 92.2% at 3-year and 90.3% at 5-year, respectively. The outcome of Cox proportional hazard regression revealed that age, gender, primary sites, and treatment regimens were important independent predictors in this model. Based on the Cox regression model, we created a nomogram for predicting OS in pediatric YST patients. The chance of death increased with age in patients. Furthermore, patients with extra-gonadal YST have a lower survival rate than those with gonadal YST. Our study revealed that age, gender, and primary site were found to be the most important predictors of the overall survival of pediatric YST, providing crucial epidemiological information for clinical management.

A Review of Ixodid Ticks (Acari: Ixodidae) Associated with Lacerta spp. (Reptilia: Lacertidae) from the Caucasus and Adjacent Territory

Based on a literature review, as well as on our own data, 14 ixodid tick species belonging to 5 genera were registered for the lizard hosts of the genus Lacerta (L. agilis, L. media, and L. strigata) in the Caucasus and the adjacent territories: Haemaphysalis sulcata, Haem. punctata, Haem. parva, Haem. caucasica, Haem. concinna, Haem. inermis, Ixodes ricinus, I. redikorzevi, Dermacentor marginatus, D. reticulatus, Hyalomma marginatum, Rhipicephalus bursa, Rh. rossicum, and Rh. turanicum. Tick species Haem. caucasica were recorded from Armenia for the first time. Our findings of Haem. punctata represent the first record of this species for Chechnya, Ingushetia (Russia), Armenia, and Azerbaijan. Most of the parasite species are associated with L. agilis (13) and L. strigata (12); L. media is a host of 6 tick species. Data on the infestation of Lacerta spp. by four tick species from our material (I. ricinus, Haem. punctata, Haem. caucasica, and Hyal. marginatum) are presented in the article. In addition, our article contains information on the range of infections associated with the above tick species. Castor bean tick I. ricinus (236 specimens), the most represented species in our collection, parasitizes all available terrestrial vertebrates including humans and can be vector of many various pathogens, so our study provides significant epidemiological information.

Complete genome analysis of echovirus 30 strains isolated from hand-foot-and-mouth disease in Yunnan province, China

BackgroundEchovirus 30 is prone to cause hand-foot-and-mouth disease in infants and children. However, molecular epidemiologic information on the spread of E30 in southwestern China remains limited. In this study, we determined and analyzed the whole genomic sequences of E30 strains isolated from the stools of patients with hand-foot-and-mouth disease in Yunnan Province, China, in 2019.MethodsE30 isolates were obtained from fecal samples of HFMD patients. The whole genomes were sequenced by segmented PCR and analyzed for phylogeny, mutation and recombination. MEGA and DNAStar were used to align the present isolates with the reference strains. The VP1 sequence of the isolates were analyzed for selection pressure using datamonkey server.ResultsThe complete genome sequences of four E30 were obtained from this virus isolation. Significant homologous recombination signals in the P2-3’UTR region were found in all four isolates with other serotypes. Phylogenetic analysis showed that the four E30 isolates belonged to lineage H. Comparison of the VP1 sequences of these four isolates with other E30 reference strains using three selection pressure analysis models FUBAR, FEL, and MEME, revealed a positive selection site at 133rd position.ConclusionsThis study extends the whole genome sequence of E30 in GenBank, in which mutations and recombinations have driven the evolution of E30 and further improved and enriched the genetic characteristics of E30, providing fundamental data for the prevention and control of diseases caused by E30. Furthermore, we demonstrated the value of continuous and extensive surveillance of enterovirus serotypes other than the major HFMD-causing viruses.

