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1.
Virus res ; 276: 197828, Jan. 2020. tab, ilus
Artículo en Inglés | Sec. Est. Saúde SP, SESSP-IIERPROD, Sec. Est. Saúde SP | ID: biblio-1047647

RESUMEN

Variations in the open reading frame (ORF) K1 gene sequence of human gammaherpesvirus 8 (HHV-8) has led to the identification of 6 major genotypic clades (A, B, C, D, E, and F) in specimens isolated from around the world. These clades exhibit clear clustering among individuals in different ethnic groups and from different geographic regions. The human population of Brazil varies greatly in ethnicity because of multiple immigration events from Africa, Europe, Asia, and indigenous communities. However, there is scant information about the HHV-8 genotypes currently circulating in Brazil. Here, we describe HHV-8 genotypic diversity in isolates from Brazilian HIV-infected patients living with Kaposi's sarcoma (KS) by analysis of the complete ORF-K1 region. We also identified the most likely geographic origins of these different Brazilian genotypes. We extracted HHV-8 DNA (24 positive samples) from individuals with HIV/KS from the states of São Paulo and Rio de Janeiro, amplified the ORF-K1 gene using nested PCR (about 870 base pairs), performed sequencing and phylogenetic analysis, and then calculated the mean genetic distances of Brazilian sequences from sequences in other regions of the world (523 sequences analyzed). Phylogenetic analysis showed that genotypes C, A, and B were present in 45.8 %, 29.2 % and 25 % of the isolates from Brazil, respectively. These isolates grouped into separate clades, rather than a single monophyletic cluster. Mean genetic distance analyses suggested that these genotypes were introduced into the Brazil multiple times from different geographical regions. HHV-8/A isolates appear to be from Ukraine, Russia, and the Tartar ethnic group; HHV-8/B isolates appear to be from Congo and Democratic Republic of the Congo; and HHV-8/C isolates appear to be from Australia, Algeria, England, and French Guiana. These results contribute to a better understanding of the genetic diversity and origins of HHV-8 strains circulating in Brazil, and will provide a foundation for further epidemiological and evolutionary studies of HHV-8


Asunto(s)
Epidemiología Molecular , Herpesvirus Humano 8/genética
3.
Hum Genet ; 139(1): 73-84, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31049651

RESUMEN

In this paper, we give an overview of methodological issues related to the use of statistical learning approaches when analyzing high-dimensional genetic data. The focus is set on regression models and machine learning algorithms taking genetic variables as input and returning a classification or a prediction for the target variable of interest; for example, the present or future disease status, or the future course of a disease. After briefly explaining the basic motivation and principle of these methods, we review different procedures that can be used to evaluate the accuracy of the obtained models and discuss common flaws that may lead to over-optimistic conclusions with respect to their prediction performance and usefulness.


Asunto(s)
Algoritmos , Enfermedad/genética , Aprendizaje Automático , Modelos Estadísticos , Epidemiología Molecular , Inteligencia Artificial , Humanos
4.
Hum Genet ; 139(1): 121-136, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31134333

RESUMEN

In the current era, with increasing availability of results from genetic association studies, finding genetic instruments for inferring causality in observational epidemiology has become apparently simple. Mendelian randomisation (MR) analyses are hence growing in popularity and, in particular, methods that can incorporate multiple instruments are being rapidly developed for these applications. Such analyses have enormous potential, but they all rely on strong, different, and inherently untestable assumptions. These have to be clearly stated and carefully justified for every application in order to avoid conclusions that cannot be replicated. In this article, we review the instrumental variable assumptions and discuss the popular linear additive structural model. We advocate the use of tests for the null hypothesis of 'no causal effect' and calculation of the bounds for a causal effect, whenever possible, as these do not rely on parametric modelling assumptions. We clarify the difference between a randomised trial and an MR study and we comment on the importance of validating instruments, especially when considering them for joint use in an analysis. We urge researchers to stand by their convictions, if satisfied that the relevant assumptions hold, and to interpret their results causally since that is the only reason for performing an MR analysis in the first place.


Asunto(s)
Variación Genética , Estudio de Asociación del Genoma Completo , Análisis de la Aleatorización Mendeliana/métodos , Epidemiología Molecular/métodos , Humanos
5.
Acta Trop ; 201: 105188, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31545949

RESUMEN

Triatoma petrocchiae is the newly member of the Triatoma brasiliensis species complex. This species overlaps with T. brasiliensis in geographic and ecotypic occupation in the sylvatic habitat because both inhabit rocky outcrops in the semi-arid portion of Brazilian northeast. In this region T. brasiliensis is the most important Chagas disease vector because it constantly colonizes domiciles. In contrast, T. petrocchiae is rarely found in peri or intradomiciliary habitats - reason why little is known about this species. Therefore, Here, we present information for the first time on. the T. petrocchiae ecotopes, genetic diversity, Trypanosoma cruzi prevalence/genotyping in comparison to T. brasiliensis. We found T. brasilensis (N = 223) and T. petrocchiae (N = 69) in co-habitation in rocky outcrops in three Districts of Paraíba and Rio Grande do Norte states. Forty-tree T. petrocchiae insects of eleven sampling spots (composing three geographic populations) were genotyped for the mitochondrial Cyt B gene and little geographic structure was observed. Tajima's D test suggested that species is evolving toward a mutation-drift equilibrium in our collection range. Sylvatic T. petrocchiae had 4% (3/68) of infected insects by T. cruzi, whereas T. brasiliensis had 26% (59/223). Fluorescent Fragment Length Barcoding demonstrated that all three T. petrocchiae harbored TcI whereas T. brasiliensis had TcI, but also TcIII, TcII/TcVI and T. rangeli genotype A, sometimes under mixed infections. None of infected T. petrocchiae were carrying mixed infections. However, this result should be confirmed using a larger pool of infected bugs. We here presented the first documentation of T. rangeli infecting T. brasiliensis. The finding of infected T. petrocchiae calls for constant vector monitoring because the epidemiologic scenario is dynamic and sylvatic vectors are progressively found in adaptation to anthropic environments.


