Molecular epidemiology and antifungal susceptibilities of Aspergillus species isolated from patients with invasive aspergillosis

SUMMARY OBJECTIVE: The aim of this study was to evaluate the demographic data, molecular epidemiology, and in vitro antifungal susceptibility results of patients with Aspergillus isolated from various clinical specimens. METHODS: A total of 44 Aspergillus strains were studied. The definition of invasive aspergillosis in patients was made according to European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) criteria. Strains were phenotypically and molecularly identified. Demographic characteristics of patients and genotypes of strains were evaluated. Phylogenetic analysis was done by the The Unweighted Pair-Group Method with Arithmetic Mean (UPGMA). Antifungal susceptibility of strains was determined according to The Clinical and Laboratory Standards Institute (CLSI)-M61-Ed2 and The European Committee on Antimicrobial Susceptibility Testing (EUCAST). RESULTS: A total of 11 patients were classified as proven and 33 as probable invasive aspergillosis. There was a statistically significant difference in age groups, subdisease, neutropenic, and receiving chemotherapy between groups. A total of 23 strains were identified as Aspergillus fumigatus, 12 as Aspergillus niger, 6 as Aspergillus flavus, and 3 as Aspergillus terreus. Phylogenetic analysis revealed five different genotypes. No statistical difference was found in the comparisons between patients groups and genotype groups. There was a statistically significant difference between genotype groups and voriconazole, posaconazole, and itraconazole Minimum Inhibition Concentration (MIC). CONCLUSION: Accurate identification of strains and antifungal susceptibility studies should be performed due to azole and amphotericin B resistance. Genotyping studies are important in infection control due to identifying sources of infection and transmission routes.

Molecular epidemiology progress of community-associated Methicillin-resistant Staphylococcus aureus infection in children / 中华实用儿科临床杂志

Antimicrobial resistance of Staphylococcus aureus is a main factor for the poor prognosis.In China, the detection rate of Methicillin-resistant Staphylococcus aureus (MRSA) in children is annually increasing, especially the community-acquired MRSA (CA-MRSA). This review discussed molecular characteristics, antimicrobial resistance mechanism and antimicrobial resistance progress of CA-MRSA, and analyzed recent molecular epidemiology and changes of drug resistance to CA-MRSA in children from China, thus providing theoretical basis for the prevention and control of CA-MRSA in children.

Study on the progress of HIV typing methods / 上海预防医学

As a retrovirus with high recombination and mutation rate， HIV targets CD4+ T lymphocytes， causing damage to the body's immune system and eventually leading to severe immune function defects. Different subtypes of the HIV virus exhibit significant sequence differences in their structural and regulatory genes， and this diversity is closely related to etiology， transmission， diagnosis， drug therapy， disease progression， and vaccine development. As a country with the largest number of HIV subtypes， rapid and accurate typing of the HIV virus holds great significance for China's efforts in disease prevention and control. This study provides a comprehensive reveiw of domestic and international HIV genotyping methods， and summarizes the clinical significance of different subtypes in order to provide reference for further research.

NDM-producing Enterobacterales prevalence associated to COVID-19 in a tertiary hospital

Abstract Colonizations/Infections caused by carbapenem-resistant Enterobacterales are of great clinical and epidemiological importance due to their rapid dissemination and high mortality rates. In this scenario, the use of antibiotics intensified by the COVID-19 pandemic has brought about a great warning on the real impact that this pandemic could have on antimicrobial management programs and long-term antimicrobial resistance rates. The objective of this study was to evaluate the increase of New Delhi Metallo β-Lactamase (NDM)-producing Enterobacterales cases in COVID-19 units of a complex Brazilian tertiary hospital. This retrospective observational study included all patients admitted to the hospital identified as colonized or infected by NDM-producing Gram negative bacilli (GNB), from January 2017 to April 2021. Forty-two NDM-producing Enterobacterales were identified in 39 patients. The rate of NDM cases per total surveillance cultures increased progressively between 2017 and 2021 (chi-2 for trend, p < 0.0001) and was associated with a higher occurrence specifically in COVID units (Fisher exact, p < 0.0001). The molecular investigation of the NDM-producing Klebsiella pneumoniae strains revealed the emergence of diverse clones during the COVID-19 period, also with possible evidence of horizontal transmission among patients within COVID units. NDM-producing Enterobacterales with multiple and different clonalities in the COVID-19 units also raised questions about the importance of other factors besides horizontal clonal transfer, including the increase of antimicrobial consumption by these patients.

A review of the recent advances on Lassa fever with special reference to molecular epidemiology and progress in vaccine development

