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1.
J Med Virol ; 95(10): e29194, 2023 10.
Artigo em Inglês | MEDLINE | ID: mdl-37881026

RESUMO

Enteroviruses (EV) and parechoviruses A (PeV-A) are commonly circulating viruses able to cause severe disease. Surveillance studies from sub-Saharan Africa are limited and show high but variable infection rates and a high variation in genotypes. This is the first study to describe EV and PeV-A circulation in children in South Sudan. Of the fecal samples collected, 35% and 10% were positive for EV and PeV-A, respectively. A wide range of genotypes were found, including several rarely described EV and PeV-A types. Coxsackie virus A (CVA) EV-C types, particularly CVA13, were the most dominant EV types. The CVA13 types had a high diversity with the majority belonging to four different previously described clusters. PeV-A1 and -A14 were the most common PeV-A genotypes. A lack of representative data from our and other studies from sub-Saharan Africa demonstrates the need for more systematic surveillance of non-polio EV and PeV-A types in this region.


Assuntos
Enterovirus Humano A , Infecções por Enterovirus , Enterovirus , Parechovirus , Infecções por Picornaviridae , Criança , Humanos , Parechovirus/genética , Filogenia , Infecções por Picornaviridae/epidemiologia , Enterovirus/genética , Infecções por Enterovirus/epidemiologia
2.
Front Pediatr ; 11: 1181698, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37744436

RESUMO

Enteroviruses are among the most common causes of acute viral illness worldwide, and in neonates, the clinical course of these infections is heterogeneous. Severe complications, such as myocarditis, are associated with high mortality rates. In this case report, we present the clinical course of premature twins born at 35 weeks of gestational age, suffering from a severe neonatal enterovirus infection with cardiac involvement, which proved fatal in one of the twins. This course led to prompt identification in the other twin and facilitated timely transfer to a neonatal intensive care unit with neonatal hemodynamic expertise, and facilitated the timely transfer to a neonatal intensive care nit with hemodynamic expertise and immediate availability of AZCMO would it have been indicated. Early supportive therapy in the other twin contributed to a positive outcome. Therefore, we emphasize the importance of early recognition in averting adverse consequences. As a recommendation, we propose routine screening of enterovirus in viral panels for febrile newborns.

3.
Brain Commun ; 5(5): fcad223, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37731906

RESUMO

Nodding syndrome is a neglected, disabling and potentially fatal epileptic disorder of unknown aetiology affecting thousands of individuals mostly confined to Eastern sub-Saharan Africa. Previous studies have identified multiple associations-including Onchocerca volvulus, antileiomodin-1 antibodies, vitamin B6 deficiency and measles virus infection-yet, none is proven causal. We conducted a case-control study of children with early-stage nodding syndrome (symptom onset <1 year). Cases and controls were identified through a household survey in the Greater Mundri area in South Sudan. A wide range of parasitic, bacterial, viral, immune-mediated, metabolic and nutritional risk factors was investigated using conventional and state-of-the-art untargeted assays. Associations were examined by multiple logistic regression analysis, and a hypothetical causal model was constructed using structural equation modelling. Of 607 children with nodding syndrome, 72 with early-stage disease were included as cases and matched to 65 household- and 44 community controls. Mansonella perstans infection (odds ratio 7.04, 95% confidence interval 2.28-21.7), Necator americanus infection (odds ratio 2.33, 95% confidence interval 1.02-5.3), higher antimalarial seroreactivity (odds ratio 1.75, 95% confidence interval 1.20-2.57), higher vitamin E concentration (odds ratio 1.53 per standard deviation increase, 95% confidence interval 1.07-2.19) and lower vitamin B12 concentration (odds ratio 0.56 per standard deviation increase, 95% confidence interval 0.36-0.87) were associated with higher odds of nodding syndrome. In a structural equation model, we hypothesized that Mansonella perstans infection, higher vitamin E concentration and fewer viral exposures increased the risk of nodding syndrome while lower vitamin B12 concentration, Necator americanus and malaria infections resulted from having nodding syndrome. We found no evidence that Onchocerca volvulus, antileiomodin-1 antibodies, vitamin B6 and other factors were associated with nodding syndrome. Our results argue against several previous causal hypotheses including Onchocerca volvulus. Instead, nodding syndrome may be caused by a complex interplay between multiple pathogens and nutrient levels. Further studies need to confirm these associations and determine the direction of effect.