Asunto(s)
Enfermedad de Chagas/transmisión , Insectos Vectores/parasitología , Simpatría , Triatoma/parasitología , Trypanosoma cruzi/genética , Animales , Brasil/epidemiología , Enfermedad de Chagas/epidemiología , Ecosistema , Variación Genética , Genotipo , Epidemiología Molecular , Prevalencia
6.
Food Microbiol ; 85: 103280, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31500706

RESUMEN

Listeria monocytogenes causes severe diseases in humans, including febrile gastroenteritis and systemic infections that has a high mortality despite antibiotic treatment. This pathogen may cause massive outbreaks associated to the consumption of contaminated food products, which highlight its importance in public health. In the last decade, L. monocytogenes has emerged as a foodborne pathogen of major importance in Chile. A previous work showed that in Chile during 2008 and 2009, L. monocytogenes serotypes 1/2a, 1/2b and 4b were the most frequently identified in food and clinical strains. Here we report the molecular characterization of L. monocytogenes strains isolated from 2008 to 2017 in the country. Our results indicate that serotypes 1/2a, 1/2b and 4b continue to be the most commonly found in food products. In addition, we identify persistent and widespread PFGE subtypes. This study reports ten years of epidemiological surveillance ofL. monocytogenes in Chile.


Asunto(s)
Monitoreo Epidemiológico , Microbiología de Alimentos , Enfermedades Transmitidas por los Alimentos/epidemiología , Listeria monocytogenes/genética , Listeriosis/epidemiología , Chile/epidemiología , Recuento de Colonia Microbiana , ADN Bacteriano/genética , Brotes de Enfermedades , Enfermedades Transmitidas por los Alimentos/microbiología , Gastroenteritis/epidemiología , Gastroenteritis/microbiología , Variación Genética , Humanos , Listeria monocytogenes/patogenicidad , Productos de la Carne/microbiología , Epidemiología Molecular , Salud Pública , Serogrupo , Serotipificación , Factores de Virulencia/genética
7.
Zhonghua Liu Xing Bing Xue Za Zhi ; 40(11): 1487-1491, 2019 Nov 10.
Artículo en Chino | MEDLINE | ID: mdl-31838826

RESUMEN

HIV molecular network is a recently reported method for studying the transmission characteristics of HIV-infected people. Countries have used this method to conduct a large number of researches on transmission relations, transmission hotspots and epidemic surveillance for the purpose of providing evidence for precise AIDS intervention and control. At present, there are three major methods for constructing molecular networks in the world, i.e. genetic distance method based on pairwise alignment, phylogenetic node support method, and joint parameter method based on the two methods. This paper reviews the progress of the three methods for constructing HIV molecular network to study the transmission characteristics of HIV-infected patients, in order to provide data support for the prevention and control of HIV. Since the emergence of the molecular network method, Beijing, Shanghai, Zhejiang, Sichuan and other provinces in China have reported relevant research results using molecular network analysis, which provided scientific data for further precise AIDS prevention and control. Recent international studies have also predicted that molecular network based transmission cluster detection is expected to become a new method to stop AIDS epidemic.


Asunto(s)
Infecciones por VIH/epidemiología , Infecciones por VIH/transmisión , VIH-1/clasificación , VIH-1/genética , Síndrome de Inmunodeficiencia Adquirida , Beijing , China , Infecciones por VIH/diagnóstico , Infecciones por VIH/genética , VIH-1/aislamiento & purificación , Humanos , Modelos Moleculares , Epidemiología Molecular , Filogenia
8.
Zhonghua Yu Fang Yi Xue Za Zhi ; 53(12): 1278-1283, 2019 Dec 06.
Artículo en Chino | MEDLINE | ID: mdl-31795586