Condemnation of bovine carcasses due to tuberculosis-gross lesions in Rio Grande do Sul, Brazil: Associated risk factors

Surveillance of bovine tuberculosis (bTB) lesions in animals at slaughterhouses is useful for controlling and eradicating the disease, besides providing epidemiological information. This study aimed to identify risk factors for bovine tuberculosis (bTB) condemnation in cattle at slaughterhouses in Rio Grande do Sul, Brazil. A logistic regression analysis was conducted using data on bTB-related condemnations. Variables examined included animal origin, number of slaughtered animals, season, inspection level (state or municipality), animal sex, and slaughterhouse location. A total of 297,817 Animal Transport Guides were evaluated, representing the transportation of 3497,521 animals. Among these, 6097 (2.05%) had at least one animal condemned due to bTB lesions. Risk factors for condemnation included larger batch sizes, female animals, slaughterhouses, and animal origin. The higher condemnation frequency in females and regions with dairy farms suggests links to milk production. Variation in condemnation rates by inspection level and slaughterhouse highlights the need for standardized procedures in identifying bTB lesions. Identifying these risk factors enables targeted interventions to enhance disease control and eradication efforts.

Hospital mortality from covid-19 in children and adolescents in Brazil in 2020-2021.

To describe cases, deaths, and hospital mortality from covid-19 in children and adolescents in Brazil, according to age group, during the evolving phases of the pandemic in 2020 and 2021. Census of patients aged up to 19 committed with severe acute respiratory syndrome, due to covid-19 or unspecified, notified to the Brazilian Influenza Epidemiological Surveillance Information System, from January 1, 2020, to December 31, 2021. The two years were divided into six phases, covering the spread of the disease-first, second and third wave-as well as the impact of vaccination. The pediatric population was categorized into infants, preschoolers, schoolchildren, and adolescents. Hospital mortality was assessed by pandemic phase and age group. A total of 144,041 patients were recorded in the two years, 18.2% of whom had confirmed cases of covid-19. Children under 5 years old (infants and preschoolers) accounted for 62.8% of those hospitalized. A total of 4,471 patients died, representing about 6.1 deaths per day. Infants were the ones who most progressed to the intensive care unit (24.7%) and had the highest gross number of deaths (n = 2,012), but mortality was higher among adolescents (5.7%), reaching 9.8% in phase 1. The first peak of deaths occurred in phase 1 (May/2020), and two other peaks occurred in phase 4 (March/2021 and May/2021). There was an increase in cases and deaths for younger ages since phase 4. Hospital mortality in the pediatric population was higher in phases 1, 4, and 6, following the phenomena of dissemination/interiorization of the virus in the country, beginning of the second wave and beginning of the third wave, respectively. The absolute number of cases of covid-19 in children and adolescents is significant. Although complete vaccination in descending order of age provided a natural deviation in age range, there was a greater gap between the curve of new hospitalized cases and the curve of deaths, indicating the positive impact of immunization.

Strong breeding colony fidelity in northern gannets following high pathogenicity avian influenza virus (HPAIV) outbreak

High pathogenicity avian influenza virus (HPAIV) caused the worst seabird mass-mortalities in Europe across 2021–2022. The northern gannet (Morus bassanus) was one of the most affected species, with tens of thousands of casualties in the northeast Atlantic between April–September 2022. Disease outbreaks can modify the movement ecology of animals by diminishing spatial consistency, thereby increasing the potential for disease transmission. To detect potential changes in movement behaviour, we GPS-tracked breeding adults following the initial HPAIV outbreak, at three of the largest northern gannet breeding colonies where major mortality of adults and chicks occurred (Bass Rock, Scotland, UK; Grassholm, Wales, UK; Rouzic, Brittany, France). We also gathered background epidemiological information and northern gannet colony dynamics during the outbreak. Our data indicate that HPAIV killed at least 50 % of northern gannets, and suggest the presence of HPAIV H5N1 antibodies in juveniles. GPS-tracked adult northern gannets remained faithful to their breeding sites despite the HPAIV outbreak and did not prospect other breeding colonies. They performed regular foraging trips at sea, similar to their behaviour before the outbreak. Comparison with GPS-tracking data gathered in 2019, i.e. before the HPAIV outbreak, suggested lower foraging effort in birds which survived HPAIV in 2022, potentially as a consequence of reduced intra- and interspecific food competition. Breeding colony fidelity of surviving adult northern gannets following HPAIV mass-mortalities indicates limited capacity for viral spread during our study. This may contrast with the behaviour of adults during the initial disease outbreak, and with that of younger individuals.