4.
Heliyon ; 9(7): e17338, 2023 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-37539175

RESUMO

Background: Male genital schistosomiasis (MGS) is an underappreciated complication of schistosomiasis, first described in 1911. However, its epidemiology, diagnostic testing and case management are not well understood in sub-Saharan Africa. To shed new light on MGS prevalence in Malawi, a longitudinal cohort study was conducted among adult fishermen along the southern shoreline of Lake Malawi using detection of schistosome DNA in participants' semen by real-time TaqMan® PCR analyses. Methods: Upon recruitment of 376 participants, 210 submitted urine samples and 114 semen samples for parasitological tests. Thereafter, the available semen samples were subsequently analysed by real-time TaqMan® PCR. Praziquantel (PZQ) treatment was provided to all participants with follow-ups attempted at 1, 3, 6 and 12-months' intervals. Results: At baseline, real-time PCR detected a higher MGS cohort prevalence of 26.6% (n = 64, Ct-value range: 18.9-37.4), compared to 10.4% by semen microscopy. In total, 21.9% of participants (n = 114) were detected with MGS either by semen microscopy and/or by real-time PCR. Subsequent analyses at 1-, 3-, 6- and 12-month follow-ups indicated variable detection dynamics. Conclusions: This first application of a molecular method, to detect MGS in sub-Saharan Africa, highlights the need for development of such molecular diagnostic tests which should be affordable and locally accessible. Our investigation also notes the persistence of MGS over a calendar year despite praziquantel treatment.

5.
Antimicrob Resist Infect Control ; 12(1): 1, 2023 01 05.
Artigo em Inglês | MEDLINE | ID: mdl-36604672

RESUMO

BACKGROUND: Methicillin resistant Staphylococcus aureus (MRSA) is a major burden for hospitals globally. However, in the Netherlands, the MRSA prevalence is relatively low due to the 'search and destroy' policy. Routine multiple-locus variable-number of tandem repeat analysis (MLVA) of MRSA isolates supports outbreak detection. However, whole genome multiple locus sequence typing (wgMLST) is superior to MLVA in identifying (pseudo-)outbreaks with MRSA. The present study describes a pseudo-outbreak of MRSA at the bacteriology laboratory of a large Dutch teaching hospital. METHODS: All staff members of the bacteriology laboratory of the Elisabeth-TweeSteden hospital were screened for MRSA carriage, after a laboratory contamination with MRSA was suspected. Clonal relatedness between the index isolate and the MRSA isolates from laboratory staff members and all previous MRSA isolates from the Elisabeth-TweeSteden hospital with the same MLVA-type as the index case was examined based on wgMLST using whole genome sequencing. RESULTS: One of the staff members was identified as the probable source of the laboratory contamination, because of carriage of a MRSA possessing the same MLVA-type as the index case. Eleven other isolates with the same molecular characteristics were found in the database, of which seven were retrospectively suspected of contamination. Clonal relatedness was found between ten isolates, including the isolate found in the staff member and the MRSA found in the index patient with a maximum of eleven alleles difference. All isolates were epidemiologically linked through the laboratory staff member, who had worked on all these cultures. CONCLUSIONS: The present study describes a MRSA pseudo-outbreak over a 2.5-year period due to laboratory contamination caused by a MRSA carrying laboratory staff member involving nine patients. In case of unexpected bacteriological findings, the possibility of a laboratory contamination should be considered.


Assuntos
Staphylococcus aureus Resistente à Meticilina , Infecções Estafilocócicas , Humanos , Staphylococcus aureus Resistente à Meticilina/genética , Infecções Estafilocócicas/epidemiologia , Infecções Estafilocócicas/microbiologia , Estudos Retrospectivos , Surtos de Doenças , Países Baixos/epidemiologia
6.
Pathogens ; 11(10)2022 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-36297127

