Dataset: 11.1K articles from the COVID-19 Open Research Dataset (PMC Open Access subset)
All articles are made available under a Creative Commons or similar license. Specific licensing information for individual articles can be found in the PMC source and CORD-19 metadata.
More datasets: Wikipedia | CORD-19
Deep Learning Technology: Sebastian Arnold, Betty van Aken, Paul Grundmann, Felix A. Gers and Alexander Löser. Learning Contextualized Document Representations for Healthcare Answer Retrieval. The Web Conference 2020 (WWW'20)
Funded by The Federal Ministry for Economic Affairs and Energy; Grant: 01MD19013D, Smart-MD Project, Digital Technologies
Among the 284 deceased patients included in this study, 163 (57%) tested positive for HIV, and a total of 17 (6%) fatal cryptococcal infections were confirmed in the CDA. All the deaths except one occurred in HIV-infected cases. Among the HIV-infected cases, cryptococcosis was responsible for 16 deaths (10%; 95% confidence interval [CI]: 6–15%). Among the Mozambican adults, 109 out of 169 (64%) were HIV-infected, and 11 died of fatal cryptococcal infection (10%). Four of these cases were maternal deaths (three pregnant women and one in the puerperal period), accounting for 11% of the 36 maternal deaths occurring in HIV-infected women. None of the 17 HIV-positive children over one month of age had cryptococcal infection. Thirty-seven out of the 61 (61%) patients from Brazil were HIV-infected, and Cryptococcus was responsible for five of these deaths (13%). The only death caused by Cryptococcus in an HIV-negative patient occurred in a six-year-old child (infected with C. gattii).
During the whole study, 3,282 medical consultations were carried out, 29% (955/3282) of
which were coded as common cold or acute upper respiratory infections of multiple and
unspecified sites. Of these 955 common cold cases, a sample of 134 patients who met the
inclusion criteria was obtained, median age 2.9 years (0.1-11.2 y), 49% male. The most
frequent symptoms were coryza (91.8%, 123/134), cough (90.3%, 121/134), fever (56%,
75/134) and wheezing (46.3%, 62/134). Respiratory viruses were detected in 73.9%
(99/134) of nasopharyngeal wash samples (1 sample per patient) with a coinfection rate
of 30.3% (30/99). The laboratory tests findings are described in Table I.
Overall, the antibiotic prescription rate was 39.6% (53/134), among which 60.4% (32/53)
was amoxicillin, 22.6% (12/53) macrolides, 9.4% (5/53) cephalosporins and 7.6% (4/53)
amoxicillin plus sulbactam (Table II). Of 53
patients who received antibiotics during the follow-up, only 30.2% (16/53) received them
judiciously and the other 69.8% (37/53) received them inappropriately. Among these 37
cases with inappropriate use, the clinical justifications for prescription of
antibiotics were: in 37.7% (20/53) to treat nasal or postnasal discharge during the
first week of common cold symptoms in patients without fever, in 18.9% (10/53) to treat
persistence of cough during the first week of symptoms, in 11.3% (6/53) to treat common
cold and in 1.9% (1/53) to treat wheezing symptom.
Among 75 children who had fever at the onset of symptoms, 45.3% (34/75) were prescribed
antibiotics whereas 32.2% (19/59) of those who did not have fever at the onset of
symptoms received antibiotics. Thus, there was no difference in the proportion of
antibiotic prescriptions between children who had fever at the onset of symptoms and
those who did not (p = 0.123).
Of a total of 53 children who received antibiotics, 34 presented fever at onset of
symptoms and of these, 29.4% (10/34) received judicious prescription of antibiotics. Of
the remaining 19 children who did not have fever at the onset of common cold symptoms
and received antibiotics, 31.6% (6/19) were prescribed antibiotics judiciously. Thus,
there was also no difference for judicious prescription of antibiotics between children
with fever and those without fever at the onset of common cold symptoms (p = 0.869).
The average time to the resolution of symptoms of children with signs of secondary
bacterial infection was of 16.7 days and, within this group, all children received
antibiotics. Among children with no signs of bacterial infection, the average time to
the resolution of symptoms was 8.9 days for the group that received antibiotics and 7.0
days for the group that did not.
Among patients with respiratory virus monoinfection, all patients with influenza
received antibiotics inappropriately (10/10), whereas those with respiratory syncytial
virus were prescribed antibiotics inappropriately in 60% (3/5) and those with rhinovirus
were prescribed antibiotics inappropriately in 44.4% of cases (5/9) (p = 0.016). Also,
of seven patients coinfected with influenza, 71.4% (5/7) received antibiotics
inappropriately, as showed in Table II. None of
the patients were vaccinated against influenza by the time of the study.
A high prevalence (68.3%) of diarrheic dogs, shown to harbor at least one pathogen by real-time PCR, was observed in the Brazilian samples, which exceeded those in the United States (54.5%), Australia (58.4%), Canada (52.0%), United Kingdom (51.7%), and Japan (49.6%), as shown in Table 4. The rate of co-infection observed here in diarrheic dogs (45.1%) was also higher than those in the other countries tested. Despite the higher prevalence of enteropathogens and co-infections in Brazil, the rates in the other countries are also relevant, indicating that infectious diarrhea may be a global phenomenon rather than a phenomenon specific to a particular country. Because all dogs with co-infections belonged to the diarrheic group and co-infections were observed in all age categories, this study highlights the importance of investigating multipathogen co-infections, especially in dogs aged 0–1 years, in which the rate of co-infection was 4-fold higher than in the other age groups.
Many enteric viruses, bacterial pathogens, and parasites probably contribute to disease both individually and in combination, and together, co-infecting pathogens may cause more severe diarrhea than infections with each pathogen alone. The pathogens involved in a co-infection can interact synergistically, for example via the host’s immune system, with the presence of one enhancing the abundance and/or virulence of the other, resulting in even greater pathogenesis and a greater contribution to the overall disease burden. Therefore, interspecific pathogen interactions can alter the pathogen dynamics, host health, and the success of control strategies.
In this study, co-infection did not increase the duration of diarrhea and there was no significant difference in the number of deaths in animals with or without co-infections. Because there was no reliable correlation between the interaction of enteropathogens in co-infections in this study, the cause–effect relationship between the presence of an organism and the occurrence of diarrhea is still unclear. Opportunistic or commensal organisms may be identified from an imbalance in the intestinal flora or dysbiosis, and not all the co-infecting agents present must be treated to produce a good outcome. However, because all the infectious agents evaluated here have been described as causing diarrhea in experimental studies, knowledge of their presence allows treatments and prevention strategies to be planned. In this study, even when diarrhea persisted for more than 10 days, the infectious diseases were still present in the differential diagnosis. Empirical treatments and the use of several antibiotics are common in routine veterinary practice and the use of a panel to detect multiples pathogens prevents the incorrect or excessive use of antimicrobial drugs, which could cause resistance. Furthermore, some of these pathogens are potential zoonotic agents, including hookworms, Giardia spp., Cryptosporidium spp., and Salmonella spp., and the identification of these organisms can reduce the risk of their transmission to humans and others animals.
Although this study focused on client-owned dogs, dogs received in animal shelters are also expected to carry pathogen co-infections, including zoonotic agents. However, differences have been observed in the prevalence of each agent, especially in terms of the co-infection rates, and dogs from shelters with diarrhea showed a higher prevalence of co-infection (96.0%) than was observed in this study (45.1%). That heterogeneous dog population had a higher rate of crowding, and the dogs may have been immunocompromised for clinical, nutritional, and/or psychological reasons, exposed to more environmental pathogens, and sometimes with inadequate health care, so their high co-infection rate cannot be compared validly with that of owned dogs in households.
