Epidemiological characteristics and antiseptic resistance gene detection of Pseudomonas aeruginosa in children in Suzhou, Jiangsu Province / 中国热带医学

@#Abstract: Objective To investigate the clinical distribution characteristics, drug resistance trends and the carrying of antiseptic resistance gene of Pseudomonas aeruginosa infection in children in Suzhou, in order to provide theoretical basis for the prevention and treatment of Pseudomonas aeruginosa infection in children. Methods The clinical distribution characteristics and drug resistance trends of Pseudomonas aeruginosa isolated from Children's Hospital of Soochow University from 2016 to 2021 were retrospectively analyzed. Forthermore, 101 strains of Pseudomonas aeruginosa were randomly selected to detect the expression of 9 antiseptic resistance genes (qacEΔ1-sul1, qacE, qacEΔ1, qacG, sugE(p), sugE©, emrE, ydgE, ydgF) by polymerase chain reaction. Results Pseudomonas aeruginosa in Soochow University Children's Hospital was mainly isolated from respiratory specimen (47.83%), pus (28.60%) and urine (11.72%); the main departments were intensive care unit(21.45%), general surgery department (15.71%) and respiratory department (12.31%). Patients were mainly aged from 1 month to 1 year old and older than 6 years old (34.31% and 25.38%). The top three drug resistance rates of Pseudomonas aeruginosa were imipenem (11.25%), aztreonam (9.26%) and meropenem (8.02%). Among the 853 strains of Pseudomonas aeruginosa, the drug-resistant strains were mainly from the intensive care unit (58/183), hematology department (33/91), neonatology department (31/96), and there were 57 strains of multi-drug-resistant strains with the detection rate of 6.68%. There were 98 strains (11.49%) of Carbapenem resistant Pseudomonas aeruginosa, and the annual detection rates were 22.06%, 8.40%, 3.60%, 5.67%, 9.85% and 17.20%, respectively. Among the 9 antiseptic resistance genes, the carrying rate of ydgF, sugE© and qacE was 98.02%, 94.06% and 0 respectively. Conclusion Pseudomonas aeruginosa has high resistance to some drugs, so attention should be paid to rational drug use. The carriage rates of of two antiseptic resistance genes exceeded 90%, indicating the need to strengthen research on the mechanism of antiseptic resistance research and rational use of disinfectants

Research on the sensitivity of Streptococcus agalactiae to omadacycline / 中国热带医学

@#Abstract: Objective　To investigate the antimicrobial activity of omadacycline (OMC) against clinical Streptococcus agalactiae (GBS) isolates, as well as its relationship with biofilm formation, resistance genes and virulence genes. Methods　A total of 136 strains of Streptococcus agalactiae isolated from Shenzhen Nanshan People's Hospital between 2015 to 2020. The minimum inhibitory concentration (MIC) of OMC against Streptococcus agalactiae was determined by broth microdilution. Crystal violet staining was used to detect the biofilm formation ability of GBS. Resistance genes (tetM, tetO, tetK, ermB, OptrA) and virulence genes (cpsⅢ, bca, fbsA, cpsA, scpB) were investigated by polymerase chain reaction (PCR). Results　Among the 136 clinical isolates of GBS, 20 strains (14.7%) were resistant to OMC, 64 (47.1%) were intermediate, and 52 (38.2%) were sensitive. Fifty-seven strains (41.9%) were biofilm-positive, 20 of which (35.1%) were sensitive to OMC. Seventy-nine strains (58.1%) were biofilm-negative, 32 of which (40.5%) were susceptible to OMC. There was a statistically significant difference in the sensitivity rates between the two groups of strains (χ2=63.062, P<0.001), but there was no significant difference in the sensitivity of OMC among the biofilm-positive strains (Fisher's exact test, P=0.824). The resistance rates of tetM, tetO, ermB and OptrA positive strains were higher than those of negative strains, while tetK was opposite. The presence of tetM (Z=0.815, P=0.415), tetO (Z=0.151, P=0.88), tetK (Z=0.567, P=0.571), ermB (Z=1.198, P=0.231) resistance genes in Streptococcus agalactiae had no significant impact on the sensitivity of OMC. However, the presence of the OptrA resistance gene showed a statistically significant effect on the sensitivity of OMC (Z=2.913, P=0.004). The virulence factors cpsⅢ, bca, fbsA, cpsA and scpB were all detected at a rate higher than 50%. The presence of the virulence genes cpsⅢ (Z=0.222, P=0.824), bca (Z=0.141, P=0.888), fbsA (Z=0.813, P=0.416), and cpsA (Z=1.615, P=0.106) in Streptococcus agalactiae had no significant impact on the sensitivity of OMC. However, there was a significant inter-group difference in the scpB virulence gene (Z=2.844, P=0.004), but the rank mean values and resistance rates of scpB-positive strains were lower than those of the negative strains. Conclusions　The formation of biofilm in Streptococcus agalactiae reduces its sensitivity to OMC, but there was no significant difference in the sensitivity to OMC among the biofilm-positive strains. The presence of resistance genes tetM, tetO, tetK, ermB, and virulence genes cpsⅢ, bca, fbsA, cpsA, scpB in Streptococcus agalactiae is not associated with OMC resistance, but the presence of the resistance gene OptrA is correlated with OMC resistance..