RESUMO

Despite extensive vaccination and booster programs, SARS-CoV-2 outbreaks in long-term care facilities (LTCF) continue to occur. We retrospectively describe a SARS-CoV-2 outbreak amongst a partially vaccinated LTCF population in The Netherlands which occurred in March 2021. The facility comprised three floors functioning as separate wards. Nasopharyngeal swabs for SARS-CoV-2 qRT-PCR were obtained from residents and staff presenting with COVID-19-like symptoms and from all residents and staff during two point prevalence screenings (PPS). Samples meeting technical criteria were included for phylogenetic analysis. Positive SARS-CoV-2 qRT-PCR were obtained from 11 (18%) of 61 residents and 8 (7%) of 110 staff members between March 8 and March 25. Seven (37%) cases and five (63%) vaccinated cases were diagnosed through PPS. Cases were found on all wards. Phylogenetic analysis (n = 11) showed a maximum difference of four nucleotides between sequences on the outer branches of the tree, but identified two identical sequences on the root differing maximum two nucleotides from all other sequences, suggesting all did belong to the same cluster. Our results imply that PPS is useful in containing SARS-CoV-2 outbreaks amongst (vaccinated) LTCF populations, as an entire LTCF might behave as a single epidemiological unit and it is preferable to maximize the number of samples included for phylogenetic analysis.

7.
PLoS Negl Trop Dis ; 16(4): e0010307, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35377880

RESUMO

BACKGROUND: It remains largely unknown where and how infections with soil-transmitted helminths (STHs; Ascaris, Trichuris, Necator and Ancylostoma) occur. We therefore aimed to identify possible sources of infection by assessing the environmental contamination in an STH-endemic area. METHODS: We first performed a series of laboratory experiments designed to optimize a soil straining-flotation method to detect and quantify Ascaris and Trichuris eggs in soil, and to validate the diagnostic performance of the optimized method when followed by microscopy and qPCR. In a second phase, we applied this method to assess the level of STH contamination in 399 environmental samples collected from 10 school compounds, 50 households and 9 open markets in Jimma Town (Ethiopia). Subsequently, we explored associations between the environmental contamination and both the corresponding STH epidemiology at the level of the schools and the household characteristics. Finally, we assessed the knowledge, attitude and practice (KAP) towards STHs in school children. PRINCIPAL FINDINGS: Our soil straining-flotation method has an analytical sensitivity of 50 eggs per 100 grams of soil and egg recovery rate of 36.0% (Ascaris) and 8.0% (Trichuris). The analysis of field samples with both microscopy and qPCR revealed the presence of 8 different helminth species of medical importance, including but not limited to the human STHs. There was a significant association between the environmental contamination and prevalence of any STH infections at the school level only. The KAP indicated a lack of knowledge and awareness of STHs. CONCLUSIONS/SIGNIFICANCE: Our optimized straining-flotation method has a moderate diagnostic performance and revealed that life stages of helminths are ubiquitous in the environment, which might be due to the poor sanitary facilities at both the schools and the households, and a poor level of KAP towards STHs. Further research is required to gain more insights into the contribution of these life stages to transmission.


Assuntos
Helmintíase , Helmintos , Animais , Ascaris , Ascaris lumbricoides , Criança , Etiópia/epidemiologia , Fezes/parasitologia , Humanos , Prevalência , Solo/parasitologia , Trichuris
8.
Euro Surveill ; 27(4)2022 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-35086613

RESUMO

BackgroundSurveillance of human leishmaniasis in Europe is mostly limited to country-specific information from autochthonous infections in the southern part. As at the end of 2021, no integrated analysis has been performed for cases seen across centres in different European countries.AimTo provide a broad perspective on autochthonous and imported leishmaniasis cases in endemic and non-endemic countries in Europe.MethodsWe retrospectively collected records from cutaneous, mucosal and visceral leishmaniasis cases diagnosed in 15 centres between 2014 and 2019. Centres were located in 11 countries: Belgium, France, Germany, Italy, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom. Data on country of infection, reason for travelling, infecting species, age and sex were analysed.ResultsWe obtained diagnostic files from 1,142 cases, of which 76%, 21% and 3% had cutaneous, visceral, and mucosal disease, respectively. Of these, 68% were men, and 32% women, with the median age of 37 years (range: 0-90) at diagnosis. Visceral leishmaniasis was mainly acquired in Europe (88%; 167/190), while cutaneous leishmaniasis was primarily imported from outside Europe (77%; 575/749). Sixty-two percent of cutaneous leishmaniasis cases from outside Europe were from the Old World, and 38% from the New World. Geographic species distribution largely confirmed known epidemiology, with notable exceptions.ConclusionsOur study confirms previous reports regarding geographic origin, species, and traveller subgroups importing leishmaniasis into Europe. We demonstrate the importance of pooling species typing data from many centres, even from areas where the aetiology is presumably known, to monitor changing epidemiology.