RESUMEN

Objective: Using field epidemiological investigation and molecular analysis to construct the molecular transmission network of human immunodeficiency virus/acquired immunodeficiency syndrome cases (HIV/AIDS) newly diagnosed in Huzhou in 2017, Zhejiang Province. Methods: A total of 160 participants were obtained through a web-based system from Chinese Center for Disease Control and Prevention (CCDC) with the features of diagnosed in Huzhou in 2017 who also had been collected samples for the first follow-up. The basic information of demographic characteristics and risk factors was extracted from the website. RNA was extracted from plasma samples of untreated cases, followed by RT-PCR and nest-PCR for pol gene amplification, sequencing. Phylogenetic tree was constructed by MEGA software for HIV gene subtyping. TN93 model was used for calculating the distance between two sequences. Cytoscape software was used for drawing molecular transmission network. And then an epidemiological survey was conducted to cases in the primary cluster. Results: A total of 138 sequenced individuals (86.3%) were acquired from 160 individuals. Among which, 123 (89.1%) were male. The highest proportion of subtype was CRF07_BC (60, 43.5%), followed by CRF01_AE (46, 33.3%), and with four cases of Unique Recombinant Form (URF, CRF01_AE and CRF07_BC) and one case of URF (subtype B and C). A total of 18 molecular clusters included 56 individuals (40.6%) were found in the transmission network under the optimal genetic distance threshold (1.0%). The clustering proportion of CRF07_BC (66.1%, 37 cases) was higher than that of CRF01_AE. There were 9 clusters formed among CRF07_BC, including 37 cases (accounting for 61.7%, 37/60). The primary transmission cluster contained 11 cases, among which 9 cases were transmitted by homosexual sex. The first time of the cases to have homosexual behavior is range from 2010 to 2016, whose media number (P(25), P(75)) of partners was 6 (3.5, 8.5). Most of the cases come from Anhui Province and engaged in garment industry (5 cases), between which there were 8 cases used Blued software to seek for casual partners, 1 case seeking for casual partners in garden. Conclusion: With CRF07_BC and CRF01_AE predominantly circulating, HIV genetic diversity had been noticed in this area. The primary cluster was consisted of high proportion of locally new infections, and a specific population aggregation in limited place existed.


Asunto(s)
Síndrome de Inmunodeficiencia Adquirida/transmisión , Infecciones por VIH/transmisión , VIH-1/genética , Síndrome de Inmunodeficiencia Adquirida/diagnóstico , China , Amplificación de Genes , Genotipo , Infecciones por VIH/diagnóstico , VIH-1/aislamiento & purificación , Humanos , Masculino , Epidemiología Molecular , Filogenia , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa
9.
Pol J Microbiol ; 68(4): 449-456, 2019 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-31880889

RESUMEN

There is an increased demand for molecular and epidemiological information regarding Hepatitis B Virus (HBV) infection as the disease severity depends on these specifications. We have aimed to analyze nucleos(t)ide analogues (NA) resistance and typical HBsAg escape mutations with the dispersion of HBV genotype/subgenotype/HBsAg serotypes on overlapping pol/S gene regions in the Turkish population. Samples were collected in Northern Cyprus. Reverse transcriptase (rt) region between 80-250 amino acids were amplified. Typical HBsAg escape mutations were determined as HBIg escape (6.48%), vaccine escape (8.34%), HBsAg misdiagnosis (9.25%), and immune escape mutations (8.34%). NAs resistances were determined as primary (2.78%), partial (2.78%), and compensatory mutations (26.85%) in overlapping pol/S gene region. The study patients were predominantly infected with HBV genotype D/D1 (98%). However, the predominant HBsAg serotype was ayw2 (99%). The most common NA resistance mutation was rtQ215H/P/S (16.67%), however, for S gene the misdiagnosis mutations were observed most frequently (9.25%). We can conclude that HBV D/D1 is the dominant strain and ayw2 is the dominant serotype in the Turkish Cypriot. Cyprus is an island located in the Eastern Mediterranean region, and it is, therefore, a key location for human trafficking and immigration; as a result of this reputation, it is necessary to analyze HBV phylogenetically for local dynamics, and our results indicate that treatment naïve population is prone to these pol/S gene mutations. However, if HBV strains were also analyzed among Greek Cypriots too, this would enable a complete island survey. With this work, we believe that we have enlightened this subject for further research.There is an increased demand for molecular and epidemiological information regarding Hepatitis B Virus (HBV) infection as the disease severity depends on these specifications. We have aimed to analyze nucleos(t)ide analogues (NA) resistance and typical HBsAg escape mutations with the dispersion of HBV genotype/subgenotype/HBsAg serotypes on overlapping pol/S gene regions in the Turkish population. Samples were collected in Northern Cyprus. Reverse transcriptase (rt) region between 80­250 amino acids were amplified. Typical HBsAg escape mutations were determined as HBIg escape (6.48%), vaccine escape (8.34%), HBsAg misdiagnosis (9.25%), and immune escape mutations (8.34%). NAs resistances were determined as primary (2.78%), partial (2.78%), and compensatory mutations (26.85%) in overlapping pol/S gene region. The study patients were predominantly infected with HBV genotype D/D1 (98%). However, the predominant HBsAg serotype was ayw2 (99%). The most common NA resistance mutation was rtQ215H/P/S (16.67%), however, for S gene the misdiagnosis mutations were observed most frequently (9.25%). We can conclude that HBV D/D1 is the dominant strain and ayw2 is the dominant serotype in the Turkish Cypriot. Cyprus is an island located in the Eastern Mediterranean region, and it is, therefore, a key location for human trafficking and immigration; as a result of this reputation, it is necessary to analyze HBV phylogenetically for local dynamics, and our results indicate that treatment naïve population is prone to these pol/S gene mutations. However, if HBV strains were also analyzed among Greek Cypriots too, this would enable a complete island survey. With this work, we believe that we have enlightened this subject for further research.