Genotyping Characteristics of Human Fecal Escherichia coli and Their Association with Multidrug Resistance in Miyun District, Beijing / 生物医学与环境科学（英文）

OBJECTIVE@#To explore the genotyping characteristics of human fecal Escherichia coli( E. coli) and the relationships between antibiotic resistance genes (ARGs) and multidrug resistance (MDR) of E. coli in Miyun District, Beijing, an area with high incidence of infectious diarrheal cases but no related data.@*METHODS@#Over a period of 3 years, 94 E. coli strains were isolated from fecal samples collected from Miyun District Hospital, a surveillance hospital of the National Pathogen Identification Network. The antibiotic susceptibility of the isolates was determined by the broth microdilution method. ARGs, multilocus sequence typing (MLST), and polymorphism trees were analyzed using whole-genome sequencing data (WGS).@*RESULTS@#This study revealed that 68.09% of the isolates had MDR, prevalent and distributed in different clades, with a relatively high rate and low pathogenicity. There was no difference in MDR between the diarrheal (49/70) and healthy groups (15/24).@*CONCLUSION@#We developed a random forest (RF) prediction model of TEM.1 + baeR + mphA + mphB + QnrS1 + AAC.3-IId to identify MDR status, highlighting its potential for early resistance identification. The causes of MDR are likely mobile units transmitting the ARGs. In the future, we will continue to strengthen the monitoring of ARGs and MDR, and increase the number of strains to further verify the accuracy of the MDR markers.

Epidemiologic and antibiotic resistance profile and detection of meca gene in Staphylococcus spp. isolates from dog-owning veterinary students / Perfil epidemiológico e de resistência a antibióticos e detecção do gene meca em Staphylococcus spp. isolados de estudantes veterinários proprietários de cães / Perfil de resistencia epidemiológica y antibiótica y detección de género meca en Staphylococcus spp. estudiantes veterinarios aislados de perros

The maintenance of pets as reservoirs of multiresistant bacteria and the transmission of microorganisms such as Staphylococcus spp. between animals and humans can affect the effectiveness of antimicrobials in human medicine. The aim of this study was to detect risk factors, evaluate the phenotypic profile of antimicrobial resistance and detect the mecA gene in Staphylococcus spp. isolated from the nasal cavity of students of veterinary medicine who own dogs. This is a field survey where 35 nasal swab samples were collected to isolate Staphylococcus spp. The antimicrobial resistance of the isolates and the classification according to the multidrug resistance profile (MDR) were determined. The presence of the mecA gene was investigated in isolates with resistance to oxacillin. In addition, the research subjects answered a questionnaire about behavior towards the dog and hygiene habits to identify risk variables for developing antimicrobial resistance. The antimicrobials tested were ampicillin, penicillin, oxacillin, cephalothin, clindamycin, gentamicin, erythromycin, enrofloxacin, and tetracycline. 92.9% of coagulase-positive staphylococci (CoPS) and 45% of coagulase-negative staphylococci (CoNS) were resistant to the beta-lactam class, and 28.6% of CoPS and 45% of CoNS showed MDR profile. Three isolates were classified as resistant to oxacillin, and the mecA gene was detected in 100% of these isolates. About half of the individuals used antimicrobials in the last 12 months (52.9%), and 75% used amoxicillin, which could explain the high antimicrobial resistance profile. Dog owners harbor Staphylococcus spp. with high resistance to beta-lactam antimicrobials and a multi-resistance profile, representing a unique One Health problem.