Lassa fever, a viral hemorrhagic fever caused by the Lassa virus (LASV), is endemic in West Africa and is associated with high morbidity and mortality. At least three of the four proposed seven lineages of LASV are found in Nigeria, where the multimammate rat, Mastomys natalensis, serves as the primary reservoir. Endemic countries report approximately 200,000 infections and 5,000 deaths annually, with Nigeria experiencing thousands of infections and hundreds of deaths including healthcare workers. The aim of this review is to provide scientific information for better understanding of the evolutionary biology, molecular epidemiology, pathogenesis, diagnosis, and prevention of Lassa fever in Nigeria and other endemic regions worldwide, which can lead to improved control efforts and reduce morbidity and mortality from recurrent epidemics. To achieve this aim, observational studies such as case series, cross-sectional and cohort studies published between December 2017 and September 2022 were searched for on various online databases including Google Scholar, Africa Journals Online (AJOL), Research Gates, PubMed, PMIC, NCDC, and WHO websites. Although the origin and evolutionary history, and the transmission dynamics of Lassa virus have been revealed through recent. molecular epidemiological studies, the factors that drive the evolution of the virus remain unclear. Genetic changes in the viral genome may have enabled the virus to adapt to humans. Diagnosis of Lassa fever has also advanced from basic serological tests to more sophisticated methods such as quantitative real time polymerase chain reaction (qRT-PCR) and sequencing, which are particularly useful for identifying outbreak strains. Several vaccines, including recombinant vesicular stomatitis virus (rVSV), virus-like particle (VLP), and DNA-based vaccines, have shown promise in animal models and some have progressed to phase 2 clinical trials. Preventing and controlling Lassa fever is critical to safeguard the health and well-being of affected communities. Effective measures such as rodent control, improved sanitation, and early detection and isolation of infected individuals are essential for reducing transmission. Ongoing research into the genetic and ecological factors that drive the evolution of Lassa virus is necessary to reduce the impacts of Lassa fever.

A review of the recent advances on Lassa fever with special reference to molecular epidemiology and progress in vaccine development

Lassa fever, a viral hemorrhagic fever caused by the Lassa virus (LASV), is endemic in West Africa and is associated with high morbidity and mortality. At least three of the four proposed seven lineages of LASV are found in Nigeria, where the multimammate rat, Mastomys natalensis, serves as the primary reservoir. Endemic countries report approximately 200,000 infections and 5,000 deaths annually, with Nigeria experiencing thousands of infections and hundreds of deaths including healthcare workers. The aim of this review is to provide scientific information for better understanding of the evolutionary biology, molecular epidemiology, pathogenesis, diagnosis, and prevention of Lassa fever in Nigeria and other endemic regions worldwide, which can lead to improved control efforts and reduce morbidity and mortality from recurrent epidemics. To achieve this aim, observational studies such as case series, cross-sectional and cohort studies published between December 2017 and September 2022 were searched for on various online databases including Google Scholar, Africa Journals Online (AJOL), Research Gates, PubMed, PMIC, NCDC, and WHO websites. Although the origin and evolutionary history, and the transmission dynamics of Lassa virus have been revealed through recent molecular epidemiological studies, the factors that drive the evolution of the virus remain unclear. Genetic changes in the viral genome may have enabled the virus to adapt to humans. Diagnosis of Lassa fever has also advanced from basic serological tests to more sophisticated methods such as quantitative real time polymerase chain reaction (qRT-PCR) and sequencing, which are particularly useful for identifying outbreak strains. Several vaccines, including recombinant vesicular stomatitis virus (rVSV), virus-like particle (VLP), and DNA-based vaccines, have shown promise in animal models and some have progressed to phase 2 clinical trials. Preventing and controlling Lassa fever is critical to safeguard the health and well-being of affected communities. Effective measures such as rodent control, improved sanitation, and early detection and isolation of infected individuals are essential for reducing transmission. Ongoing research into the genetic and ecological factors that drive the evolution of Lassa virus is necessary to reduce the impacts of Lassa fever

La fièvre de Lassa, une fièvre hémorragique virale causée par le virus de Lassa (LASV), est endémique en Afrique de l'Ouest et est associée à une morbidité et une mortalité élevées. Au moins trois des quatre lignées proposées de LASV se trouvent au Nigeria, où le rat multimammaire, Mastomys natalensis, sert de réservoir principal. Les pays endémiques signalent environ 200,000 infections et 5,000 décès par an, le Nigéria connaissant des milliers d'infections et des centaines de décès, y compris des travailleurs de la santé. L'objectif de cette revue est de fournir des informations scientifiques pour une meilleure compréhension de la biologie évolutive, de l'épidémiologie moléculaire, de la pathogenèse, du diagnostic et de la prévention de la fièvre de Lassa au Nigeria et dans d'autres régions endémiques du monde, ce qui peut conduire à des efforts de contrôle améliorés et réduire la morbidité et la mortalité des épidémies récurrentes. Pour atteindre cet objectif, des études observationnelles telles que des séries de cas, des études transversales et de cohorte publiées entre décembre 2017 et septembre 2022 ont été recherchées sur diverses bases de données en ligne, notamment Google Scholar, Africa Journals Online (AJOL), Research Gate, PubMed, PMIC, Sites Web du NCDC et de l'OMS. Bien que l'origine et l'histoire évolutive, ainsi que la dynamique de transmission du virus de Lassa aient été révélées par des études épidémiologiques moléculaires récentes, les facteurs qui déterminent l'évolution du virus restent flous. Des modifications génétiques du génome viral pourraient avoir permis au virus de s'adapter à l'homme. Le diagnostic de la fièvre de Lassa est également passé des tests sérologiques de base à des méthodes plus sophistiquées telles que la réaction quantitative en chaîne par polymérase en temps réel (qRTPCR) et le séquençage, qui sont particulièrement utiles pour identifier les souches épidémiques. Plusieurs vaccins, y compris le virus recombinant de la stomatite vésiculeuse (rVSV), les particules pseudo-virales (VLP) et les vaccins à base d'ADN, se sont révélés prometteurs dans des modèles animaux et certains ont progressé vers des essais cliniques de phase 2. La prévention et le contrôle de la fièvre de Lassa sont essentiels pour préserver la santé et le bien-être des communautés touchées. Des mesures efficaces telles que le contrôle des rongeurs, l'amélioration de l'assainissement et la détection et l'isolement précoces des personnes infectées sont essentielles pour réduire la transmission. Des recherches continues sur les facteurs génétiques et écologiques qui déterminent l'évolution du virus de Lassa sont nécessaires pour réduire les impacts de la fièvre de Lassa.