The highest rate of co-infection in this study involved the association of viral and bacterial agents, in contrast to the highest co-infection in dogs in the United States, which was caused by viruses and protozoans. The highest co-infection rates were for CPV-2 and CPA, observed in 9/12 (75.0%) samples from dogs in Brazil, and for CCoV and Giardia spp., which occurred together in 35.4% of dogs from the United States. These co-infections may have clinical effects and may require more-intensive efforts to ensure the appropriate treatments to eliminate specific pathogens and to correct electrolyte, acid–base, and nutritional disturbances, potential sepsis, and other metabolic consequences.
The alpha toxin gene is present in all strains of Clostridium perfringens and may be found in asymptomatic dogs as part of the normal intestinal microflora, as in 14% of the control dogs in the present study. Data from some studies indicate that conventional PCR that targets only CPA will almost always be positive and of virtually no clinical use. However, a recent study demonstrated that the quantification of CPA may be used as a diagnostic marker for association of the agent in patients with diarrhea. Using the same methodology and cutoff value as a previous study, we observed a significant difference between the control group (4/43, 9.3%) and in the diarrheic group (37/104, 35.6%; P = 0.0025) in the proportion of animals positive for > 300,000 copies of CPA. The higher amount of CPA in the diarrheic dogs than in the control dogs suggests that the high concentrations of toxins produced by this organism exert a pathogenic effect on the gastrointestinal tract. In the present study, diarrheic dogs co-infected with CPA had 3-fold more copies than those that were infected with only CPA. We hypothesize that in these cases, C. perfringens overgrowth in the bacterial flora increases the toxin expressed, which contributes to the dog’s diarrhea.
All the control dogs were negative for CPV-2, which was strongly associated with diarrhea (P = 0.000004), with an overall occurrence of 36/104 (34.6%) in the diarrheic dogs. The same prevalence (18/51, 34.6%) was observed in a study also conducted in Brazil but performed only with puppies up to 6 months old and corroborated with previous surveys, which reported rates varying from 16% to 58%. Although CPV-2 has been considered to be primarily disease of puppies, the present study has shown the importance of also investigating adult dogs for CPV-2, since occurred in 11.1% of 1–8 year old dogs and in 12.0% of dogs older than 8 years. The CPV-2 was most prevalent agent involved in co-infections in this study, in which 58.3% of the diarrheic samples positive for CPV-2 were associated with others agents, contrasting with only 3.8% CPV-2 co-infection observed in the study with puppies. This variability may be related to the geographic regions examined, the populations studied, agents investigated and the diagnostic techniques used. Although the date of live-modified vaccination was not the focus of this study, the CPV-2 cutoff value used was able to differentiate vaccine strains from wild-type infections. Despite the use of vaccination, the CPV-2 was still spread among the dogs as observed in this study, in which only 13/36 (36.1%) of the positive animals for CPV-2 had no history of vaccination. Still remains unclear whether type-2 vaccines can provide protection against the new variants of the CPV, but a recent study observed that the cases of vaccine failure are most likely not associated to the mutations detected in the sequenced regions. Thus, further studies should elucidate whether local parvovirus strains are effectively controlled by the currently available vaccines and which factors may be associated with the vaccination efficacy. CPV-2 was the most prevalent agent associated with dual co-infections in the present study, which may be attributable to highly contaminated environments or low dog immunity.
Although the detection rate of CCoV was higher in the diarrheic dogs (11.54%) than in the control dogs (6.98%), the lack of a statistically significant difference in these rates may indicate a secondary role for CCoV as an intestinal pathogen in dogs. Although the shedding of CPV-2 seemed to be associated with clinical signs of gastroenteritis, CCoV was also detected in healthy dogs, as previously reported. Although CCoV infections are characterized by high morbidity and low mortality, with typically mild enteritis in dogs, 11/12 (91.7%) diarrheic dogs with CCoV were co-infected with other enteric pathogens, which may have aggravated their clinical signs and even caused higher mortality, as reported earlier for CPV-2, canine adenovirus type 1, and CDV. CDV tended to be significantly higher in the diarrheic dogs than in the control dogs; although not significant, the P value was very close to the limit of significance (P = 0.059).
Whereas some enteropathogens, such as Salmonella spp., Cryptosporidium spp., and Giardia spp., showed similar prevalences in the various countries tested (Table 4), CDV and CPV-2 were approximately 4-fold more prevalent in Brazil, indicating that the higher incidence of viral diseases may be related to differences in strain pathogenicity, vaccination status, and environmental factors.
Although the CPV-2 strain and vaccine status/response may play important roles in viral infection and host immunity, further studies are required to fully understand this specific pattern of CPV-2 infections in Brazil.
Although intestinal parasites contribute to diarrhea, 95.7% of positive and 49.2% negative samples on the parasitological tests were also positive on the real-time PCR diarrhea panel, indicating that fecal parasitological tests alone should not be used as a single diagnostic tool.
The prevalence of diarrheic dogs observed in the Brazilian samples (68.3%) was similar to that observed in the United States (54.5%), Australia (58.4%), Canada (52.0%), United Kingdom (51.7%), and Japan (49.6%), as shown in Table 4. The rate of co-infection observed in Brazilian diarrheic dogs (45.1%) was also higher than those in the other countries tested (Table 4) and a significant difference was observed between United States (P < 0.0001), Australia (P = 0.01) and Canada (P = 0.04).
QALY for H1N1 infections managed in outpatient services was 0.50 and those admitted to hospital or intensive care was 0.23 based on a study with patients infected with H1N1 during the 2009 pandemic (Hollmann et al., 2013). Adverse events reduced QALY in 0.195 (Appendix A). The QALY for the healthy state was 0.885, the mean QALY measured in two population-based Brazilian studies (Zimmermann et al., 2016; Silva et al., 2017). QALY for death was 0 (
The demographic features, HIV status, clinical presentation and management of the 17 patients with fatal cryptococcal infection are summarized in Table 1. The median age was 34 years (range 6–44 years); 11 cases (65%) were men. In 13 out of the 16 (81%) HIV-infected patients, a positive HIV test result was reported in the clinical records and was apparently unknown by the clinician in the other 3 cases. Four out of the 16 (25%) HIV-infected patients were on ART, but the duration of ART was only reported in one case.
Headache was the most common symptom (13 patients, 76%), followed by fever and vomiting (eight cases each, 47%). Upon admission to hospital, eight patients (47%) were confused and/or agitated, two patients (12%) were lethargic, and another two (12%) were fully comatose. Meningeal signs were detected in seven patients (41%). The mean time from admission to death was 9.3 days (95%CI: 2.4–16.2). Cryptococcal infection was considered the first clinical diagnostic option in only 4/17 (23%) of the confirmed cases, whereas it was included in the differential diagnosis in eight patients (47%). Antifungal treatment (fluconazole or Amphotericin B) had been prescribed to seven patients but to only five of the clinically suspected cases. Seven of the patients (41%) died within 72 hours of admission, and 12 out of the 16 HIV-positive patients (75%) died within one week of admission.
The clinical records of the remaining 267 cases included in this study were reviewed for clinical diagnosis of cryptococcal infection. Among these, three HIV-infected patients were clinically diagnosed with cryptococcal meningitis, but no evidence of cryptococcal infection was found in the autopsy (the cause of death was identified as toxoplasmosis in two cases and tuberculosis in one case).
Cost with prophylaxis was BRL 39.42, based on average expenditure of Brazilian Ministry of Health with the antivirals (Appendix B). Treatment of prophylaxis’ adverse cost BRL 292.05, calculated from the cost of each main adverse event (headache, nausea, and psychiatric event) weighted to each adverse event incidence (Appendix A).