Assuntos
Leishmaniose Cutânea , Leishmaniose Visceral , Leishmaniose , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , Pré-Escolar , Europa (Continente)/epidemiologia , Feminino , Humanos , Lactente , Recém-Nascido , Leishmaniose/diagnóstico , Leishmaniose Cutânea/diagnóstico , Leishmaniose Cutânea/epidemiologia , Leishmaniose Visceral/diagnóstico , Leishmaniose Visceral/epidemiologia , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Viagem , Adulto Jovem
9.
Expert Rev Mol Diagn ; 22(6): 595-601, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-34424112

RESUMO

INTRODUCTION: Although, in the past few decades molecular diagnostics of parasitic infections have been accepted as first-line diagnostics, laboratories tend to be reluctant of introducing nucleic acid based tests as they dread the validation of laboratory developed tests (LDTs) compliant with ISO1589. AREAS COVERED: This paper describes how to set tailor-made performance characteristics for the validation of laboratory developed tests (LDTs) for the molecular diagnosis of intestinal parasitic infections complying with the ISO 15189 guidelines. Then, just as important, maintaining these tests by daily monitoring, external quality assessment schemes, and reassessment of the test set-up. EXPERT OPINION: Tailoring performance characteristics for the validation of LDTs defining criteria that make sense and actually leading to a process of continuous quality improvement in the day-to-day practice of a diagnostic laboratory. It is essential or even obligatory to modify these characteristics, skip, or to add additional characteristics based on personal or changing insights fitted for a specific setting.


Assuntos
Laboratórios , Patologia Molecular , Humanos
10.
Clin Microbiol Infect ; 28(5): 695-700, 2022 May.
Artigo em Inglês | MEDLINE | ID: mdl-34363945

RESUMO

OBJECTIVES: To evaluate the performance of nasal mid-turbinate self-testing using rapid antigen detection tests (RDT) for persons with suspected coronavirus disease 2019 (COVID-19) in the community. Self-testing for COVID-19 infection with lateral flow assay severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RDT, provides rapid results and could enable frequent and extensive testing in the community, thereby improving the control of SARS-CoV-2. METHODS: Participants visiting a municipal SARS-CoV-2 testing centre, received self-testing kits containing either the BD Veritor System (BD-RDT) or Roche SARS-CoV-2 antigen detection test (Roche-RDT). Oro-nasopharyngeal swabs were collected from the participants for quantitative RT-PCR (qRT-PCR) testing. As a proxy for contagiousness, viral culture was performed on a selection of qRT-PCR positive samples to determine the Ct-value at which the chance of a positive culture dropped below 0.5 (Ct-value cut-off). Sensitivity and specificity of self-testing were compared to qRT-PCR with a Ct-value below the Ct value cut-off. Determinants independently associated with a false-negative self-test result were determined. RESULTS: A total of 3201 participants were included (BD-RDT n = 1595; Roche-RDT n = 1606). Sensitivity and specificity of self-testing compared with the qRT-PCR results with a Ct-value below the Ct-value cut-off were 78.4% (95% CI 73.2%-83.5%) and 99.4% (95% CI 99.1%-99.7%), respectively. A higher age was independently associated with a false-negative self-testing result with an odds ratio of 1.024 (95% CI 1.003-1.044). CONCLUSIONS: Self-testing using currently available RDT has a high specificity and relatively high sensitivity to identify individuals with a high probability of contagiousness.


Assuntos
COVID-19 , Antígenos Virais/análise , COVID-19/diagnóstico , Teste para COVID-19 , Humanos , SARS-CoV-2/genética , Autoteste , Sensibilidade e Especificidade
11.
Ned Tijdschr Geneeskd ; 1652021 05 27.
Artigo em Holandês | MEDLINE | ID: mdl-34346585

RESUMO

Malaria should always be ruled out in patients with fever who visited the tropics in the recent past. Even a long period of time after returning or after antimalarial treatment, malaria may be present due to relaps, recrudescence or a postponed first episode. Hypnozoites of P. vivax and P. ovale are dormant stages in the liver and not detectable in the blood, but can wake moths after inoculation. In this case, we show a patient with a mixed infection with P. falciparum and P. ovale. However, due to the absence of the erythrocytic stage of P. ovale, this species was not detected and caused symptoms weeks after treatment with artemisinin based therapy.