Molecular Epidemiology of Plasmodium species in Conflicted Federally Administered Tribal Area (FATA) Pakistan / Epidemiologia molecular de espécies de plasmódio em área tribal sob administração federal em conflito do Paquistão

Military conflicts have been significant obstacles in detecting and treating infectious disease diseases due to the diminished public health infrastructure, resulting in malaria endemicity. A variety of violent and destructive incidents were experienced by FATA (Federally Administered Tribal Areas). It was a struggle to pursue an epidemiological analysis due to continuing conflict and Talibanization. Clinical isolates were collected from Bajaur, Mohmand, Khyber, Orakzai agencies from May 2017 to May 2018. For Giemsa staining, full blood EDTA blood samples have been collected from symptomatic participants. Malaria-positive microscopy isolates were spotted on filter papers for future Plasmodial molecular detection by nested polymerase chain reaction (nPCR) of small subunit ribosomal ribonucleic acid (ssrRNA) genes specific primers. Since reconfirming the nPCR, a malariometric study of 762 patients found 679 positive malaria cases. Plasmodium vivax was 523 (77%), Plasmodium falciparum 121 (18%), 35 (5%) were with mixed-species infection (P. vivax plus P. falciparum), and 83 were declared negative by PCR. Among the five agencies of FATA, Khyber agency has the highest malaria incidence (19%) with followed by P. vivax (19%) and P. falciparum (4.1%). In contrast, Kurram has about (14%), including (10.8%) P. vivax and (2.7%) P. falciparum cases, the lowest malaria epidemiology. Surprisingly, no significant differences in the distribution of mixed-species infection among all five agencies. P. falciparum and P. vivax were two prevalent FATA malaria species in Pakistan's war-torn area. To overcome this rising incidence of malaria, this study recommends that initiating malaria awareness campaigns in school should be supported by public health agencies and malaria related education locally, targeting children and parents alike.

Os conflitos militares têm sido obstáculos significativos na detecção e tratamento de doenças infecciosas devido à diminuição da infraestrutura de saúde pública, resultando na endemicidade da malária. Uma variedade de incidentes violentos e destrutivos foi vivida pelas FATA (áreas tribais administradas pelo governo federal). Foi uma luta busca ruma análise epidemiológica devido ao conflito contínuo e à talibanização. Isolados clínicos foram coletados de agências Bajaur, Mohmand, Khyber e Orakzai, de maio de 2017 a maio de 2018. Para a coloração de Giemsa, amostras de sangue completo com EDTA foram coletadas de participantes sintomáticos. Isolados de microscopia positivos para malária foram colocados em papéis de filtro para futura detecção molecular plasmódica por reação em cadeia da polimerase aninhada (nPCR) de primers específicos de genes de subunidade ribossômica de ácido ribonucleico (ssrRNA). Desde a reconfirmação do nPCR, um estudo malariométrico de 762 pacientes encontrou 679 casos positivos de malária. Plasmodium vivax foi 523 (77%), Plasmodium falciparum 121 (18%), 35 (5%) eram com infecção de espécies mistas (P. vivax mais P. falciparum) e 83 foram declarados negativos por PCR. Entre as cinco agências da FATA, a agência Khyber tem a maior incidência de malária (19%), seguida por P. vivax (19%) e P. falciparum (4,1%). Em contraste, Kurram tem cerca de 14%, incluindo 10,8% casos de P. vivax e 2,7% P. falciparum, a epidemiologia de malária mais baixa. Surpreendentemente, não há diferenças significativas na distribuição da infecção de espécies mistas entre todas as cinco agências. P. falciparum e P. vivax foram duas espécies prevalentes de malária FATA na área devastada pela guerra no Paquistão. Para superar essa incidência crescente de malária, este estudo recomenda que o início de campanhas de conscientização sobre a malária na escola deve ser apoiado por agências de saúde pública e educação relacionada com a malária localmente, visando crianças e pais.

Molecular Epidemiology of Plasmodium species in Conflicted Federally Administered Tribal Area (FATA) Pakistan

Abstract Military conflicts have been significant obstacles in detecting and treating infectious disease diseases due to the diminished public health infrastructure, resulting in malaria endemicity. A variety of violent and destructive incidents were experienced by FATA (Federally Administered Tribal Areas). It was a struggle to pursue an epidemiological analysis due to continuing conflict and Talibanization. Clinical isolates were collected from Bajaur, Mohmand, Khyber, Orakzai agencies from May 2017 to May 2018. For Giemsa staining, full blood EDTA blood samples have been collected from symptomatic participants. Malaria-positive microscopy isolates were spotted on filter papers for future Plasmodial molecular detection by nested polymerase chain reaction (nPCR) of small subunit ribosomal ribonucleic acid (ssrRNA) genes specific primers. Since reconfirming the nPCR, a malariometric study of 762 patients found 679 positive malaria cases. Plasmodium vivax was 523 (77%), Plasmodium falciparum 121 (18%), 35 (5%) were with mixed-species infection (P. vivax plus P. falciparum), and 83 were declared negative by PCR. Among the five agencies of FATA, Khyber agency has the highest malaria incidence (19%) with followed by P. vivax (19%) and P. falciparum (4.1%). In contrast, Kurram has about (14%), including (10.8%) P. vivax and (2.7%) P. falciparum cases, the lowest malaria epidemiology. Surprisingly, no significant differences in the distribution of mixed-species infection among all five agencies. P. falciparum and P. vivax were two prevalent FATA malaria species in Pakistans war-torn area. To overcome this rising incidence of malaria, this study recommends that initiating malaria awareness campaigns in school should be supported by public health agencies and malaria-related education locally, targeting children and parents alike.