A manutenção de pets como reservatórios de bactérias multirresistentes e a transmissão de microrganismos como Staphylococcus spp. entre animais e humanos podem afetar a eficácia de antimicrobianos na medicina humana. O objetivo deste estudo foi detectar fatores de risco, avaliar o perfil fenotípico de resistência antimicrobiana e detectar o gene mecA em Staphylococcus spp. isolados da cavidade nasal de estudantes de medicina veterinária proprietários de cães. Trata-se de pesquisa de campo onde 35 amostras de swab nasal foram coletadas para isolar Staphylococcus spp. A resistência antimicrobiana e a classificação segundo o perfil de multirresistência (MDR) dos isolados foram determinadas. A presença do gene mecA foi investigada em isolados resistentes à oxacilina. Os estudantes responderam a um questionário sobre comportamento em relação ao cão e hábitos de higiene para identificar variáveis de risco para o desenvolvimento de resistência antimicrobiana. Foram testados os antimicrobianos ampicilina, penicilina, oxacilina, cefalotina, clindamicina, gentamicina, eritromicina, enrofloxacina e tetraciclina. 92,9% dos estafilococos coagulase-positivos (CoPS) e 45% dos estafilococos coagulase-negativos (CoNS) foram resistentes à classe dos beta- lactâmicos e 28,6% CoPS e 45% CoNS apresentaram perfil MDR. Três isolados foram classificados como resistentes à oxacilina e o gene mecA foi detectado em 100% destes isolados. Mais da metade dos indivíduos fez uso de antimicrobiano nos últimos 12 meses (52,9%), 75% fizeram uso de amoxicilina, o que poderia explicar o alto perfil de resistência antimicrobiana. Os donos de cães abrigam Staphylococcus spp. com alta resistência aos antimicrobianos beta-lactâmicos e apresentam MDR, o que representa um problema de saúde única.

El mantenimiento de las mascotas como reservorios de bacterias multiresistentes y la transmisión de microorganismos como Staphylococcus spp. entre animales y seres humanos pueden afectar a la eficacia de los antimicrobianos en la medicina humana. El objetivo de este estudio fue detectar factores de riesgo, evaluar el perfil fenotípico de la resistencia antimicrobiana y detectar el gen meccaA en Staphylococcus spp. aislado de la cavidad nasal de estudiantes veterinarios dueños de perros. Se trata de una investigación de campo en la que se recogieron 35 muestras de hisopo nasal para aislar Staphylococcus spp. Se determinó la resistencia antimicrobiana y la clasificación de los aislados por perfil de multiresistencia (MDR). La presencia del gen de la mecaA se ha investigado en aislados resistentes a oxacilina. Los estudiantes respondieron a un cuestionario sobre comportamiento de perros y hábitos de higiene para identificar variables de riesgo para el desarrollo de resistencia antimicrobiana. Se han estudiado antimicrobianos como ampicilina, penicilina, oxacilina, cefalotina, clindamicina, gentamicina, eritromicina, enrofloxacina y tetraciclina. El 92,9% de los estafilococos coagulasa-positivos (CoPS) y el 45% de los estafilococos coagulasa- negativos (CoNS) fueron resistentes a la clase beta-lactam y el 28,6% de los CoPS y el 45% de los CoNS tenían un perfil de MDR. Se clasificaron tres aislados como resistentes a la oxacilina y se detectó el gen de la mecaA en el 100% de estos aislamientos. Más de la mitad de los individuos utilizaron antimicrobianos en los últimos 12 meses (52,9%), el 75% utilizó amoxicilina, lo que podría explicar el alto perfil de resistencia antimicrobiana. Los dueños de perros albergan Staphylococcus spp. con alta resistencia a los antimicrobianos beta-lactámicos y tienen MDR, lo que representa un único problema de salud.