Assuntos
Antimaláricos , Malária Falciparum , Malária , Antimaláricos/uso terapêutico , Causalidade , Humanos , Malária/tratamento farmacológico , Recidiva
12.
Diagn Microbiol Infect Dis ; 101(2): 115392, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34161880

RESUMO

Real-time reverse transcription-polymerase chain reaction (RT-PCR) on upper respiratory tract (URT) samples is the primary method to diagnose SARS-CoV-2 infections and guide public health measures, with a supportive role for serology. We reinforce previous findings on limited sensitivity of PCR testing, and solidify this fact by statistically utilizing a firm basis of multiple tests per individual. We integrate stratifications with respect to several patient characteristics such as severity of disease and time since onset of symptoms. Bayesian statistical modelling was used to retrospectively determine the sensitivity of RT-PCR using SARS-CoV-2 serology in 644 COVID-19-suspected patients with varying degrees of disease severity and duration. The sensitivity of RT-PCR ranged between 80% - 95%; increasing with disease severity, it decreased rapidly over time in mild COVID-19 cases. Negative URT RT-PCR results should be interpreted in the context of clinical characteristics, especially with regard to containment of viral transmission based on 'test, trace and isolate'. Keywords: SARS-CoV-2, RT-PCR, serology, sensitivity, public health.


Assuntos
Teste de Ácido Nucleico para COVID-19 , COVID-19/diagnóstico , SARS-CoV-2/isolamento & purificação , Idoso , Idoso de 80 Anos ou mais , Teorema de Bayes , COVID-19/prevenção & controle , COVID-19/transmissão , Teste Sorológico para COVID-19 , Busca de Comunicante , Reações Falso-Negativas , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Países Baixos/epidemiologia , Quarentena , Estudos Retrospectivos , SARS-CoV-2/genética , SARS-CoV-2/imunologia , Sensibilidade e Especificidade , Índice de Gravidade de Doença
13.
Microb Genom ; 7(4)2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33843573

RESUMO

Cefotaxime (CTX) is a third-generation cephalosporin (3GC) commonly used to treat infections caused by Escherichia coli. Two genetic mechanisms have been associated with 3GC resistance in E. coli. The first is the conjugative transfer of a plasmid harbouring antibiotic-resistance genes. The second is the introduction of mutations in the promoter region of the ampC ß-lactamase gene that cause chromosome-encoded ß-lactamase hyperproduction. A wide variety of promoter mutations related to AmpC hyperproduction have been described. However, their link to CTX resistance has not been reported. We recultured 172 cefoxitin-resistant E. coli isolates with known CTX minimum inhibitory concentrations and performed genome-wide analysis of homoplastic mutations associated with CTX resistance by comparing Illumina whole-genome sequencing data of all isolates to a PacBio sequenced reference chromosome. We mapped the mutations on the reference chromosome and determined their occurrence in the phylogeny, revealing extreme homoplasy at the -42 position of the ampC promoter. The 24 occurrences of a T at the -42 position rather than the wild-type C, resulted from 18 independent C>T mutations in five phylogroups. The -42 C>T mutation was only observed in E. coli lacking a plasmid-encoded ampC gene. The association of the -42 C>T mutation with CTX resistance was confirmed to be significant (false discovery rate <0.05). To conclude, genome-wide analysis of homoplasy in combination with CTX resistance identifies the -42 C>T mutation of the ampC promotor as significantly associated with CTX resistance and underlines the role of recurrent mutations in the spread of antibiotic resistance.