Asunto(s)
Virus de la Hepatitis B/genética , Virus de la Hepatitis B/aislamiento & purificación , Hepatitis B/virología , Adolescente , Adulto , Anciano , Niño , ADN Viral/genética , Femenino , Genotipo , Antígenos de Superficie de la Hepatitis B/genética , Virus de la Hepatitis B/clasificación , Humanos , Islas/epidemiología , Masculino , Persona de Mediana Edad , Epidemiología Molecular , Mutación , Filogenia , Turquia/epidemiología , Adulto Joven
10.
Parasitol Res ; 118(12): 3195-3204, 2019 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-31724068

RESUMEN

Whole genomic sequencing (WGS) and comparative genomics are increasingly used in the characterization of Cryptosporidium spp. They are facilitated by the establishment of procedures for WGS analysis of clinical specimens without laboratory propagation of pathogens. Results of recent comparative genomics analysis suggest that gene duplication might be associated with broad host ranges of some zoonotic Cryptosporidium species and subtypes, while genetic recombination could be involved in the emergence of virulent subtypes. The availability of WGS data has further facilitated the development of advanced molecular typing tools. The use of these tools together with comparative genomics analyses has begun to improve the investigations of outbreaks in industrialized nations. More WGS data, however, are needed from both industrialized nations and developing countries before we can have in-depth understanding of the population genetics and evolution of Cryptosporidium spp. and genetic determinants of various phenotypic traits in human-pathogenic subtypes.


Asunto(s)
Criptosporidiosis/epidemiología , Cryptosporidium/genética , Genómica , Animales , Criptosporidiosis/parasitología , Criptosporidiosis/transmisión , Cryptosporidium/clasificación , Cryptosporidium/patogenicidad , Genoma de Protozoos/genética , Genotipo , Especificidad del Huésped/genética , Humanos , Epidemiología Molecular , Virulencia/genética
11.
Mikrobiyol Bul ; 53(4): 374-387, 2019 Oct.
Artículo en Turco | MEDLINE | ID: mdl-31709935

RESUMEN

Human immunodeficiency virus (HIV) comprises two genotypes, namely HIV-1 (group M, N, O and P) and HIV-2 (group A to H), which differ in their envelope glycoproteins and other antigenic epitopes despite their morphological and biological resemblance.Group M of HIV-1 responsible for 95% of HIV infections worldwide is composed of nine subgroups. In addition to subgroups, group M contains also two recombinant forms, known as circulating recombinant form (CRF) and unique recombinant form (URF). The first case of HIV/acquired immun deficiency virus (AIDS) in Turkey was reported in 1985 and the current number of cases reached a total of 18.557 including 1736 with AIDS based upon the surveillance data of Ministry of Health between October 1985 and November 2018. The aim of this study was to determine the prevalence of HIV-1 strains isolated from HIV positive autopsy cases detected by HIV polymerase chain reaction (PCR) and determine drug resistance. Twenty eight cases [17 males, 11 female: age ranged between 3 months and 66 years (median: 35 years)] found to be HIV positive among the autopsy cases sent for HIV1 PCR study and serological screening between 2011-2017 were recruited in the study. For identification of subtypes in HIV-1 isolates, most-preferred analysis tool was used [HIVdb Stanford University Genotypic Resistance Interpretation Algorithm (www.hivdb.stanford.edu)]. Phylogenetic tree was made according to direct sequencing of HIV-1 reverse transcriptase (pol) region and phylogenetic analysis was evaluated in 23 cases. Los Alamos National Laboratory were trimmed from full-length genomes. Phylogenetic analysis of the 870 base pair of the pol gene region was performed using CLC Sequence Viewer v8.0 (Qiagen Aarhus A/S, www.qiagenbioinformatics.com) software. The phylogenetic tree was obtained according to the neighbor-joining method and the Jukes-Cantor nucleotide distance scale and bootstrap value was set at 1000. In our study, subtype B was found to be most frequent type (39.3%; 11/28). Subtype A (17.9%; 5/28), CRF02_AG (14.3%; 4/28), subtype C (10.7%; 3/28), B+CRF02_AG recombinant (3.6%; 1/28), CRF01_AE (3.6%; 1/28), subtype D (3.6%; 1/28), as well as subtype F (3.6%; 1/28) and subtype G (3.6%; 1/28) strains were also detected in the circulation. Analysis of our results showed that 32.1% (9/28) of the samples exhibited resistance mutations. Detected mutations were as follows: M41L, T215C, K65R, M184V, responsible for nucleoside reverse transcriptase inhibitor (NRTI) resistance; K103N, Y181C, G190A, responsible for non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance; D30N, M46I, responsible for protease inhibitor (PI) resistance. NRTI, NNRTI and PI mutation rates in the samples were found as 21.4%, 7.1% and 3.6%, respectively. Although number of samples analyzed in our study is low, we can propose that they resemble the strains circulating in Turkey. The results of our study; although the subtype B is still dominant in our country, it supports other studies reporting that there are non-B subtypes and an increase in CRF rates in recent years. Phylogenetic analysis is widely regarded as the gold standard technique to determine the subtypes of HIV-1. Molecular epidemiologic studies related to HIV may be important in monitoring HIV subtype patterns and spreading pathways in that country. As a result; the opportunity to collect postmortem HIV sequences in a database appears to have occurred, and as this database expands, its usability is available. Therefore, it is thought that HIV subtypes and mutation information may be useful.