Outpatient care cost BRL 12.47 according to SUS reimbursement for an urgent care consultation. Cost of hospital admission was estimated in BRL 5,727.59 and for intensive care, BRL 19,217.25 (
The 330 patients included in the study exhibited the classical clinical symptoms of the disease and were divided according to the progression of infection into two groups: patients that presented severe acute respiratory syndrome (SARS) and were hospitalized (n = 156) following Brazilian Ministry of Health protocol and patients with mild symptoms non-hospitalized (n = 174) (Table 1). There was a predominance of women among the patients studied (61.5%) and the mean patient age was 24.7 years (1–80 years). Forty-seven of the women were pregnant and 28 were hospitalized. Radiologic alterations were found in 51.9% of hospitalized patients. Most hospitalized patients had no comorbidities (59%). However, patients with comorbidities (metabolic disorders, immunosuppression and obesity) were significantly more frequent in the group of hospitalized patients. Deaths occurred in 55.7% of hospitalized patients. The population studied exhibited a mean European genetic contribution of 57.4%, a mean Native American contribution of 26.4% and a mean African contribution of 16.2% (Table 1) in agreement with previously data from Brazilian populations [13, 15]. In non-hospitalized patients the mean European contribution was 60% ranging from 4.6 to 91.9%, the mean Native American contribution was 25% ranging from 3.2 to 93.2%, and the mean African contribution was 15% ranging 2.2–61%. In hospitalized patients, genetic contribution was European 54.4% ranging from 5.9 to 93%, Native American 28% ranging from 3.5 to 90.6%, and African 17,6% ranging 2.4–67.6% (Additional files 1, 2). European and African genetic ancestry showed statistical differences between groups (p = 0.006 and p = 0.010, respectively).
There were no significant differences in the allele or genotype frequencies of the CCR5Δ32 polymorphism between non-hospitalized and hospitalized patients (p = 0.289 and 0.431, respectively) (Table 2). A logistic regression analysis was performed to assess the effect of CCR5Δ32 polymorphism on infection severity controlling for European and African ancestry and the presence of comorbidities to avoid confounding effects. No association between patients carrying the Δ32 allele and severity was found (Table 3).
Here, in a screening of dog fecal samples, 26% (71/269) of the dogs with and without diarrhea were MAstV5 positive, as determined using RT-PCR. Likewise, non-viral agents and factors such as bacteria, intestinal parasites, malnutrition and intoxications are able to promote enteric disease mainly in the young dog population. The search for other enteric viruses in the MAstV5-positive samples from dogs with gastroenteritis showed that the dogs were also infected with other known pathogens. Moreover, we found that single MAstV5 infection was associated only with the asymptomatic state, although there is a risk that the results will be biased, since the analyzes were conducted on the basis of convenience sampling and we can not exclude the possibility that the long term of viral shedding could be an explanation for the MAstV5-positive samples detected in asymptomatic dogs, based on previous study that demonstrated the comparison between virus load and clinical manifestation26 (Fig. 1 and Table 3). These findings were not unexpected, as mixed infections are common, but more studies will be necessary to real deduce the role of MAstV5 in the cases reported here.15, 16, 17, 18, 19, 20, 21, 22, 23, 24
Several reports of MAstV5 suggest a clinical association of virus molecular detection and diseased dog clinical samples.18, 20, 21, 22, 23, 26, 33 Furthermore, studies of the prevalence of MAstV5 in China showed that 12% (22/183) of the puppies displaying clinical signs of diarrhea were positive for MAstV5, as determined using RT-PCR, compared to none of 138 healthy dogs, although these studies did not look for other viruses that may be associated with diarrhea.19 In a study conducted in Italy, 24% of 110 stool samples collected from dogs with clinical signs tested positive for the presence of MAstV5 RNA, and 9% (10/110) of the samples showed an MAstV5-single infection, although other asymptomatic animals (9% of 75) were also positive for MAstV533. Therefore, the association with clinical signs and the shedding of the virus was described only in a case study of 2 animals, which is apparently an isolated case.26 A prevalence study in France found that 21% (66/316) of the puppies in 42% (14/33) of the breeding kennels surveyed were MAstV5 positive, as determined using RT-PCR.21 In the same report, the authors observed that puppies that were less than 7 weeks old were especially susceptible to MAstV5 infection, although a direct association with clinical signs was not possible.21 Lastly, recent studies found a MAstV5 prevalence of 6% in the United Kingdom and an infection rate of 33% in puppies under three months in Japan.22, 23
The partial genomic sequencing and characterization of selected samples revealed a remarkable genetic heterogeneity of MAstV5 of Brazilian origin. Because it was hypothesized that two strains of human AstV with less than 95% identity at the nucleotide level are serologically distinguishable,34 the lower identities (<85%) shown between the capsid gene sequences analyzed here may reflect the need for a novel species classification into four genotypes – MAstV5a to MAstV5d. Additionally, phylogenetic analysis indicated that the four MAstV5 strains reported here represent a lineage that is more closely related to the Chinese strains than to the others strains, based on the high sequence identity (97%) of ORF2, according to the species demarcation criteria established by the ICTV5 (Table 2).
In summary, we found 26% MAstV5-positive fecal samples in dogs with or without gastroenteritis. Based on sequence analysis of the partial genome from four MAstV5-positive samples, we proposed a novel species classification into four genotypes – MAstV5a to MAstV5d. More studies are required to understand the biology and attempt the clinical and antigenic implications of astrovirus genotypes in dogs to elucidate the relative veterinary importance of different canine AstV types.
A total of 333 viruses were found in 270 samples, and the most common virus detected corresponded to IBV, showing a 58.9% (196/333) occurrence, followed by ANV with 12.6% (42/333), FAdV-I with 8.4% (28/333), CAstV with 8.1% (24/333), ChPV with 6.6% (22/333), ARtV with 5.1% (17/333), and AReo with 0.3% (1/333). Single infections were found in 86.3% (233/270) of the samples, with IBV being the most predominant virus diagnosed as a unique agent. ANV, CAstV, IBV, ChPV, and ARtV were found in simple and combined (2 to 5 viruses) infections. FAdV-I was found in unique and combined (2 to 3 viruses) infections. Multiple infection analysis showed that 2 viral infections were found in 6.3% (17/270) of samples, followed by 3 viral infections in 5.6% (15/270), 4 viral infections in 1.5% (4/270), and 5 viral infections in 0.4% (1/270). Single and multiple viral infections are described in Table 2. Multiple infections occurred with 25 profile combinations of viruses (Table 3). ANV, CAstV, IBV, ChPV, and ARtV were present in combination with each other, resulting in between two and five virus combinations. FAdV-I was present in combination with ChPV, ANV, and IBV. AReo showed a single infection. The variance analysis showed no significant difference between the frequencies of single and multiple viruses (p = 0.36).
Inappropriate use of antibiotics for viral common colds is an important problem
worldwide but, until now, we did not have clinical studies addressing this problem in
Brazil. During the clinical course of a common cold, secondary bacterial infections may
occur, however, antimicrobials are frequently used inappropriately for events that are
normal during the clinical course of a viral infection (Dowell et al. 1998b). In our
study, this practice was particularly evident in cases of viral rhinosinusitis, since
37.7% (20/53) of patients received antibiotics for the presence of nasal or postnasal
discharge during the first week of common cold symptoms without fever. During childhood,
20-40% of common colds can be complicated by AOM (Wald
et al. 1991, Chonmaitree et al. 2008)
and although current recommendations on management of AOM encourage the initial
observation of nonsevere AOM cases in selected children (i.e., “watchful waiting”)
(AAP 2004), there are still controversies
around the diagnosis and management of AOM (Hoberman et
al. 2011,Shaikh et al. 2011). In
routine practice, the over diagnosis of AOM is frequent but, considering that there are
difficulties in confirming the diagnosis, in our study we considered all indications of
antibiotic for AOM as adequate regardless of the patients' age, severity of symptoms and
certainty of diagnosis. We believe that rates of inappropriate use of antibiotics could
be even greater if stringent diagnostic criteria were applied for AOM diagnosis.