Assuntos
Antibacterianos/farmacologia , Cefotaxima/farmacologia , Farmacorresistência Bacteriana , Infecções por Escherichia coli/microbiologia , Escherichia coli/genética , Genoma Bacteriano , Heteroplasmia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Escherichia coli/classificação , Escherichia coli/efeitos dos fármacos , Escherichia coli/isolamento & purificação , Humanos , Testes de Sensibilidade Microbiana , Mutação , Plasmídeos/genética , Regiões Promotoras Genéticas , beta-Lactamases/genética , beta-Lactamases/metabolismo
15.
Pathogens ; 10(2)2021 Feb 09.
Artigo em Inglês | MEDLINE | ID: mdl-33572338

RESUMO

This study aimed to assess standard and harsher nucleic acid extraction schemes for diagnostic helminth real-time PCR approaches from stool samples. A standard procedure for nucleic acid extraction from stool and a procedure including bead-beating as well as proteinase K digestion were compared with group-, genus-, and species-specific real-time PCR assays targeting helminths and nonhelminth pathogens in human stool samples. From 25 different in-house and commercial helminth real-time PCR assays applied to 77 stool samples comprising 67 historic samples and 10 external quality assessment scheme samples positively tested for helminths, higher numbers of positive test results were observed after bead-beating-based nucleic acid extraction for 5/25 (20%) real-time PCR assays irrespective of specificity issues. Lower cycle threshold values were observed for one real-time PCR assay after the standard extraction scheme, and for four assays after the bead-beating-based scheme. Agreement between real-time PCR results after both nucleic acid extraction strategies according to Cohen's kappa ranged from poor to almost perfect for the different assays. Varying agreement was observed in eight nonhelminth real-time PCR assays applied to 67 historic stool samples. The study indicates highly variable effects of harsh nucleic acid extraction approaches depending on the real-time PCR assay used.

16.
J Clin Virol ; 135: 104720, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33418142

RESUMO

BACKGROUND: Apart from major health concerns associated to the SARS-coronavirus-2 (SARS-CoV-2) pandemic, also the diagnostic workflow encountered serious problems. Limited availability of kit components, buffers and even plastics has resulted in suboptimal testing procedures worldwide. Alternative workflows have been implemented to overcome these difficulties. Recently a liquid based sample prep has been launched as solution to overcome limitations in relation to nucleic acid extraction. OBJECTIVE: Multicenter evaluation of the QIAprep& Viral RNA UM kit (QIA P&A) for rapid sample preparation and real-time PCR detection of SARS-CoV-2 in comparison to standardized laboratory testing methods. STUDY DESIGN: Selected samples of the routine diagnostic workflow at Clinical Microbiology Laboratories of four Dutch hospitals have been subjected to the rapid QIA P&A protocol and the results have been compared to routine diagnostic data. RESULTS: Combining results of manual and automated procedures, a total of 377 clinical samples of which 202 had been tested positive with a wide range of CT values, showed almost complete concordance in the QIA P&A assay for samples up to CT values of 33 with one exception of CT 31. Prospectively 60 samples were tested and also showed 100 % concordance with 5 positives. The method has been automated by two centres. CONCLUSIONS: Despite an input of only 8 µL of clinical sample, the QIA P&A kit showed good performance for sample preparation and amplification of SARS-CoV-2 and can contribute as a rapid molecular testing strategy in managing the CoV-2 pandemic.


Assuntos
Teste para COVID-19/métodos , COVID-19/diagnóstico , COVID-19/virologia , Programas de Rastreamento/métodos , Reação em Cadeia da Polimerase em Tempo Real/métodos , SARS-CoV-2/genética , Técnicas de Laboratório Clínico/métodos , Humanos , Técnicas de Diagnóstico Molecular/métodos , Pandemias/prevenção & controle , Estudos Prospectivos , Manejo de Espécimes/métodos , Fluxo de Trabalho
18.
Microorganisms ; 8(11)2020 Nov 08.
Artigo em Inglês | MEDLINE | ID: mdl-33171694

RESUMO

Distinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission. We compared IncI1-pST12 plasmids from both human and livestock origin and explored the degree of sequence similarity between plasmids from Enterobacteriaceae with different epidemiological links. Short-read sequence data of Enterobacteriaceae cultured from humans and broilers were screened for the presence of both a blaCMY-2 gene and an IncI1-pST12 replicon. Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid assembly, pairwise single nucleotide polymorphisms (SNPs) were determined. The plasmids were annotated, and a pan-genome was constructed to compare genes variably present between the different plasmids. Nine Escherichia coli sequences of broiler origin, four Escherichia coli sequences, and one Salmonella enterica sequence of human origin were selected for the current analysis. A circular contig with the IncI1-pST12 replicon and blaCMY-2 gene was extracted from the assembly graph of all fourteen isolates. Analysis of the IncI1-pST12 plasmids revealed a low number of SNP differences (range of 0-9 SNPs). The range of SNP differences overlapped in isolates with different epidemiological links. One-hundred and twelve from a total of 113 genes of the pan-genome were present in all plasmid constructs. Next generation sequencing analysis of blaCMY-2-containing IncI1-pST12 plasmids isolated from Enterobacteriaceae with different epidemiological links show a high degree of sequence similarity in terms of SNP differences and the number of shared genes. Therefore, statements on the horizontal transfer of these plasmids based on genetic identity should be made with caution.