Resumo Os conflitos militares têm sido obstáculos significativos na detecção e tratamento de doenças infecciosas devido à diminuição da infraestrutura de saúde pública, resultando na endemicidade da malária. Uma variedade de incidentes violentos e destrutivos foi vivida pelas FATA (áreas tribais administradas pelo governo federal). Foi uma luta buscar uma análise epidemiológica devido ao conflito contínuo e à talibanização. Isolados clínicos foram coletados de agências Bajaur, Mohmand, Khyber e Orakzai, de maio de 2017 a maio de 2018. Para a coloração de Giemsa, amostras de sangue completo com EDTA foram coletadas de participantes sintomáticos. Isolados de microscopia positivos para malária foram colocados em papéis de filtro para futura detecção molecular plasmódica por reação em cadeia da polimerase aninhada (nPCR) de primers específicos de genes de subunidade ribossômica de ácido ribonucleico (ssrRNA). Desde a reconfirmação do nPCR, um estudo malariométrico de 762 pacientes encontrou 679 casos positivos de malária. Plasmodium vivax foi 523 (77%), Plasmodium falciparum 121 (18%), 35 (5%) eram com infecção de espécies mistas (P. vivax mais P. falciparum) e 83 foram declarados negativos por PCR. Entre as cinco agências da FATA, a agência Khyber tem a maior incidência de malária (19%), seguida por P. vivax (19%) e P. falciparum (4,1%). Em contraste, Kurram tem cerca de 14%, incluindo 10,8% casos de P. vivax e 2,7% P. falciparum, a epidemiologia de malária mais baixa. Surpreendentemente, não há diferenças significativas na distribuição da infecção de espécies mistas entre todas as cinco agências. P. falciparum e P. vivax foram duas espécies prevalentes de malária FATA na área devastada pela guerra no Paquistão. Para superar essa incidência crescente de malária, este estudo recomenda que o início de campanhas de conscientização sobre a malária na escola deve ser apoiado por agências de saúde pública e educação relacionada com a malária localmente, visando crianças e pais.

Genetic typing, virulence genes and drug resistance analysis of Campylobacter fetus subsp. testudinum / 中华微生物学和免疫学杂志

Objective:To analyze the molecular epidemiological characteristics of Campylobacter fetus subsp. testudinum ( Cft). Methods:Fifteen strains of Cft collected in our laboratory from 2010 to 2022 were subjected to whole-genome sequencing. Their epidemiological characteristics were analyzed based on the global genome data of Cft on GenBank database. MLST-GrapeTree software was used to obtain the genetic structure of Cft strains. A phylogenetic tree was constructed using core-genome single nucleotide polymorphism (cgSNP) analysis, and the sequence clusters were identified using rhierBAPS. Virulence genes and drug resistance genes of Cft strains were annotated using CARD, ResFinder and VFDB database. Their susceptibility to antibiotics was tested using E-test method and the results were analyzed using the CLSI-M45 sensitivity standard for Campylobacter jejuni/ Campylobacter coli. Results:Based on average nucleotide identity (ANI) analysis, the genome data of 41 Cft strains including 24 isolated from human, 13 from animals and four of unknown sources were collected from GenBank database. Among the 24 human-derived strains, 20 were linked to Asian descent and only one was linked to Caucasian descent (spouse of Asian descent), showing statistically significant differences in human ethnicity. All of the 13 animal-derived strains were originated from reptilian sources, including six from turtles, four from snakes and three from lizards. MLST revealed that ST46 was the predominant ST in China, while ST15 was the major sequence type in the United States. Grapetree analysis also demonstrated that the genetic diversity in China was greater than that in the United States. The phylogenetic tree constructed based on cgSNP and BAPS identified six distinct sequence clusters. The Chinese isolates were scattered in diverse sequence clusters and closely related to animal-derived strains, while the American isolates mainly belonged to ST15. The genes encoding virulence factors such as flagella, glycosylation systems and adhesins were carried by all of the 41 Cft strains (100.00%). The invasion-related virulence genes, such as the genes encoding the IV type secretion system ( virB4, virB9, virD4) and the resistance-related tetO efflux pump gene were specifically identified in the emerging ST74 clones. In vitro drug susceptibility testing of 15 Chinese isolates revealed 46.67% of the Cft strains were resistant to ciprofloxacin and 100.00% were sensitive to erythromycin. Conclusions:The global sequence clusters of Cft isolates showed a great genetic diversity. Most of the people with Cft infection had basic immune diseases and might have eaten or had contact with reptiles. Notably, the Chinese domestic infection of ST46 and the emerging ST74 should arouse our more attention.