Amoxicillin was the first choice for antibiotic therapy accounting for 60.4% (32/53) of
all prescriptions but, on the other hand, the second most prescribed antibiotics were
macrolides (22.6%, 12/53) which is not in accordance with current guidelines (Bradley et al. 2011). Predominantly in the paediatric
outpatient population, the growing emergence of bacterial resistance to macrolides is
related to delayed cure and is responsible for a great proportion of costs currently
associated with antibiotic resistant pneumococcal infections (Kawai et al. 2012, Reynolds et al.
2014). Continuing medical education programs aimed not only to reduce the
inappropriate use of antibiotics, but also to teach the best practices of antibiotic
therapy could be of great help to improve this scenario.
Diagnostic uncertainty, which is defined as the difficulty in distinguishing a
self-limited viral infection from a bacterial infection requiring antibiotic therapy is
identified by researchers as a factor that contributes for antibiotic overuse (Arnold et al. 2005). Thus, the difficulty in
predicting a bacterial infection in febrile children could lead to the misuse of
antibiotics. Bacterial infections are associated with worsening of clinical conditions
with a consequent longer time for the resolution of symptoms. However, common colds
without secondary infections follow a self-limited course of seven-10 days with no
reduction of the duration of symptoms with the use of antibiotic, as it was observed in
this study and as reported elsewhere in the medical literature (Kaiser et al. 2001, Brandileone et
al. 2006, Li et al. 2009, Carranza-Martinez et al. 2010).
Although our study was not designed to evaluate the influence of fever in medical
decision to prescribe antibiotics, we observed that there was no difference in the
proportion of antibiotic prescriptions for patients who had fever at the onset of
symptoms and for those who did not, as well as in the proportion of judicious
prescription of antibiotics for these two groups of patients. Additional research is
needed to identify the local factors that are determinants of antibiotic misuse.
Although it is well known that influenza vaccination is the primary strategy to prevent
influenza, the Brazilian Health Ministry started public vaccination campaigns against
influenza for children in 2010 so that part of the population had no access to influenza
vaccine by the time of the study. None of the patients of the study were vaccinated
against influenza and this fact could explain the high frequency of influenza infection
in our patients (23.1%; 31/134), as showed in Table
Antiviral treatment also plays an important role in decreasing influenza-related
morbidity and mortality, but none of 33 patients with laboratory confirmed influenza
infection received antiviral therapy, whereas all patients with influenza monoinfection
received antibiotics inappropriately (10/10) and those coinfected with influenza and
other viruses also received antibiotics inappropriately in a great proportion of cases
(71.4%; 5/7). A recent study in the United States of America reported that during
2012-2013, antiviral medications were underprescribed and antibiotics may have been
inappropriately prescribed to a large proportion of outpatients with influenza (Havers et al. 2014). The referred study emphasises
that the use of sensitive and specific tests for the rapid diagnosis of influenza and
other respiratory viruses is strongly recommended and could decrease antibiotic use and
guide appropriate use of antiviral agents in both outpatient and inpatient settings
(Bradley et al. 2011). In Brazil, diagnostic
tests for respiratory virus are still expensive and are not easily available for the
vast majority of the population, especially for low income people.
This study was conducted at one primary care facility and it is not possible to
generalise the results to all Brazilian primary health care services, however, these
preliminary data will help us to better understand antibiotic misuse among children with
common cold viral infections. We believe that continuing education on appropriate
antibiotics and antivirals use as well as accessibility to influenza vaccination,
sensitive and specific tests for the rapid diagnosis of respiratory viruses and
antiviral medication are essential to improve primary healthcare quality.
Since the demonstration of the protective role of a 32-bp deletion in the CCR5 gene in two individuals exposed to, but not infected with HIV, studies on the protective or regulatory role of this deletion have multiplied. The protective role of this polymorphism in HIV infection was extensively studied and utilized as model for the development of new therapeutics for AIDS.
However, the presence of the deletion can be a determinant factor of morbidity and mortality in the case of other infectious diseases. In a meta-analysis of four cohorts evaluating the deletion in patients with West Nile fever, genetic deficiency of the CCR5 gene was a strong risk factor of symptomatic arbovirus infection. In another study comparing 129 patients with a diagnosis of tickborne encephalitis virus infection and 79 subjects with aseptic meningitis negative for tickborne encephalitis and 134 healthy controls, a higher frequency of the homozygous Δ32/Δ32 genotype was observed among patients with tickborne encephalitis, particularly among severe cases of the disease.
In the present study, no difference in the Δ32 deletion of the CCR5 gene was observed between the groups of individuals infected with Influenza A(H1N1)pdm09 in a Brazilian admixed population, who presented the classical clinical symptoms. Thus, no correlation could be established between the presence of the mutation and a more severe outcome of the disease. The present results agree with those reported in a recent study involving an Italian population, but disagree with the findings obtained for a Canadian population.
The Brazilian population was formed by extensive admixture of Native American, European and African populations, nevertheless European genetic ancestry is predominantly in Brazil [13, 15]. In the population studied the mean European contribution was around 57% and the CCR5Δ32 allele frequency was 3.6%, similar to previously described for Brazilian populations. Despite ethnic differences with the populations previously analyzed, in the present study thirteen heterozygous and one homozygous for the Δ32 deletion were found in patients with mild symptoms and eight heterozygous for this deletion were found in hospitalized group showing no evidence of this allele effect on severity.
Previous researches adopted different criteria for severe patients [7, 11], which could contribute for conflicting results among studies, but despite those differences, we emphasize the large size of the sample studied here compared to previously published studies, supporting the hypothesis that the Δ32 mutation is not a predisposing factor for severe Influenza A(H1N1)pdm09 infection.
The post-BMT patients in our study had a median age of 22 years (ranging from 9 to 40 years). Males accounted for 67% of the individuals. Patients who underwent BMT before or within 6 months of A(H1N1)pdm09 diagnosis were stratified because this time frame is critical for immunosuppression after BMT. Two immunosuppressed patients, one with graft-versus-host disease (GVHD) and the other with chronic lung injury (CLI), received BMT 6 months prior to influenza diagnosis (Table 1). The other seven patients received BMT more than 6 months prior to influenza infection (Table 1). However, two patients in this last group were immunocompromised, due to remission of cancer or chronic neutropenia (<1.500 cells/mm3) (Table 1). Viruses infecting these patients were infectious, because they have been isolated in cell culture. Although we have searched for other respiratory viruses infection, all patients were negative (Fast-Track Diagnostic, Luxembourg, Luxembourg).
The A(H1N1)pdm09 HA was sequenced from all clinical samples. In eight cases, mutant viruses were found. The ESH strain was found in 7 patients, while one sample had the K-15E, P83S and Q293R mutations (Figure 1). In another patient, a strain with wild-type (WT) residues K-15 and Q293, and mutant P83S, was detected (KSQ strain; patient 2 in Table 1). The predisposing conditions of the patients indicate that they should be more likely to have worse clinical outcomes. Additionally, confirmed diagnosis with a presumably more virulent strain of A(H1N1)pdm09 could be even more critical for these individuals. Despite that, these patients displayed mild symptoms of infection, and hospitalization was not required. Comparisons of the influenza A(H1N1)pdm09 HA sequences from post-BMT patients with those from Lee et al, and other control groups (otherwise healthy individuals with severe/fatal outcomes or non-immunocompromised individuals with mild infection) are shown (Figure 1). As we can see, there is no specific pattern to cluster sequences together (Figure 1). In fact, this phylogenetic tree has low bootstrap values for the different branches (Figure 1); suggesting that independently of the clinical outcomes and/or predisposing condition, the different virus strains from this period looked alike.