Epidemiological Characterisation of blaNDM-Positive Enterobacterales from Food-Producing Animal Farms in Southwest China.

Carbapenems are atypical β-lactam antibiotics with a broade antibacterial spectrum and strong antibacterial activity; however, the emergence and spread of carbapenemases have led to a decline in their effectiveness. New Delhi metallo-β-lactamase (NDM) is an important carbapenemase that has attracted widespread attention and poses a major threat to public health. To investigate the epidemiological characteristics of blaNDM in swine and chicken farms in southwestern China, we isolated 102 blaNDM-positive Enterobacterales strains from 18 farms in Sichuan and Yunnan provinces in 2021, with Escherichia coli and Klebsiella spp. being the main reservoirs of blaNDM, variant blaNDM-5 being the most prevalent, and all strains being multi-drug resistant. Whole-genome sequencing analysis of 102 blaNDM-positive Enterobacterales strains revealed that blaNDM had spread primarily through its carriers on the same farm and among the 18 farms in this study. A high degree of genetic similarity between animal-derived blaNDM-positive Escherichia coli strains and human-derived strains was also identified, suggesting a potential mutual transmission between them. Nanopore sequencing results indicated that blaNDM is predominantly present on the IncX3 plasmid, that an insertion sequence might be important for recombination in the blaNDM genetic environment, and that most of the plasmids carrying blaNDM are transferable. Collectively, our results enrich the current epidemiological information regarding blaNDM in pig and chicken farms in Southwest China, revealing its transmission pattern, as well as the potential risk of transmission to humans, which could help to better understand and control the spread of blaNDM.

Autism Spectrum Disorders Registry in Hamadan, Iran: A Study Protocol

: Autism spectrum disorder (ASD) begins in early childhood and has short-term and long-term effects in later life. Deficits in social communication, social interaction, and limited and repetitive behaviors characterize this disorder. We aimed to develop and design a registration system for ASD patients in Hamadan Province to have comprehensive and valuable epidemiological data for researchers about the frequency, distribution, and causes of ASD. This epidemiological information can help target prevention measures and plan care. By designing and developing a patient registry system for ASD, valuable uniform epidemiological information about the web of causes and consequences of ASD is available. The next step is to utilize valid and reliable information for public health, clinical, or policy purposes.

Four-year field survey on francisellosis in Yesso scallops Mizuhopecten yessoensis cultured in southern Hokkaido, Japan

Lethal impact of the bacterium Francisella halioticida on Yesso scallops Mizuhopecten yessoensis has been experimentally demonstrated, but epidemiological information for this bacterium infection in scallop farms has been limited. Thus, the present study conducted a monthly epidemiological survey for 4 years on adult scallops ear-hung from 2017 to 2020 on a scallop farm in northern Japan. As a result, the prevalence of F. halioticida in low temperature period increased for all year groups, but any association with scallop mortality was recognized. On the other hand, in the 2017–2019 year groups, increase of the prevalence and rapid declines of scallop survival were recognized in high-temperature periods. Additionally, overall survival in these year groups were apparently lower than the 2020 year group without increase of the prevalence in high-temperature period, suggesting that infection of F. halioticida in high-temperature periods may be associated with mortality of scallops. Abscess lesions in the adductor muscle were found to be associated with F. halioticida infection, but not always formed in infected scallops. Thus, presence of abscess lesions may serve as an indicator for francisellosis, but not necessarily a definitive symptom for this disease.

Serological profile of respiratory viruses in unvaccinated steers upon their arrival at Brazilian feedlot facilities.