Detección clonal de cepas parentales de streptococcus agalactiae Lehmann y Neumann por amplificación aleatoria de ADN polimórfico / Clonal detection of streptococcus agalactiae Lehmann and Neumann parental strains by random amplification of polymorphic DNA

RESUMEN Streptococcus agalactiae (SGB) produce infecciones invasivas en neonatos siendo la transmisión materna la más frecuente. Estudios epidemiológicos utilizan técnicas moleculares que evalúan la diversidad genética, entre ellas la de amplificación aleatoria de ADN polimórfico (RAPD) que resulta ser accesible, sensible y utiliza cebadores arbitrarios para amplificar segmentos polimórficos de ADN mediante PCR. El objetivo fue determinar la relación clonal entre aislamientos de SGB recuperados de madres y sus respectivos recién nacidos. Se estudiaron por RAPD cuatro parejas de aislamientos de SGB obtenidos de hisopados vagino-rectales de madres y de hemocultivos de sus neonatos. Se utilizaron los cebadores OPS11, OPB17 y OPB18 para seleccionar uno con capacidad de discriminar entre cepas no relacionadas genéticamente. Se utilizó la fórmula de Hunter-Gaston que establece el índice de discriminación (D), cuando D>0,90 se considera que los aislamientos pertenecen a clones diferentes. Los perfiles de amplificación para los ocho aislamientos, empleando independientemente cada cebador, permitieron calcular un D=1 para OPS11, y D=0,84 para OPB17 y OPB18. Por lo tanto, OPS11 fue seleccionado para el estudio de la relación clonal de los aislamientos, encontrándose perfiles de amplificación similares por RAPD para cada par de cepas madre-recién nacido. Se observaron diferentes perfiles de amplificación entre los pares de cepas madre-recién nacido, lo que revela la discriminación entre cepas no relacionadas, resultados confirmados por electroforesis en campo pulsante (PFGE). Estos resultados indican transmisión vertical para cada caso estudiado y robustez del cebador OPS11. Se encontraron condiciones apropiadas del ensayo de RAPD, lo que es útil para estudios epidemiológicos.

ABSTRACT Streptococcus agalactiae (GBS) causes invasive infections in newborns, being the most frequent the maternal transmission. Epidemiological studies use molecular techniques that assess genetic diversity, including random amplification of polymorphic DNA (RAPD) that is found to be accessible, sensitive and uses arbitrary primers to amplify polymorphic segments of DNA by PCR. The objective was to determine the clonal relationship between GBS strains recovered from mothers and their respective newborns. Four pairs of GBS isolates obtained from vaginal-rectal swabs of mothers and blood cultures of their newborns were studied with RAPD. Primers OPS11, OPB17 and OPB18 were used to select one with the ability to discriminate between non-genetically related strains. The Hunter-Gaston formula that establishes the discrimination index (D) was used; when D>0.90, it is considered that the isolates belong to different clones. The amplification profiles for the eight isolates, using each primer independently, allowed to calculate a D=1 for OPS11, and D=0.84 for OPB17 and OPB18. Therefore, OPS11 was selected for the study of the clonal relationship of the isolates, and similar amplification profiles were found by RAPD for each mother-newborn pair of GBS isolates. Different amplification profiles were observed between pairs of mother-newborn strains, which reveals the discrimination between unrelated strains, confirmed by pulsating field electrophoresis (PFGE). These results indicated vertical transmission for each studied case and robustness of the OPS11 primer. Appropriate conditions of the RAPD trial were found, which is useful for epidemiological studies.

Molecular epidemiology of Japanese encephalitis in pigs and risk factors associated with causing Japanese encephalitis in pigs of Lakhimpur, the first case reported in the district of North East India

Background & objectives: Japanese encephalitis (JE) is a major public health problem in India. The first outbreaks of JE have been reported from the North-eastern regions of Assam, particularly from the Lakhimpur district of Assam between July–August 1989. In Assam every year many people died due to JE. This study was performed to investigate the molecular epidemiology of JE in pigs in Lakhimpur district of Assam and the risk factors associated with causing Japanese encephalitis in pigs. This study will help to map out the endemic regions and to know where and when to apply the most control strategies towards the prevention and control of the disease. Methods: A total of 342 serum samples from pigs were collected from 10 organized and 20 unorganized farms from 9 blocks and recorded to age, sex and breed and tested by RT-PCR. Pig farms and the surrounding environment were studied for assessment of farm-level risk factors responsible for JEV infection in pigs. Results: Out of 342 samples tested for detection of the E gene of JEV, 14 samples were found to be positive with a prevalence rate of 4.09%. Age, sex and breed-wise higher cases were found in at the age group above 12 months, sex wise female and breed-wise local pigs. Pig farms less than 500 meters from risk factors like rice field, stagnant water source, wild bird exposure to farm and mosquito exposure at farm/ bite to pigs, found to be more numbers of JE cases. Interpretation & conclusion: Molecular epidemiology of JE in pigs, and humans; positive at Lakhimpur recommend the need for uninterrupted surveillance of this virus in pigs specially those areas where pig population is more and all risk factors are present.