Next, we compared the exposure to the virus carrying the three polymorphisms, ESH strain, as a risk factor to lead to different outcomes in post-BMT individuals and other control groups of patients. Of note, another required control would be a viral strain without the three polymorphisms. In our dataset, viruses genetically closer to the A/California/04/2009, also carry the change P83S. Mutation P83S is found in influenza A(H1N1)pdm09 viruses from clades 6 and 7, and in Brazilian strains from the mitigation phase of the pandemics and afterwards. Since mutations K-15E and Q293H are the main ones associated with increased influenza virulence,, comparisons between ESH and KSQ strains correlation with disease severity could still be feasible. By selecting Brazilian samples from the pandemic period from our dataset, we found 73 sequenced samples from potential control groups. Among these, 21 cases were from healthy individuals, with registered information about absence of any comorbidity, and 51 cases were from non-immunocompromised individuals. Among healthy individuals, 3 had mild infection (no ESH virus detected), 13 had severe infection (5 ESH viruses) and 5 deceased (1 ESH virus). Out of the non-immunocompromised individuals, 11 had mild outcome (5 ESH viruses), 22 had severe infection (7 ESH viruses) and 18 deceased (7 ESH viruses). In Table 2, we compared ESH as a risk factor, over the KSQ strain, for post-BMT patients and other groups. Although ESH is presumably more lethal, the mild clinical outcome is more likely to occur in post-BMT patients than severe or fatal outcomes in otherwise healthy individuals (OR = 14.32, 95% CI 1.4–767.3; P<0.05) (Table 2, upper half). When the exposure to ESH is analyzed by comparing two groups with mild outcomes, post-BMT vs. non-immunocompromised patients, no significant difference is observed (Table 2, lower half). Despite that, there is a greater tendency of ESH-infected post-BMT patients progress to mild clinical infection than non-immunocompromised individuals (OR = 8.53 and 95% CI 0.71–495.4). Altogether, data from phylogenetic tree and contingency table, suggest that ESH strain correlation with severity or fatality may be questionable.
Ours findings oppose the previously observed impact of the ESH strain on the general population,,. Our patients were easily distinguishable in terms of their specific genetic backgrounds, ethnicity and previous history of treatments and clinical interventions. Therefore, it seems unlikely that an impaired virus replication could have occurred as a consequence of any specific cancer- or BMT-related interventions. Although the works on influenza infection in post-BMT patients is, in general, limited by the small number of patients (around a dozen individuals), contributions such as this are important for further meta-analysis investigations – which may strengthen the isolated findings displayed in the literature.
Except for Salmonella spp. and both coronaviruses, all other agents commonly associated with diarrhea in pigs were detected in varying proportions in the 184 animals examined in the present study. One to six different agents were found at each farm, and one to four pathogens were detected in stool samples of infected animals.
Most studies of diarrhea in pigs have focused on a single agent, which can result in a biased view of the relevance to the disease of a particular pathogen. Calderaro et al., however, studied 21 swine herds in the state of São Paulo, Brazil, from 1996 to 1997 and determined the frequency of bacterial, viral, and protozoan agents in the feces of piglets with clinical signs of diarrhea. Among the 174 samples tested in their study, 40.2 % were positive for E. coli, 31.6 % for C. suis, 10.9 % for rotavirus, and 1.2 % for Cryptosporidium parvum, with some samples having more than one pathogen present. Interestingly, 32.8 % of the samples tested negative for any agent. More recently, a matched case–control study evaluated the frequency of rotavirus, haemolytic E. coli, C. difficile, C. perfringens types A and C, Eimeria spp., Cystoisospora spp., and Cryptosporidium spp. associated with neonatal mild diarrhea in piglets. The study was carried out in litters of 1- to 7-day-old piglets from 28 pig farms in the state of Rio Grande do Sul, Brazil. Despite a wide range of frequencies of the different agents in case and control groups, no agent was significantly associated with diarrhea in case litters when compared to controls. Thus, the authors stressed the need for caution when interpreting laboratory diagnosis of mild diarrhea, as the detection of a single agent does not necessarily indicate that it causes the problem.
Fecal samples from suckling (n = 205) and weaned piglets (n = 82) with diarrhea from 24 farms in Southern Germany were examined. C. suis was diagnosed in 26.9 % and C. parvum in 1.4 % of the piglets investigated. It was found that 17.6 % of the animals were infected with enterotoxigenic E. coli and 4 % were positive for rotavirus. The occurrence of the pathogens was significantly associated with the age of the animals examined.
Rotaviruses represent one of the most frequently detected viral agents associated with diarrhea in swine worldwide, especially in 1- to 4-week-old pigs [17, 18]. In 75 % of the visited farms, almost 40 % of stool samples tested were positive for RV-A, indicating the high frequency of this viral infection among piglets in Brazil. Nevertheless, this viral agent was equally distributed between case and control groups. According to Svensmark et al., rotaviruses are more frequently detected in semiliquid and loose stools than in normal or watery stools. However, when rotavirus infection was studied in 1090 litters from 26 intensively managed Danish sow herds, an association between virus detection and diarrhea could not be demonstrated. On the other hand, a significant difference has been reported regarding the frequency of RV-A in diarrheic and non-diarrheic fecal samples. These previous results, together with ours, indicate that in spite of the wide distribution of rotaviruses, additional factors may be involved in the development of clinical cases.
Negative RT-PCR results obtained in this study for coronaviruses confirm previous reports of the absence of serological evidence of these infections in Brazilian pig herds [14, 21, 22].
Although campylobacteriosis is one of the most common causes of diarrhea in humans, the role of Campylobacter spp. in swine gastrointestinal disorders is still controversial. In 2005, a study suggested that pigs represent an important C. coli reservoir in Germany. However, the clinical relevance of this finding was not evaluated, because this broad study aimed at monitoring foodborne pathogens. An experimental infection conducted to evaluate the colonization and translocation ability of a porcine strain of C. coli showed that all ten infected animals remained in very good health, although overall fecal consistency, rated on a five-point scale, decreased from 4.0 to 3.5 over 4 days. In another study, no statistically significant difference was found in the number of pigs with Campylobacter spp. between diarrheic and healthy animals. However, CFU counts were significantly different in the two groups, suggesting that Campylobacter spp. may play a role as a cofactor in pig diarrhea. Despite the fact that C. coli was the most frequent bacteria found in the present study, with almost 40 % of samples positive and 81.25 % of farms positive, no difference in frequency was found between case and control groups, which is in agreement with previous reports. Nevertheless, in one industrialized well-managed indoor farm, we found that all animals that were positive only for C. coli had severe diarrhea, while control animals were negative for all pathogens tested. Altogether, these results suggest that C. coli may play a role in pathogenesis, although it is important to consider other agents or factors not tested in this work.
Clostridium perfringens type A was found in almost 23 % of diarrheic and non-diarrheic samples from 62.5 % of the farms, yet again there was no statistical difference between case and control groups, even when the subgroup of C. perfringens carrying the cpb2 gene was investigated (21.2 % positive samples). Chan et al. identified C. perfringens as the causal agent of gastrointestinal tract illness in 28 of 237 studied cases, and genotyping of 17 strains showed that they belonged to toxinotype A and had the cpb2 gene. In another study, intestinal positivity for C. perfringens was detected in 73 % of diarrheic and 78 % of healthy piglets. Those bacteria were mostly present in the intestinal lumen. In 20 % of diarrheic and 30 % of healthy animals, bacteria were found within the mucus layer and in direct contact with the intestinal epithelium. However, presence and location of C. perfringens in the intestinal tissue did not significantly correlate with histological lesions. Other authors necropsied and took intestinal samples from 46 piglets from 10 farms with a consistent history of type-A C. perfringens neonatal diarrhea. Samples were compared to those from an unaffected cohort of piglets. Based on the number of intestinal bacteria, presence of consensus cpb2 in C. perfringens isolates, expression of cpb2 in piglet intestines, and known or unknown causes of diarrhea, these investigators were unable to distinguish between healthy and diarrheic piglets. The role of cpb2-harboring C. perfringens in the development of diarrhea was also investigated through the assessment of cytotoxicity to porcine IPI-21 and human Caco-2 cell-lines. Supernatants of cpb2-harboring C. perfringens were cytotoxic to both cells to variable extents. However, toxin removal by anti-beta 2 toxin antibodies or degradation by trypsin did not reduce the cytotoxic effect of supernatants. These results indicate the need for further studies focused on elucidating the role of cpb2-positive C. perfringens type A in neonatal diarrhea.