Asunto(s)
Infecciones por VIH , VIH-1 , Epidemiología Molecular , Adolescente , Adulto , Anciano , Antivirales/farmacología , Autopsia , Niño , Preescolar , Farmacorresistencia Viral , Femenino , Genotipo , Infecciones por VIH/epidemiología , Infecciones por VIH/virología , VIH-1/clasificación , VIH-1/efectos de los fármacos , Humanos , Lactante , Masculino , Persona de Mediana Edad , Mutación , Filogenia , Turquia/epidemiología
12.
Vet Microbiol ; 238: 108426, 2019 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-31648722

RESUMEN

Felis catus gammaherpesvirus 1 (FcaGHV1), a novel gammaherpesvirus of domestic cats identified in 2014, has been detected in different countries demonstrating a worldwide distribution. The aim of this study was to establish the prevalence of FcaGHV1 in Italy using a molecular epidemiological approach. FcaGHV1 DNA was detected with virus-specific real-time PCR in ≃1% of 2659 feline blood samples tested. Analysis of risk factors showed that being male and coinfection with feline immunodeficiency virus (FIV) increase the likelihood of FcaGHV1 detection. One-third of FcaGHV1-positive cats also tested positive for FIV provirus, whereas coinfections with feline panleukopenia virus were not demonstrated. Further studies are necessary to confirm the risk factors for FcaGHV1 detection and the pathobiology of the virus.


Asunto(s)
Enfermedades de los Gatos/diagnóstico , Infecciones por Herpesviridae/veterinaria , Animales , Enfermedades de los Gatos/epidemiología , Enfermedades de los Gatos/virología , Gatos , Coinfección/epidemiología , Coinfección/veterinaria , Síndrome de Inmunodeficiencia Adquirida del Felino/complicaciones , Femenino , Gammaherpesvirinae/genética , Infecciones por Herpesviridae/complicaciones , Infecciones por Herpesviridae/epidemiología , Virus de la Inmunodeficiencia Felina/genética , Italia/epidemiología , Masculino , Epidemiología Molecular , Prevalencia , Reacción en Cadena en Tiempo Real de la Polimerasa/veterinaria , Factores de Riesgo , Factores Sexuales
13.
Adv Parasitol ; 106: 209-254, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31630759

RESUMEN

A total of eight Giardia species are accepted. These include: Giardia duodenalis (syn. Giardia intestinalis and Giardia lamblia), which infects humans and animals, Giardia agilis, Giardia ardeae, Giardia psittaci, Giardia muris, Giardia microti, Giardia peramelis and G. cricetidarum, which infect non-human hosts including amphibians, birds, rodents and marsupials. Giardia duodenalis is a species complex consisting of eight assemblages (A-H), with assemblages A and B the dominant assemblages in humans. Molecular studies to date on the zoonotic potential of Giardia in animals are problematic and are hampered by lack of concordance between loci. Livestock (cattle, sheep, goats and pigs) are predominantly infected with G. duodenalis assemblage E, which has recently been shown to be zoonotic, followed by assemblage A. In cats and dogs, assemblages A, B, C, D and F are commonly reported but relatively few studies have conducted molecular typing of humans and their pets and the results are contradictory with some studies support zoonotic transmission but the majority of studies suggesting separate transmission cycles. Giardia also infects a broad range of wildlife hosts and although much less well studied, host-adapted species as well as G. duodenalis assemblages (A-H) have been identified. Fish and other aquatic wildlife represent a source of infection for humans with Giardia via water contamination and/or consumption of undercooked fish and interestingly, assemblage B and A predominated in the two molecular studies conducted to date. Our current knowledge of the transmission dynamics of Giardia is still poor and the development of more discriminatory typing tools such as whole genome sequencing (WGS) of Giardia isolates is therefore essential.


Asunto(s)
Giardiasis/epidemiología , Epidemiología Molecular , Medicina Veterinaria , Zoonosis/epidemiología , Animales , Giardia , Giardiasis/parasitología , Giardiasis/transmisión , Humanos , Medicina Veterinaria/tendencias , Zoonosis/parasitología , Zoonosis/transmisión
14.
BMC Infect Dis ; 19(1): 908, 2019 Oct 29.
Artículo en Inglés | MEDLINE | ID: mdl-31664926