Prevalence of Streptococcus agalactiae capsular types among pregnant women in Rio de Janeiro and the impact of a capsular based vaccine

Abstract Streptococcus agalactiae (group B Streptococcus, GBS) remains one major neonatal pathogen, being maternal colonization a risk factor for infection development. Despite effective, the usage of antibiotics to prevent neonatal infections has limitations. The bacterial polysaccharide capsule is a virulence determinant, a target for vaccine directed to pregnant women, and also the most useful epidemiological marker of GBS infections. Capsular polysaccharides are diverse and disease severity varies according to the expressed type. Here, capsular typing of 124 GBS isolates recovered from pregnant women was determined by a multiplex PCR-based method. The most frequent types were Ia (33.0%), II (25.8%) and V (21.8%). Other types found were Ib (8.9%), III (8.9%) and IV (1.6%). While type Ia was prevalent during the whole period (2002-2018), fluctuations in distribution of other types, specially V, were observed over time. Capsular type III, traditionally associated with severe neonatal infections, was poorly detected. Distribution of maternal GBS capsular types in the metropolitan area of Rio de Janeiro, with prevalence of Ia and II, is quite different from other parts of the world. The knowledge about GBS capsular type distribution is essential to predict the theoretical impact of developing capsule-based vaccines in the local population.

Laboratory-based study of drug resistance and genotypic profile of multidrug-resistant tuberculosis isolates in Salvador, Bahia, Brazil

Abstract Background: Surveillance of multidrug resistant/extensively drug-resistant tuberculosis (MDR/XDR-TB) is essential to guide disease dissemination control measures. Brazil contributes to a significant fraction of tuberculosis (TB) cases worldwide, but only few reports addressed MDR/XDR-TB in the country. Methods: This cross-sectional, laboratory-based study describes the phenotypic resistance profiles of isolates obtained between January 2008 and December 2011 in Bahia, Brazil, and sociodemographic, epidemiological, and clinical characteristics (obtained from mandatory national registries) of the corresponding 204 MDR/XDR-TB patients. We analyzed the mycobacterial spoligotyping and variable number of tandem repeats of mycobacterial interspersed repetitive units in 12-loci profiles obtained from Salvador. Results: MDR/XDR-TB patients were predominantly male, had a median age of 43 years, belonged to black ethnicity, and failed treatment before MDR-TB diagnosis. Nearly one-third of the isolates had phenotypic resistance (evaluated by mycobacteria growth indicator tube assay) to second-line anti-TB drugs (64/204, 31%), of which 22% cases (14/64) were diagnosed as XDR-TB. Death was a frequent outcome among these individuals and was associated with resistance to second-line anti-TB drugs. Most isolates successfully genotyped belonged to the Latin-American Mediterranean (LAM) Family, with an unprecedented high proportion of LAM10-Cameroon subfamily bacilli. More than half of these isolates were assigned to a unique cluster by the genotyping methods performed. Large clusters of identical genotypes were also observed among LAM SIT42 and SIT376 strains. Conclusions: We highlight the need for strengthening local and national efforts to perform early detection of TB drug resistance and to prevent treatment discontinuation to limit the emergence of drug-resistant strains.

Retrospective analysis of 201 clinical isolates of Aspergillus fumigatus from a hospital in Nanjing: clinical characteristics of infected patients and azole resistance / 中华皮肤科杂志

Objective:To summarize clinical characteristics of patients with Aspergillus fumigatus infection in a hospital in Nanjing, to preliminarily assess azole resistance in clinical isolates of Aspergillus fumigatus, and to investigate risk factors for the emergence of azole-resistant Aspergillus fumigatus. Methods:Clinical isolates of Aspergillus fumigatus were collected from inpatients in Department of Laboratory, Nanjing Drum Tower Hospital from March 2017 to February 2021. Clinical data on these infected patients were analyzed, azole sensitivity testing and mutation analysis of the cyp51A gene and its promoter region were performed for these Aspergillus fumigatus isolates. Results:A total of 201 strains of Aspergillus fumigatus were collected, and mainly isolated from sputum specimens. Among the infected patients, there were 131 males and 70 females, and their age were 64.2 ± 15.8 years. The patients were mainly collected from department of respiratory medicine (79 cases), department of intensive medicine (34 cases), department of rheumatology (19 cases), etc. Among these patients, common underlying diseases included interstitial pneumonia (32 cases), malignant tumors (18 cases), pneumonia (13 cases), trauma (12 cases), systemic lupus erythematosus (8 cases), etc. Drug susceptibility testing showed that 6 (2.99%) strains of Aspergillus fumigatus were resistant to itraconazole and posaconazole, and 3 patients infected with azole-resistant Aspergillus fumigatus had used antifungal drugs before testing. Sequencing was performed on the cyp51A gene and its promoter region in the 6 strains of azole-resistant Aspergillus fumigatus, and showed TR34/L98H/S297T/F495I mutation in 5 strains and TR34/L98H mutation in 1 strain. Conclusion:Compared with previously published data about azole resistance in China during 2010 -2015, the resistance of Aspergillus fumigatus to azoles in Nanjing Drum Tower Hospital did not increase from 2017 to 2021, and the mechanism of azole resistance was mostly associated with TR34/L98H/S297T/F495I mutation in the cyp51A gene and its promoter region.