Neonatal intestinal infection with E. coli causes severe diarrhea and frequently kills piglets. Different strains are described as responsible for clinical conditions, especially strains that produce enterotoxins such as the heat-labile enterotoxin (LT) and the heat-stable enterotoxin (ST) [31, 32]. In the present study, less than 12 % of examined samples were positive for ST (STa or STb), and no statistically significant difference between case and control groups was found. In Canada, from 2001 to 2010, 31 % of 237 samples submitted for gastrointestinal disease laboratory diagnoses had enterotoxigenic E. coli (ETEC) infection, and ETEC was less likely to be recovered when C. difficile, C. perfringens or rotavirus were detected (p < 0.05). In four commercial Danish swine herds, intestinal positivity for E. coli was found in 88 % and 80 % of the small intestines of diarrheic and non-diarrheic piglets, respectively. Nevertheless, diarrheic piglets had large numbers of E. coli more frequently than non-diarrheic piglets. Our results showed that 25 and 43.75 % of the farms were positive for E. coli STa and STb toxins, respectively, which represents a risk of outbreaks and of selection of resistant pathogenic strains.
Salmonella spp. was not found in the examined samples. These findings were expected, because this agent is not usually found in such young piglets [33, 34].
The equal distribution of bacterial agents between groups may have resulted from the extensive use of antibiotics in Brazilian swine production. This finding reinforces the need for a reassessment of the use of antibiotics in food-producing livestock.
Based on parasitological analysis, only two farms and 3.8 % of samples were positive for nematode eggs, and no statistically significant difference between case and control groups was found. These results suggest that systematic use of anthelminthic drugs associated with indoor housing systems and hygiene procedures can control infection by breaking the chain of transmission. However, animal welfare concerns are leading to changes in management practices. During recent decades, the number of organic and “green” swine herds has increased, and this may be an indication that former risk factors could arise again.
The detection frequency of Eimeria spp. was 8.15 % among tested samples (37.5 % of farms), and there was a statistically significant difference between case (18.60 %) and control (4.44 %) groups (p = 0.047). Some authors consider Eimeria spp. infection in piglets an uncommon cause of clinical signs [36–39]. However, more recently, Eimeria spp. was identified in 13 % of fecal samples from suckling piglets with diarrhea.
C. suis was the most commonly detected coccidian agent, present in 34.78 % of samples and widespread in the studied farms (87.5 %). A significant difference was again observed between case (53.49 %) and control (31.11 %) groups (p = 0.034). The ability of C. suis to cause diarrhea in piglets is well documented [41, 42], as is its frequency of infection in young piglets: 17.3 % in the Republic of Korea, 53.8 % in Germany, 31.6 % in Brazil, 6.3 % in Canada, and 8.9 % in Cuba. Our results differ from those of another study that was recently published in Brazil in which no statistical difference between case and control groups was found. Methodological aspects of the two studies could explain the differing results. We collected samples from 1-day- to 4-week-old animals, while piglets between 1 and 7 days of age were sampled in the previous Brazilian study. Age of piglets seems to be crucial for the outcome. C. suis infections in piglets undoubtedly have a high impact. However, encouraging the use of drugs to control this agent could lead to abuses similar to those seen with antibiotic use. Coccidian oocysts are generally regarded as relatively resistant to environmental factors and apt to survive for considerable periods. However, high temperature (25–30 °C) in combination with low relative humidity (53–62 %) rapidly reduces the viability of C. suis oocysts. This finding might point to a possible control mechanism requiring only some environmental control and proper management of farrowing pens, like by allowing a few extra days in-between litters or by increasing desiccation somehow, might be able to reduce the number of infective C. suis oocysts that has escaped pen cleaning.
According to Mengel et al., newborn piglets exposed to natural C. perfringens type A infection and to low-level experimental infection with C. suis showed an increase in clinical disease, mortality, and metabolically active C. perfringens type A. In the present study, analyses of 28 possibilities of co-infection by two agents and 55 possibilities of co-infection by three agents identified a potential for worsening conditions only in the combination of C. suis and C. perfringens type A (cpb2 gene) (p = 0.014), corroborating the hypothesis that simultaneous infection with these agents soon after birth may lead to an increase in the severity of clinical disease in piglets.
Recently, a non-hemorrhagic diarrhea during the first week of life, with no detection of known infectious agents and characterized by a milk-filled stomach and flaccid intestines at necropsy was described. The syndrome is not related to starvation or infection by enterotoxigenic E. coli, C. perfringens type A or C, C. difficile, rotavirus, coronavirus, Cryptosporidium spp., Giardia spp., C. suis or Strongyloides ransomi. The existence of neonatal diarrhea with unspecific lesions and without known pathogens is not a new phenomenon, but this study also reinforces the importance of laboratory diagnosis and correct interpretation of results as well as the relevance of control and prophylactic measures.
The present study showed a high rate of HRSV detection in infants hospitalized with bronchiolitis. Five genotypes were found, with a predominance of genotype A ON1, which was recently described in other countries and not identified in previous studies in the southeast region of Brazil. The clinical and epidemiological characteristics of infants that were infected with HRSV A ON1 were similar to infants with infections by other genotypes identified in the study.
Raising awareness of the risk of ZIKV infection to those groups at risk is of critical importance. The population groups to be targeted will vary according to whether they are in a region or country where there is ZIKV activity. In those areas where ZIKV transmission is occurring, the entire population needs to be aware of the disease and vigilant of the risk in order for them to be motivated to undertake risk mitigation measures. Apart from the general public, specific stakeholder groups in the risk communication strategy should include pregnant women, women of reproductive age and their partners, community organizations, schools, health care workers, the media, local and international organizations involved in reproductive health, and local policymakers (WHO, 2016c). Key messages should include prevention of unintended pregnancies by the use of reversible contraception methods; using insect repellents, mosquito nets and other mosquito avoidance measures; and assisting in local vector control activities, such as reducing the mosquito breeding sites on private property. This last issue is essential, because the majority of breeding sites of Ae. albopictus and Ae. aegypti in urbanized areas are usually found on private property, where the simple preventive measure of water source elimination by owners can significantly reduce the risk.
The advice of health ministries of some Zika-countries for women to defer pregnancy for considerable periods to lessen the risk to their newborns is unprecedented and controversial. Apart from the attendant population planning risks of a distorted population profile resulting from a diminished birth cohort, some of these countries have high rates of unplanned pregnancies, strict abortion laws, a lack of sexuality education programs in schools, and poor access to contraception, leading to difficulties in implementation of this policy (Ahmed, 2016).
Because of the rarity of the complication of GBS, raising awareness among clinicians is likely to be the more effective risk communication strategy. However, the fact that cases may have mild, or no, symptoms of ZIKV infection preceding it means that clinicians won’t necessarily be aided by a clinical prompt, hence delays in diagnosis are likely.
In countries where ZIKV is not active and not receptive to the virus, the focus of awareness-raising is on those citizens planning to travel to Zika-affected areas, in particular, to individuals or couples who are pregnant or planning to become pregnant. Avoiding or deferring travel is advised, and if the person does decide to travel, the messages focus on mosquito avoidance and contraception advice, and symptoms to be aware of on return. Again, the high rate of asymptomatic infection means that the advice needs to relate to anyone traveling to endemic areas, not just those who develop symptoms. Based on available evidence of risk of sexual transmission of ZIKV, the WHO recommends men and women returning from areas where transmission of ZIKV is known to occur to abstain from unprotected sex for at least 6 months upon return to prevent ZIKV infection through sexual transmission and that women who are planning a pregnancy wait at least 6 months before trying to conceive to ensure that possible ZIKV infection has cleared (WHO, 2016b). Disease control agencies from individual countries advise a lesser risk period for women to defer pregnancy following their (or their partner’s) return from Zika-affected areas (CDC, 2017).