19.
PLoS Negl Trop Dis ; 14(9): e0008511, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32976499

RESUMO

BACKGROUND: Soil-transmitted helminthiasis (STH) is endemic in Fiji but its prevalence is not known and likely to have changed after a decade of mass drug administration (MDA) for lymphatic filariasis (LF). By linking with LF transmission assessment surveys (LF-TAS), we undertook the first nation-wide assessment of STH in Fijian primary schools, as well as an analysis of factors associated with STH infections. METHODOLOGY/PRINCIPAL FINDINGS: A cross-sectional assessment for STH was conducted in all four Divisions of Fiji from 2014 to 2015. In the Western, Central, and Northern Divisions, schools were sub-sampled after LF-TAS, while, in the Eastern Division, schools were selected via simple random sampling. For the diagnosis of STH, stool samples were examined by coproscopy with a single Kato-Katz thick smear (KK) and the formol-ether-acetate concentration technique, except for the samples from the Eastern Division where only KK was used. Mean prevalence of any STH among class 1-2 students at the national level was 10.5% (95% CI: 6.9-15.5). Across the three Divisions via LF-TAS, the prevalence levels for ascariasis were 8.7% (95% CI: 4.3-16.6), hookworm 3.9% (95% CI: 2.3-6.6) and trichuriasis 0%. In the Eastern Division, ascariasis prevalence was 13.3% (95% CI: 6.4-25.6), and hookworm 0.7% (95% CI: 0.2-2.5), with one case of trichuriasis. Among class 3-8 students, ascariasis prevalence was lower. Lower risk of any STH was associated with wearing shoes (adjusted OR 0.54, 95% CI: 0.32-0.90) and having piped water from the Fiji Water Authority at home (adjusted OR 0.48, 95% CI: 0.25-0.92). CONCLUSIONS: After a decade of community-based LF-MDA, STH in school-age children in Fiji is now close to 10%, but localities of endemicity remain. Preventive chemotherapy should be maintained in areas with elevated STH prevalence alongside targeted delivery of integrated WASH interventions. LF-TAS has provided an opportunity to develop future public health surveillance platforms.


Assuntos
Ascaríase/epidemiologia , Infecções por Uncinaria/epidemiologia , Tricuríase/epidemiologia , Adolescente , Ancylostomatoidea/isolamento & purificação , Animais , Ascaris/isolamento & purificação , Criança , Pré-Escolar , Estudos Transversais , Filariose Linfática/epidemiologia , Feminino , Fiji/epidemiologia , Helmintíase/epidemiologia , Humanos , Masculino , Contagem de Ovos de Parasitas , Prevalência , Sapatos , Estudantes , Inquéritos e Questionários , Trichuris/isolamento & purificação , Abastecimento de Água
20.
Ned Tijdschr Geneeskd ; 1642020 07 02.
Artigo em Holandês | MEDLINE | ID: mdl-32613784

RESUMO

BACKGROUND: Since December 2019, the world is captivated by SARS-CoV-2, a new coronavirus that shows a lot of similaritieswith previous coronaviruses such as SARS and MERS. Although it was initially seen mainly in China and the surrounding countries, now it also reached Europe, where a large region in northern Italy, in particular, encountered many infections. CASE DESCRIPTION: Here we describe the first Dutch patient with COVID-19, a 56-year-old man whose infection appeared to be related to a trip to Northern Italy one week before presentation. In the days that followed, the brother of the patient with whom he had traveled, his wife and daughter also tested positive. CONCLUSION: At the moment much is still unclear and it is particularly important to quickly identify patients with an increased risk of complications and to prevent unrestrained spread in the Netherlands.


Assuntos
Betacoronavirus , Busca de Comunicante , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Viagem , COVID-19 , Europa (Continente) , Humanos , Masculino , Pessoa de Meia-Idade , Países Baixos , Pandemias , SARS-CoV-2
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