Molecular epidemiological investigation on Theileria in yellow cattle from Xiangxi Autonomous Prefecture of Hunan Province / 中国血吸虫病防治杂志

Objective To investigate the prevalence and genetic variation of Theileria in yellow cattle in Xiangxi Autonomous Prefecture of Hunan Province. Methods A total of 184 blood specimens were collected from Fenghuang, Huanyuan and Baojing counties of Xiangxi Autonomous Prefecture during the period from August 2018 through August 2019, and were detect using PCR assay with the specific 18S ribosomal rRNA (18S rRNA) gene targeting Theileria. The gene sequences of positive specimens were aligned with the sequences recorded in GenBank, and a phylogenetic tree was created with Plasmodium ovale 18S rRNA as an outgroup. Results A total of 143 blood samples were positive for Theileria, with a mean detection rate of 77.7%. Theileria was prevalent in the blood samples from yellow cattle in all three counties, with detection rates of 85.0% in Fenghuang County, 88.3% in Huayuan County and 61.0% in Baojing County, respectively. There was no significant difference in the detection rate of Theileria between Xiangxi yellow cattle and normal yellow cattle (77.2% vs. 79.5%; χ2 = 0.08, P > 0.05), while the detection of Theileria was significantly lower in the housed yellow cattle than in free-range cattle (68.9% vs. 89.7%; χ2 = 22.36, P < 0.01). A total of 18 PCR positive samples were randomly selected for sequencing and analysis, and all samples showed more than 99.0% homology with T. luwenshuni isolates. Phylogenetic analysis showed that the 18 positive samples were clustered into the same branch with T. luwenshuni, but were far away from other isolates. Conclusions The prevalence of Theileria is high in yellow cattle from Xiangxi Autonomous Prefecture of Hunan Province, and T. luwenshuni may be the dominant parasite species.

Molecular epidemiological characteristics of the virus in 96 children with acute diarrhea in Changdu of Tibet, China / 中国当代儿科杂志

OBJECTIVES@#To study the molecular epidemiological characteristics of the virus in children with acute viral diarrhea in Changdu of Tibet, China.@*METHODS@#Fecal specimens were collected from 96 children with acute diarrhea who visited the People's Hospital of Changdu, Tibet, from November 2018 to November 2020 and were tested for adenovirus, norovirus, astrovirus, sapovirus, and rotavirus. Gene sequencing was performed for the genotypes of these viruses.@*RESULTS@#The overall positive rate of the five viruses was 39% (37/96), among which astrovirus had the highest positive rate of 17%, followed by norovirus (9%), rotavirus (8%), adenovirus (7%), and sapovirus (5%). There was no significant difference in the positive rate of the five viruses among different age groups (P>0.05). Only the positive rate of astrovirus was significantly different among the four seasons (P<0.05). For adenovirus, 6 children had F41 type and 1 had C2 type; for norovirus, 6 had GⅠ.3 type, 1 had GⅠ.7 type, 1 had GⅡ.3 type, and 2 had GⅡ.4 Sydney_2012 type; HAstrV-1 type was observed in all children with astrovirus infection; for sapovirus, 1 child each had sporadic GⅠ.2, GⅠ.6, and GⅡ.1 sapovirus and 2 children had unknown type; 6 children had rotavirus G9[P8].@*CONCLUSIONS@#Astrovirus and norovirus are important pathogens in children with acute diarrhea in Changdu, Tibet. The positive rate of adenovirus, norovirus, astrovirus, sapovirus, and rotavirus is not associated with age, and only the positive rate of astrovirus has obvious seasonality. F41 type is the dominant genotype of adenovirus; GⅠ.3 is the dominant genotype of norovirus; HAstrV-1 is the dominant genotype of astrovirus; sporadic GⅠ.2, GⅠ.6, and GⅡ.1 are the dominant genotypes of sapovirus; G9[P8] is the dominant genotype of rotavirus.

Molecular epidemiology of HIV-1 among blood donors in Dalian: 2011~2020 / 中国输血杂志

【Objective】 To investigate HIV-1 subtype distribution and trend among Dalian blood donors between 2011 and 2020, in order to provide information to improve blood safety and HIV prevention. 【Methods】 HIV RNA was purified from plasma samples of Dalian blood donors with confirmed HIV infection, which were collected between 2011 and 2020. The HIV pol gene was amplified and sequenced. HIV-1 subtypes were determined by phylogenetic analysis. 【Results】 HIV RNA was successfully genotyped in 174 samples from HIV-infected donors. The main subtypes among Dalian blood donors were CRF01_AE(69.5%), CRF07_BC(17.2%), B(5.2%), CRF02_AG(2.9%), C(1.1%), CRF55_01B(1.1%), CRF08_BC(0.6%), CRF59_01B(0.6%) and CRF79_0107(0.6%). There were still 2 cases (1.1%) unclassified. Significant difference was observed when comparing with the published national data. The prevalence of CRF01_AE strains decreased over the years, while CRF07_BC increased significantly. CRF02_AG carriers differed from donors infected with other HIV subtypes by being mostly females (40.0% vs. 2.4%), aged (median: 35y vs. 26y) and lower educational background(junior school degree or below). And 96.7% of local CRF01_AE cases were related to HIV strains, which were reported to circulate in Northeast China and in the MSM population. 【Conclusion】 HIV-1 among Dalian blood donors had unique molecular epidemiology and the trends of 07_BC increasing and 01_AE decreasing lagged behind the overall national data. Donor education on blood safety and consultation services to high risk group before donation still need improvement.