A third category includes those countries where ZIKV infection is not endemic but are receptive to the virus as they harbor competent vectors. The key population health messages in these countries relate to raising awareness of the symptoms of ZIKV infection so that cases are ascertained early and disease control measures rapidly instigated. Travelers from these countries to endemic areas need to be especially aware of risk mitigation measures whilst traveling to endemic areas, as well as symptoms of the infection, as they are at risk of triggering an outbreak on their return.
Microcephaly cases and neurological disorders have only been associated with infection with strains of ZIKV from the Asian lineage, detected in French Polynesia and in the Americas. To determine the inhibition spectrum of chloroquine against ZIKV infection, Vero cells were infected with the Brazilian isolate of the Asian lineage (ZIKV BR). Chloroquine decreases the percentage of cells infected with the Brazilian isolate from 70% to 30% and 5% at 12.5 and 25 μM, respectively (Figure 2A,C). Moreover, viral RNA levels in the supernatant of Vero cells were quantified as a direct measurement of ZIKV infection. Treatment with 25 μM chloroquine led to a 16-fold reduction in the level of viral RNA detected in the supernatant (Figure 2B).
The samples received for viral diagnostics were from broilers, layers, and breeders of all ages. According to the age of birds, the samples corresponding to layer and breeder hens were divided into 5 groups, with intervals of 10 weeks of age, from week 1 to week 50, and two more groups, one for birds older than 51 weeks, and a group for which the ages were not reported (N/R; Table 4).
The samples corresponding to broilers were divided into 6 groups with intervals of 7 days of age, from day 1 to day 42, and two more groups, one for birds older than 43 days, and an N/R age group (Table 5).
Positive samples from layer and breeder hens older than 51 weeks of age showed the highest frequency of viral infections: 22.4% for layers and 37.8% for breeders. The viral infection frequencies of the other layer groups were 18.4% for the 11–20-week group, 16.3% for the 1–10-week and 31–40-week groups, 4.1% for the 21–30-week group, and 22.4% for the N/R age group. In the case of breeders, the frequency of viral infections was 18.9% for the 1–10-week and 41–50-week groups, 13.5% for the 31–40-week group, and 10.8% for the N/R age group (Table 4). Broilers showed the highest frequency of viral infections, at 37.8% for the 36–42-day group. Viral infection rates in the other groups were 15.3% for the 8–14-day group, 14.7% for the 15–21-day group, 11.7% for the 43-day group, 7.4% for the 1–7-day group, 6.7% for the 22–28-day group, 4.9% for the 29–35-day group, and 6.7% for the N/R age group (Table 5). Single viral infections were found mostly in broilers, with 129/233 (55.4%), followed by 49/233 (21%) in layers and 34/233 (14.6%) in breeders. Multiple viral infections were found with more frequency in broilers, with 14/17 (82.4%) with two viruses, 15/15 (100%) with three viruses, and 4/4 (100%) with four viruses. The only sample with five viral infections also belonged to the broilers group. A total of 3/17 (17.6%) samples with multiple viral infections (3 viruses) were found in samples from breeders (Table 6).
The organs corresponding to positive results for FAdV, ChPV, CAstV, and ARtV included the liver, intestines, and pancreas. AReo was present in one sample of intestines and IBV was present in all the five organs used for this study (Table 7).
FAdV-I was found in samples from breeders (12/28) and broilers (14/28). ChPV was found in samples from broilers (20/22). CAstV was found in samples from breeders (10/27) and broilers (17/27). ANV was found in samples from broilers (41/42). IBV was found in samples from layers (49/196), breeders (16/196), and broilers (116/196). AReo was found in one sample, but the origin was not reported. ARtV was found in samples from breeders (2/17) and broilers (15/17). All data describing the positive samples according to the age of layers, breeders, and broilers affected by the enteric viruses in this study are shown in Table 8.
To our knowledge, the present study revealed for the first time the presence of RASs in the NS5A and NS5B regions of HCV genotype 1 Uruguayan strains from patients who have not been previously treated with DAAs and is one of the few South American countries to report on this matter. It is currently unclear if preexisting viral variants with reduced susceptibility to DAAs are clinically relevant for the prediction of virologic treatment failure. However, individualized DAA therapy based on baseline resistance analysis may be beneficial for optimizing treatment efficacy in patients with HCV genotype 1 infection and risk factors for treatment failure. Therefore, the potential role of baseline resistance testing remains an area of critical research and clinical questions.
The presence of known pathogens in piglets alone does not seem to determine the occurrence of diarrhea. The indiscriminate use of antibiotic and anthelminthic medication should be reassessed. The importance of laboratory diagnosis and correct interpretation of data as well as the relevance of control and prophylactic measures should be reinforced.
The aim of this case–control study was to assess the association between a variety of pathogens and the occurrence of diarrhea episodes in 1-day- to 4-week-old piglets. Statistically significant differences in pathogen frequency between animals in case and control groups were found for the protozoan agents C. suis and Eimeria spp., and C. suis and C. perfringens type A co-infection. This finding may indicate that coccidian agents should be independently considered in disease control and monitoring programs.
Overall, 13 patients (five adults and eight children) were admitted to the ICU. Six patients were directly admitted from the emergency department, and the other seven patients were transferred from other hospital wards (Table S2). Ventilatory support was given to 12 patients (Table 1 and S9). Invasive mechanical ventilation was performed in 10 patients (76.9%), and non invasive ventilation (NIV) was performed in 3 patients (23.1%; Table 1). Among the NIV patients, one required subsequent endotracheal intubation and mechanical ventilation, and all three patients were discharged from the hospital. Extra-pulmonary organ failure occurred in eight patients (33.3%; Table 1 and S9).
Of the 13 critically ill patients, 12 were treated with oseltamivir, and treatment was initiated 48 h after the first signs/symptoms of viral infection in 5 of them. Adjunct or non-conventional supportive therapies for ARDS were performed for 12 of the 13 patients that entered the ICU (92.3%). A total of 10 patients (76.9%) received systemic corticosteroids (eight due to previous use and two for shock and persistent ARDS); five (38.5%) were ventilated in a prone position, and four (30.8%) required recruitment maneuvers. No patient received extra-corporeal membrane oxygenation.
Two cases of encephalopathy syndromes, with seizures or electroencephalographic changes, were seen in Martinique as part of ZIKV infection, probably due to encephalitis (Roze et al., 2016). Carteaux et al. (2016) reported a case of an 81-year old man from France who was admitted to an Intensive Care Unit 10 days after a cruise to Pacific islands, with fever and decreased level of consciousness, being diagnosed with meningoencephalitis and had a positive RT-PCR for ZIKV in his cerebrospinal fluid. The patient later recovered and was discharged after 17 days, with cognitive function fully recovered after 38 days and residual weakness in his left arm. In Brazil, a 47-year old pregnant patient was admitted to an Intensive Care Unit with confusion, dysarthria and lower limb weakness, 4 days after presenting a rash and arthralgia (Soares et al., 2016). The patient was diagnosed with encephalitis and had a positive PCR for ZIKV in her urine and IgM ZIKV antibody in her cerebrospinal fluid and serum, and passed away after 11 days (Soares et al., 2016). Since these observations have only recently been described, very little is known about the frequency of a direct central nervous system (CNS) infection by ZIKV. A possible confounder is the simultaneous occurrence of various arboviruses, such as Chikungunya and DENV, since these arboviruses can cause a direct CNS invasion with myelitis, encephalitis, and meningitis (Moulin et al., 2016).