RESUMEN

BACKGROUND: Drug-resistant tuberculosis (TB) is a major public health concern threathing the success of TB control efforts, and this is particularily problematic in Central Asia. Here, we present the first analysis of the population structure of Mycobacterium tuberculosis complex isolates in the Central Asian republics Uzbekistan, Tajikistan, and Kyrgyzstan. METHODS: The study set consisted of 607 isolates with 235 from Uzbekistan, 206 from Tajikistan, and 166 from Kyrgyzstan. 24-loci MIRU-VNTR (Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeats) typing and spoligotyping were combined for genotyping. In addition, phenotypic drug suceptibility was performed. RESULTS: The population structure mainly comprises strains of the Beijing lineage (411/607). 349 of the 411 Beijing isolates formed clusters, compared to only 33 of the 196 isolates from other clades. Beijing 94-32 (n = 145) and 100-32 (n = 70) formed the largest clusters. Beijing isolates were more frequently multidrug-resistant, pre-extensively resistant (pre-XDR)- or XDR-TB than other genotypes. CONCLUSIONS: Beijing clusters 94-32 and 100-32 are the dominant MTB genotypes in Central Asia. The relative size of 100-32 compared to previous studies in Kazakhstan and its unequal geographic distribution support the hypothesis of its more recent emergence in Central Asia. The data also demonstrate that clonal spread of resistant TB strains, particularly of the Beijing lineage, is a root of the so far uncontroled MDR-TB epidemic in Central Asia.


Asunto(s)
Epidemias , Genotipo , Mycobacterium tuberculosis/genética , Tuberculosis Resistente a Múltiples Medicamentos/epidemiología , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Niño , Estudios Transversales , Femenino , Humanos , Kirguistán/epidemiología , Masculino , Persona de Mediana Edad , Repeticiones de Minisatélite/genética , Epidemiología Molecular , Tipificación Molecular , Mycobacterium tuberculosis/aislamiento & purificación , Fenotipo , Tayikistán/epidemiología , Tuberculosis Resistente a Múltiples Medicamentos/microbiología , Tuberculosis Resistente a Múltiples Medicamentos/prevención & control , Uzbekistán/epidemiología , Adulto Joven
15.
Wei Sheng Yan Jiu ; 48(4): 545-559, 2019 Jul.
Artículo en Chino | MEDLINE | ID: mdl-31601334

RESUMEN

OBJECTIVE: Real-time reverse transcription-polymerase chain reaction(real-time RT-PCR) assay based on Taqman and phylogenetic tree were developed for detecting hepatitis E virus in swine feces of pig farms from several provinces and city. METHODS: Designing prime and probe refering to HEV genotype sequences of Genbank, we developed a Taqman-based real-time RT-PCR assay and nested RT-PCR according to HEV conserved domain after optimizing reaction system, then detected the prevalence of HEV infection of pig farms. RESULTS: The sensitivity of the real-time RT-PCR assay established in this experiment was 19. 9 copies/µL, the amplification efficiency was 92. 9%-109. 1%, there was no cross reaction with Sapovirus, Norovirus and Hepatitis A. A total of 342 samples of swine feces were detected. There were two hundred and ten positive samples, and positive rate was 61. 4%. The positive rate of before-fattening was 56. 6%, and after-fattening was 66. 9%. The positive rate of before and after fattening samples had statistical difference(χ~2=24. 8, P<0. 05). The genotype identification system determined that the positive strains isolated in this study were HEV-4 type, and three subtypes of 4 b, 4 d and 4 h were detected. CONCLUSION: The pig farms of several provinces and city are contaminated by HEV extensively. The genotypes of the isolated strains are all HEV-4 type. The infection rate and infection subtype of pigs in different provinces and cities are different.


Asunto(s)
Heces/virología , Virus de la Hepatitis E , Epidemiología Molecular , Animales , Genotipo , Hepatitis E , Filogenia , ARN Viral , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Transcripción Reversa , Porcinos , Enfermedades de los Porcinos/virología
16.
Vet Microbiol ; 237: 108408, 2019 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-31585650

RESUMEN

Information on the epidemiology of C. difficile infection (CDI) in South-East Asian countries is limited, as is data on possible animal reservoirs of C. difficile in the region. We investigated the prevalence and molecular epidemiology of C. difficile in piglets and the piggery environment in Thailand and Malaysia. Piglet rectal swabs (n = 224) and piggery environmental specimens (n = 23) were collected between 2015 and 2016 from 11 farms located in Thailand and Malaysia. All specimens were tested for the presence of C. difficile with toxigenic culture. PCR assays were performed on isolates to determine the ribotype (RT), and the presence of toxin genes. Whole genome sequencing was used on a subset of isolates to determine the evolutionary relatedness of RT038 (the most prevalent RT identified) common to pigs and humans from Thailand and Indonesia. C. difficile was recovered from 35% (58/165) and 92% (54/59) of the piglets, and 89% (8/9) and 93% (13/14) of the environmental specimens from Thailand and Malaysia, respectively. All strains from Thailand, and 30 strains from Malaysia (23 piglet and 7 environmental isolates) were non-toxigenic. To our knowledge, this is the first and only report with a complete lack of toxigenic C. difficile among piglets, a feature which could have a protective effect on the host. The most common strain belonged to RT038 (ST48), accounting for 88% (51/58) of piglet and 78% (7/9) of environmental isolates from Thailand, and all 30 isolates tested from Malaysia. Piglet RT038 isolates from Thailand and Malaysia differed by only 18 core-genome single nucleotide variants (cgSNVs) and both were, on average, 30 cgSNVs different from the human strains from Thailand and Indonesia, indicating a common ancestor in the last two decades.