Genomic epidemiology analysis of Enterobacter hormaechei subsp. hoffmannii / 中华检验医学杂志

Objectives:To investigate the genetic characteristics of the blaNDM-1-carrying plasmid of the multidrug resistant Enterobacter hormaechei subsp. hoffmannii clinical isolate C37, and constructing a phylogenetic tree of the 66 publicly available genomes of the Enterobacter hormaechei subsp. hoffmannii to explore its global epidemic situation. Methods:Carbapenem-resistant Enterobacter cloacae complex (CRECC) strains isolated from the First Affiliated Hospital of Sun Yat-sen University from August 2014 to August 2021 were collected. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rDNA Sanger sequencing were used for species identification. Micro broth dilution method was used for antibacterial susceptibility test. The polymerase chain reaction (PCR) was used to detect the β-lactamase resistance gene and plasmid-mediated quinolone resistance (PMQR) gene carried by the C37 strain. The conjugation experiment was used to confirm the conjugative metastasis of the resistance genes in C37 strain. Whole genome of the C37 strain was sequenced. Core genome was extracted and the phylogenetic analysis of 66 publicly available Enterobacter hormaechei subsp. hoffmannii was performed. Results:Enterobacter hormaechei subsp. hoffmannii C37 strain is resistant to third-generation cephalosporins, carbapenems, aminoglycosides and quinolones, and carries blaACT-5, blaNDM-1, qnrA1, aac(6′)-Ib-cr, oqxAB, fosA, dfrA15 and other resistance genes, as well as IncX3, IncX4, IncFIB and IncFII plasmids. Multilocus sequence typing (MLST) analysis showed that C37 strain belongs to the ST78 type of Enterobacter cloacae complex (ECC). Conclusions:ST78 type Enterobacter hormaechei subsp. hoffmannii is closely related to the spread of carbapenem resistance genes. It is a potential high-risk clone to spread carbapenem resistance genes. The prevalence and trends of ST78 type Enterobacter hormaechei subsp. Hoffmannii should be monitored.

Progress in genetic epidemiology of gestational diabetes mellitus / 中华围产医学杂志

Gestational diabetes mellitus poses a substantial threat to the short- and long-term health of women and their offspring. Previous studies have identified a number of genetic risk factors for gestational diabetes through candidate gene strategy and whole genome studies. Many of these identified genetic variations have also been proved to be associated with type 2 diabetes, abnormal glycometabolism as well as insulin secretion and resistance. This article reviews the recent progress in the genetic epidemiology of gestational diabetes mellitus.

Estructura genética de cepas de Mycobacterium tuberculosis farmacorresistentes en Perú con base en haplotipos obtenidos de un ensayo de sonda lineal / Genetic structure of drug-resistant strains of Mycobacterium tuberculosis in Peru based on haplotypes obtained from a linear probe assay

RESUMEN Objetivo. Determinar la estructura genética de las cepas drogorresistentes de Mycobacterium tuberculosis que circularon en todo el Perú durante los años 2011-2015 a través de haplotipos obtenidos de un ensayo con sondas en línea. Materiales y métodos. Se analizaron 6589 muestras que ingresaron al Instituto Nacional de Salud para el diagnóstico rutinario mediante el ensayo GenoType® MTBDRplus v2, durante el periodo de estudio. Se crearon haplotipos resistentes mediante la concatenación de 21 sitios polimórficos de los genes evaluados por el ensayo con sondas en línea, y se realizó el análisis de asociación con fenotipos obtenidos por el método de proporciones agar 7H10. Resultados. Las mutaciones de mayores frecuencias fueron: rpoB S531L (55,4%) y rpoB D516V (18,5%) para la resistencia a rifampicina, y katG S315T (59,5%) e inhA c-15t (25,7%) para la resistencia a isoniacida. Se obtuvieron 13 haplotipos representativos (87,8% de muestras analizadas) de los cuales seis correspondieron al genotipo multidrogorresistente, cuatro al genotipo monorresistente a isoniacida y tres al genotipo monorresistente a rifampicina. Dieciocho departamentos, y la provincia del Callao, presentaron una alta diversidad haplotípica; cuatro presentaron moderada diversidad y dos presentaron baja diversidad. Conclusiones. Existe una alta diversidad haplotípica en la mayoría de los departamentos, además de una concentración de las cepas de Mycobacterium tuberculosis drogorresistentes en las ciudades de Lima y Callao. Asimismo, las cepas de Mycobacterium tuberculosis con perfil drogorresistente que circulan en el Perú contienen principalmente los marcadores genéticos de mayor prevalencia a nivel mundial asociados con la resistencia frente a rifampicina e isoniacida.

ABSTRACT Objective. To determine the genetic structure of drug-resistant strains of Mycobacterium tuberculosis that circulated throughout Peru during the years 2011-2015, by using haplotypes obtained from a line probe assay. Materials and methods. A total of 6589 samples that were admitted to the Instituto Nacional de Salud for routine diagnosis using the GenoType® MTBDRplus v2 assay were analyzed during the study period. Resistant haplotypes were created by concatenating 21 polymorphic sites of the evaluated genes using the line probe assay; and the association analysis was carried out with phenotypes obtained by the 7H10 agar ratio method. Results. The most frequent mutations were: rpoB S531L (55.4%) and rpoB D516V (18.5%) for rifampicin resistance, and katG S315T (59.5%) and inhA c-15t (25.7%) for isoniazid resistance. We obtained 13 representative haplotypes (87.8% of analyzed samples), 6 corresponded to the multidrug-resistant genotype, 4 to the isoniazid mono-resistant genotype and 3 to the rifampicin mono-resistant genotype. Eighteen regions and the province of Callao showed high haplotype diversity; four showed moderate diversity and two showed low diversity. Conclusions. Most regions showed high haplotype diversity; in addition, most drug-resistant strains of Mycobacterium tuberculosis were concentrated in the cities of Lima and Callao. Likewise, drug-resistant Mycobacterium tuberculosis strains circulating in Peru mainly contain the genetic markers with the highest prevalence worldwide, which are associated with resistance to rifampicin and isoniazid.