Throughout the ZIKV epidemic in French Polynesia, an increase in the number of patients presenting with GBS was seen (Paploski et al., 2016). Other arboviral infections such as dengue, chikungunya, Japanese encephalitis, and West Nile fever (WNF) have been associated with GBS (Ravi et al., 1994; Lebrun et al., 2009; Leis and Stokic, 2012; Verma et al., 2014). Cao-Lormeau et al. (2016) published a case-control study reporting the occurrence of 42 cases of GBS after a Zika outbreak between October 2013 and April 2014, in comparison to 5–10 cases in the same period in previous years. All 42 patients had neutralizing antibodies against ZIKV, whereas only 56% of neutralizing antibodies were found in the serum from a control group of 98 patients without GBS. The majority of GBS patients (93%) had detectable ZIKV IgM and 88% had a systemic febrile disease with symptoms that corresponded to ZIKV infection before the development of the neurological symptoms. This cohort of ZIKV associated GBS was classified electrophysiologically as acute motor axonal neuropathy (AMAN) with a rapid onset of disease (4 days to reach the plateau). Approximately one-third of patients required intensive medical therapy with mechanical ventilation (Cao-Lormeau et al., 2016). Anti-glycolipid antibodies were found in 31% of patients. However, anti-ganglioside antibodies typical of AMAN were rarely present (Cao-Lormeau et al., 2016). Dos Santos et al. (2016) performed an analysis of ministry of health websites and International Health Regulations channels to compare the occurrence of GBS before and after the Zika outbreak. They found an increase of 877% in Venezuela, 400% in Suriname, 211% in Colombia, 172% in the Brazilian state of Bahia, 150 % in the Dominican Republic, 144% in Honduras and 100% in El Salvador.
During the study period, 44 hospitalized cancer patients with a suspected influenza infection were screened, and 24 had a confirmed influenza A diagnosis using a rapid indirect immunofluorescence (IFI) test or World Health Organization (WHO)-recommended real-time RT-PCR (rRT-PCR) (Figure 1 and Table S1). Among these, 20 patients were confirmed to be positive for the H1N1pdm virus using rRT-PCR (Figure 1 and Table S1). The remaining four patients were positive for influenza A using IFI only. Considering the pandemic case definitions with reference to international guidelines, these last four cases were categorized as H1N1pdm-confirmed cases. Altogether, these 24 cases constituted the study population. All of the respiratory samples collected from the 20 rRT-PCR-confirmed patients were inoculated in cell cultures. We recovered the virus from 13 individuals after at least two passages in MDCKs, constituting 15 isolated samples. These isolates were also analyzed for oseltamivir resistance using a functional assay.
Patients diagnosed with H1N1pdm were young (median age = 14.5, range 3–69 years). In total, 14 (58.3%) were under 18 years old, and 17 (70.8%) were less than 50 years old. Hematologic cancer occurred in 75% (18) of the patients, whereas solid tumors occurred in 25% (6) patients (Tables S2 and S3). A total of 22 (∼92%) patients had received immunosuppressive therapy in the previous 30 days. Among these individuals, 18 patients (75%) were on chemotherapy, 14 (58.3%) received systemic corticosteroids and 1 (4%) received radiation therapy (Table 1 and S4). No patient received erythropoietin (EPO) or immunomodulatory agents. A total of 14 patients (58.3%) presented febrile neutropenia (<500 neutrophils/mm3) at the time H1N1pdm was diagnosed. The median duration of neutropenia after the onset of viral disease was two days (ranging from one to six days; Table S5). According to the Brazilian National Cancer Institute's protocol, all patients that presented neutropenia received G-CSF until normalization of neutrophil counts. The clinical characteristics and comparisons among groups are shown in Table 1 and Tables S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, and S11. The overall mortality in our cohort was around 21% (n = 5), and four patients (n = 16.6%) had at least one comorbidity besides cancer. Of these patients with comorbidities, one died. No pregnant or morbidly obese patients were identified.
A total of 23 (95.8%) patients were treated with oseltamivir, and the median time from the initial symptoms to the initiation of therapy was three days (0–15 days; Tables 1, S2 and S6). One patient that died due to severe acute respiratory failure 24 h after clinical suspicion of H1N1pdm infection never received antiviral treatment. Oseltamivir was used for a median of seven days (0–19 days), and double doses (150 mg bid for adults and twice the recommended dose per kg for children) were administered for 11 (47.8%) patients (Table S6). A total of 11 (47.8%) patients received oseltamivir for more than seven days. Six patients (25%) received this antiviral within 48 h of clinical suspicion. All patients that died received oseltamivir more than 48 h after the onset of the illness. However, when we compared the mortality of patients that received oseltamivir either within or after 48 h of the onset illness, no significant difference was observed (0/6 vs. 5/18, p = 0.28). No differences in prolonged viral shedding were observed between these two groups.
At presentation, all patients were treated with broad-spectrum intravenous antimicrobial agents to combat community-acquired pneumonia and/or febrile neutropenia, and five (20.8%) had concomitant positive cultures (Tables S7 and S8). Hypoxemia was frequent, and the median PaO2/FiO2 on the first arterial blood gas evaluation was 192 mmHg (range: 64–367 mmHg).
AHEI is a small-vessel leukocytoclastic vasculitis that causes benign purpura in children typically between the ages of 4 and 24 months. It classically presents with rapidly progressive purpuric lesions over the face, extremities, and bilateral ears, accompanied by nonpitting edema of the extremities. The presence of bilateral auricular swelling and purpura in a well-appearing child should raise particular clinical suspicion for AHEI. Fewer than 10% of patients diagnosed with AHEI exhibit extracutaneous manifestations, which include glomerulonephritis, abdominal pain, arthralgia, testicular torsion, and intussusception. Diagnosis is clinical and can be made without a skin biopsy. If skin biopsy is performed, a leukocytoclastic vasculitis is present with IgA immunofluorescence in approximately one-third of patients. Laboratory testing is typically reassuring without evidence of renal or hematologic compromise. Some physicians have made the diagnosis via telemedicine, relying on cellphone photos to monitor the progression of the disease.
About 75% of cases of AHEI are preceded by respiratory infections, diarrheal illnesses, or urinary tract infections. Viruses including rotavirus, herpes simplex virus, and adenovirus have been implicated. Additionally, antibiotics and vaccinations have been identified as triggers. Although the exact triggering pathogen for AHEI is rarely identified, our case demonstrates that coronavirus can precede this disease. Our patient's symptoms of cough and conjunctivitis are consistent with coronavirus infection, and the result is unlikely to be a false positive given the low rate of coronavirus detection observed in healthy children. Specifically, coronavirus NL63 has been associated with petechial rash, but this is the first case to our knowledge to be associated with AHEI.
Several case reports note rapid improvement of purpura or edema after the administration of corticosteroids [3, 11]. Given the improvement in our patient's purpura by 48 hours after onset, we made the decision not to administer corticosteroids. Our case illustrates that symptoms of AHEI can have rapid onset as well as swift resolution without steroid intervention. This suggests that some previously reported patients may have improved even without corticosteroids, though at least one case has noted relapse of symptoms when steroids were removed. While use of corticosteroids remains controversial, most reports suggest that corticosteroids only be considered in severe presentations with complications or inability to maintain fluid intake [7, 11, 12].
With or without corticosteroids, most patients with AHEI make a complete recovery within one to three weeks of presentation. To our knowledge, our case is the fourth report in which a recurrence of symptoms occurred. In most cases, the recurrence occurred in a three-week time frame from onset of symptoms, though one case series reported a familial occurrence of AHEI in which three sons have had frequent relapses of purpuric circular rash into adulthood.
This patient was admitted to the hospital, underwent significant laboratory workup, received intravenous antibiotics, and was evaluated by multiple subspecialty services prior to diagnosis. While keeping in mind more worrisome diagnoses, providers should consider the diagnosis of AHEI in well-appearing young children with purpuric lesions on the face and ears and nonpitting edema of the extremities. Awareness and early recognition of AHEI may prevent hospital admission, invasive workup, and parental and provider concern.