Asunto(s)
Infecciones por Clostridium/veterinaria , Clostridium difficile/genética , Enfermedades de los Porcinos/microbiología , Animales , Infecciones por Clostridium/epidemiología , Infecciones por Clostridium/microbiología , Microbiología Ambiental , Variación Genética , Vivienda para Animales , Malasia/epidemiología , Epidemiología Molecular , Prevalencia , Porcinos , Tailandia/epidemiología , Secuenciación Completa del Genoma
17.
Medicine (Baltimore) ; 98(40): e17269, 2019 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-31577718

RESUMEN

This study examined the characteristics of norovirus (NoV) gastroenteritis associated with convulsions in children and its molecular epidemiology. From July 2006 through December 2015, NoV infection was confirmed by the genome detection using reverse transcriptase polymerase chain reaction. Viral genotyping with strain validation was achieved using sequence analyses with Basic Local Alignment Search Tool genome identification. The patients' clinical features were assessed retrospectively, focusing on convulsive disorders. The diagnosis of encephalitis followed the International Encephalitis Consortium. Seizures occurred in 52 (20.9%) of 249 NoV infections. GII.4 Den_Haag_2006b (n = 22, 42.3%) and GII.4 Sydney 2012 (n = 10, 19.2%) were major variants correlated with convulsions. Patient with convulsions tend to have GII.4 genotype infection (P < .001), short vomiting (≤2 days) (P < .001), and no fever (P = .002). Compared to GII.4 Den_Haag_2006b, the GII.4 Sydney 2012-associated convulsions had similar manifestations except without significant winter preponderance (P = .049). The NoV infection with convulsions had less febrile course, specific genotype (GII.4) infections, and with shorter symptom of vomiting. Continuous surveillance is important for uncommon disease associated with emerging NoV strain infections. The prevention of NoV diseases requires the development of vaccines targeting highly virulent variants.


Asunto(s)
Infecciones por Caliciviridae/epidemiología , Infecciones por Caliciviridae/genética , Gastroenteritis/epidemiología , Convulsiones/epidemiología , Adolescente , Niño , Preescolar , Encefalitis/epidemiología , Femenino , Fiebre/epidemiología , Gastroenteritis/virología , Genotipo , Humanos , Lactante , Masculino , Epidemiología Molecular , ARN Viral/genética , Estudios Retrospectivos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Estaciones del Año , Análisis de Secuencia de ADN , Taiwán/epidemiología
18.
PLoS Pathog ; 15(9): e1008067, 2019 09.
Artículo en Inglés | MEDLINE | ID: mdl-31513651

RESUMEN

The molecular clock and its phylogenetic applications to genomic data have changed how we study and understand one of the major human pathogens, Mycobacterium tuberculosis (MTB), the etiologic agent of tuberculosis. Genome sequences of MTB strains sampled at different times are increasingly used to infer when a particular outbreak begun, when a drug-resistant clone appeared and expanded, or when a strain was introduced into a specific region. Despite the growing importance of the molecular clock in tuberculosis research, there is a lack of consensus as to whether MTB displays a clocklike behavior and about its rate of evolution. Here we performed a systematic study of the molecular clock of MTB on a large genomic data set (6,285 strains), covering different epidemiological settings and most of the known global diversity. We found that sampling times below 15-20 years were often insufficient to calibrate the clock of MTB. For data sets where such calibration was possible, we obtained a clock rate between 1x10-8 and 5x10-7 nucleotide changes per-site-per-year (0.04-2.2 SNPs per-genome-per-year), with substantial differences between clades. These estimates were not strongly dependent on the time of the calibration points as they changed only marginally when we used epidemiological isolates (sampled in the last 40 years) or three ancient DNA samples (about 1,000 years old) to calibrate the tree. Additionally, the uncertainty and the discrepancies in the results of different methods were sometimes large, highlighting the importance of using different methods, and of considering carefully their assumptions and limitations.


Asunto(s)
Relojes Biológicos/genética , Mycobacterium tuberculosis/genética , Teorema de Bayes , Relojes Biológicos/fisiología , ADN Bacteriano/genética , Evolución Molecular , Genoma Bacteriano , Humanos , Modelos Biológicos , Epidemiología Molecular , Mycobacterium bovis/genética , Mycobacterium bovis/fisiología , Mycobacterium tuberculosis/patogenicidad , Mycobacterium tuberculosis/fisiología , Filogenia , Polimorfismo de Nucleótido Simple , Factores de Tiempo , Tuberculosis/epidemiología , Tuberculosis/microbiología
19.
Artículo en Inglés | MEDLINE | ID: mdl-31522664