Bovine viral diarrhea virus (BVDV), bovine alphaherpesvirus 1 (BoAHV1), bovine respiratory syncytial virus (BRSV), and bovine parainfluenza virus 3 (BPIV-3) are involved in bovine respiratory disease. These viruses can infect the respiratory system and cause considerable economic losses to beef and dairy cattle herds. This study aimed to determine the serological profiles of steers for BVDV, BoAHV1, BRSV, and BPIV-3 upon their arrival at Brazilian feedlot facilities. A total of 1,282 serum samples from unvaccinated steers were obtained on the first day of feeding. Samples were collected from 31 beef cattle herds reared in an extensive rearing system in six Brazilian states. Antibodies against BVDV, BoAHV1, BRSV, and BPIV-3 were detected using a virus neutralization test. The steers were distributed in agreement with their age and the Brazilian state of origin. The highest seropositivity was for BoAHV1 and BPIV-3 at 92.1% (1,154/1,253) and 86.6% (1,100/1,270), respectively. The seropositivity of BRSV was 77.1% (959/1,244). BVDV presented a lower rate, at slightly more than 50% (51.8%; 656/1,266). Age was a risk factor for the presence of antibodies against BVDV, BoAHV1, and BPIV-3 but not BRSV. A positive correlation was identified between BoAHV1 and BPIV-3 (P = 0.85) and between BRSV and BPIV-3 (P = 0.47). The high rate of seropositive steers for these four respiratory viruses on the first day of confinement identified in this serological survey provides important epidemiological information on respiratory infections, as the seropositivity of the four main bovine respiratory viruses in Brazilian beef cattle herds in an extensive rearing system.

Emergence of carbapenem-resistant enterobacterales co-harboring blaOXA−78 and blaOXA−58 from India

BackgroundCarbapenem-Resistant Enterobacterales (CRE) has been categorized as pathogens of critical priority by World Health organization (WHO) as they pose significant threat to global public health. Carbapenemase production considered as the principal resistance mechanism against carbapenems and with the recent surge and expansion of carbapenemases and its variants among clinically significant bacteria in India, the present study reports expansion blaOXA−78 and blaOXA−58 of in CRE of clinical origin.MethodsBacterial isolates were collected from a tertiary referral hospital and identified through VITEK® 2 Compact automated System (Biomerieux, France). Rapidec® Carba NP (Biomerieux, France) was used to investigate carbapenemase production followed by antibiotic susceptibility testing through Kirby-Bauer Disc Diffusion method and agar dilution method. Class D carbapenemase genes were targeted through PCR assay followed by investigation of horizontal transmission of blaOXA−58 and blaOXA−78. Whole genome sequencing was carried out using Illumina platform to investigate the genetic context of blaOXA−58 and blaOXA−78 genes and further characterization of the CRE isolates.ResultsThe carbapenem-resistant Escherichia coli (BJD_EC456) and Serratia marcescens (BJD_SM81) received during the study from the tertiary referral hospital were isolated from sputum and blood samples respectively. PCR assay followed by whole genome sequencing revealed that the isolates co-harbor blaOXA−58 and blaOXA−78, a variant of blaOXA−51. Horizontal transfer of blaOXA−58 and blaOXA−78 genes were unsuccessful as these genes were located on the chromosome of the study isolates. Transposon Tn6080 was linked to blaOXA−78 in the upstream region while the insertion sequences ISAba26 and ISCfr1 were identified in the upstream and downstream region of blaOXA−58 gene respectively. In addition, both the isolates were co-harboring multiple antibiotic resistance genes conferring clinical resistance towards beta-lactams, aminoglycosides, fluroquinolones, sulphonamides, tetracyclines. BJD_EC180 belonged to ST2437 while BJD_SM81 was of an unknown sequence type. The nucleotide sequences of blaOXA−78 (OQ533021) and blaOXA−58 (OQ533022) have been deposited in GenBank.ConclusionsThe study provides a local epidemiological information regarding carbapenem resistance aided by transposon and insertion sequences associated blaOXA−78 and blaOXA−58 genes associated and warrants continuous monitoring to prevent their further dissemination into carbapenem non-susceptible strains thereby contributing to carbapenem resistance burden which is currently a global concern.