RESUMEN

From 1 January to 31 December 2017, 36 institutions around Australia participated in the Australian Enterococcal Sepsis Outcome Programme (AESOP). The aim of AESOP 2017 was to determine the proportion of enterococcal bacteraemia isolates in Australia that were antimicrobial resistant, and to characterise the molecular epidemiology of the E. faecium isolates. Of the 1,137 unique episodes of bacteraemia investigated, 95.2% were caused by either E. faecalis (52.9%) or E. faecium (42.3%). Ampicillin resistance was not detected in E. faecalis but in 89.6% of E. faecium. Vancomycin non-susceptibility was reported in 0.3% and 47.0% of E. faecalis and E. faecium respectively. Overall 50.9% of E. faecium harboured vanA or vanB genes. For the vanA/B positive E. faecium isolates, 49.6% harboured vanB genes and 49.2% vanA genes; 1.2% harboured vanA and vanB genes. The percentage of E. faecium bacteraemia isolates resistant to vancomycin in Australia is significantly higher than that seen in most European countries. E. faecium consisted of 76 multilocus sequence types (STs) of which 77% of isolates were classified into nine major STs containing ten or more isolates. All major STs belong to clonal cluster (CC) 17, a major hospital-adapted polyclonal E. faecium cluster. Seven of the nine predominant STs (ST80, ST1421, ST17, ST296, ST555, ST203 and ST18) were found across most regions of Australia. The most predominant clone was ST17 which was identified in all regions except the Australian Capital Territory, the Northern Territory and Tasmania. Overall 60.7% of isolates belonging to the nine predominant STs harboured vanA or vanB genes. The AESOP 2017 has shown enterococcal bacteraemias in Australia are frequently caused by polyclonal ampicillin-resistant high-level gentamicin resistant vanA or vanB E. faecium which have limited treatment options.


Asunto(s)
Antiinfecciosos/farmacología , Bacteriemia/epidemiología , Farmacorresistencia Bacteriana Múltiple , Enterococcus/efectos de los fármacos , Infecciones por Bacterias Grampositivas/epidemiología , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Australia/epidemiología , Bacteriemia/microbiología , Niño , Preescolar , Enterococcus/clasificación , Enterococcus/genética , Enterococcus faecalis/clasificación , Enterococcus faecalis/efectos de los fármacos , Enterococcus faecalis/genética , Enterococcus faecium/clasificación , Enterococcus faecium/efectos de los fármacos , Enterococcus faecium/genética , Femenino , Infecciones por Bacterias Grampositivas/microbiología , Humanos , Lactante , Recién Nacido , Masculino , Persona de Mediana Edad , Epidemiología Molecular , Adulto Joven
20.
Artículo en Inglés | MEDLINE | ID: mdl-31522665

RESUMEN

From 1 January to 31 December 2017, 36 institutions around Australia participated in the Australian Staphylococcus aureus Sepsis Outcome Programme (ASSOP). The aim of ASSOP 2017 was to determine the proportion of Staphylococcus aureus bacteraemia (SAB) isolates in Australia that are antimicrobial resistant, with particular emphasis on susceptibility to methicillin and to characterise the molecular epidemiology of the methicillin-resistant isolates. A total of 2,515 S. aureus bacteraemia episodes were reported, of which 77% were community-onset. Approximately one in five S. aureus (19.0%) were methicillin resistant. The 30-day all-cause mortality associated with methicillin-resistant SAB was 18.7% which was significantly higher than the 14.0% mortality associated with methicillin-susceptible SAB. With the exception of the ß-lactams and erythromycin, antimicrobial resistance in methicillin-susceptible S. aureus was rare. However in addition to the ß-lactams approximately 42% of methicillin-resistant S. aureus (MRSA) were resistant to erythromycin and ciprofloxacin and approximately 14% resistant to co-trimoxazole, tetracycline and gentamicin. When applying the EUCAST breakpoints teicoplanin resistance was detected in five S. aureus isolates. Resistance was not detected for vancomycin and linezolid. Resistance to non-beta-lactam antimicrobials was largely attributable to two healthcare-associated MRSA clones: ST22-IV [2B] (EMRSA-15) and ST239-III [3A] (Aus-2/3 EMRSA). ST22-IV [2B] (EMRSA-15) is the predominant healthcare-associated clone in Australia. Seventy-five percent of methicillin-resistant SAB were due to community-associated clones. Although polyclonal approximately 74% of community-associated clones were characterised as ST93-IV [2B] (Queensland CA-MRSA), ST5-IV [2B], ST45-VT [5C2&5] and ST1-IV [2B]. CA-MRSA, in particular the ST45-VT [5C2&5] clone has acquired multiple antimicrobial resistance determinants including ciprofloxacin, erythromycin, clindamycin, gentamicin and tetracycline. ST45-VT [5C2&5] accounted for 12.8% of CA-MRSA. As CA-MRSA is well established in the Australian community it is important antimicrobial resistance patterns in community- and healthcare-associated SAB is monitored as this information will guide therapeutic practices in treating S. aureus sepsis.


Asunto(s)
Antiinfecciosos/farmacología , Bacteriemia/epidemiología , Farmacorresistencia Bacteriana Múltiple , Infecciones Estafilocócicas/epidemiología , Staphylococcus aureus/efectos de los fármacos , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Australia/epidemiología , Bacteriemia/microbiología , Niño , Preescolar , Infecciones Comunitarias Adquiridas/epidemiología , Infecciones Comunitarias Adquiridas/microbiología , Infección Hospitalaria/epidemiología , Infección Hospitalaria/microbiología , Femenino , Humanos , Lactante , Recién Nacido , Masculino , Staphylococcus aureus Resistente a Meticilina/efectos de los fármacos , Persona de Mediana Edad , Epidemiología Molecular , Infecciones Estafilocócicas/microbiología , Adulto Joven
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