Antibióticos innovadores contra la farmacorresistencia bacteriana obtenido por tecnología de edición genética CRISPR/Cas9 / Innovative antibiotics against bacterial drug resistance obtained by CRISPR/cas9 gene editing technology

Introducción: El aumento de la resistencia a los antimicrobianos constituye actualmente una peligrosa amenaza para la salud. Ante este problema global de falta de antimicrobianos, es perentorio intervenir de forma coordinada e idear fórmulas para incentivar la investigación a nivel internacional. Objetivo: Realizar una revisión actualizada sobre las causas y mecanismos de la resistencia a los antibióticos y la adaptación del sistema CRISPR/Cas para el desarrollo de innovadores antimicrobianos como parte esencial de una estrategia altamente específica en el tratamiento de infecciones producidas por bacterias resistentes. Métodos: Se realizó una revisión documental, se empleó la bibliografía nacional e internacional especializada publicada en los últimos 5 años. Se utilizó el motor de búsqueda Google Académico y se consultaron artículos de libre acceso en las bases de datos Pubmed, SciELO, LILACS, CUMED y HINARI, en el período comprendido entre marzo de 2020 hasta el mes de enero de 2021. Se revisaron un total de 41 artículos. Las consultas se hicieron en inglés y español. Para la búsqueda se tuvo en cuenta las palabras clave: eligobióticos; resistencia a antibióticos; CRISPR/Cas. Resultados: La evidencia recopilada sustenta que muchas enfermedades son inducidas por alteraciones del equilibrio de la microbiota humana y la técnica de edición genética CRISPR/Cas permitirá el desarrollo de novedosos antibióticos como los eligobióticos que eliminarán las bacterias patógenas multirresistentes y dejarán intacto el microbioma. Conclusiones: el esclarecimiento de los enigmas de la microbiota y su diseño con terapia génica permitirán el progreso de innovadores antibióticos con empleo del sistema CRISPR/Cas que ineludiblemente modificarán la práctica médica para siempre(AU)

Introduction: The increase in antimicrobial resistance is currently a dangerous threat to health. Faced with this global problem of lack of antimicrobials, it is imperative to intervene in a coordinated manner and devise formulas to encourage research at the international level. Objective: To review on the update causes and mechanisms of antibiotic resistance and the adaptation of CRISPR/Cas system for the development of innovative antimicrobials as an essential part of a highly specific strategy in the treatment of infections caused by resistant bacteria. Methods: A documentary review was carried out in the specialized national and international bibliography published in the last 5 years. Google Scholar search engine was used and free access articles were consulted in Pubmed, SciELO, LILACS, CUMED and HINARI databases, from March 2020 to January 2021. A total of 41 articles were retrieved. The consultations were made in English and Spanish. For the search, we took into account the keywords eligobiotics, antibiotic resistance, CRISPR/Cas. Results: The reviewed evidence supports that many diseases are induced by alterations in the balance of the human microbiota; and CRISPR/Cas gene editing technique will allow the development of novel antibiotics such as eligobiotics that will eliminate multi-resistant pathogenic bacteria and leave the microbiome intact. Conclusions: The clarification of the enigmas of the microbiota and its design with gene therapy will allow the progress of innovative antibiotics using CRISPR/Cas system that will inevitably change medical practice forever(AU)

High Throughput Sequencing in Antimicrobial Resistance-the State of the Art / 中国生物化学与分子生物学报

Antimicrobial resistance (AMR) is one of the greatest concerns for human health globally. Developing rapid and accurate methods to identify and characterize AMR is critical to improve patient outcome and limit the spread of antibiotic resistance. High throughput sequencing allows for high-throughput massively sequencing of thousands to billions of DNA fragments independently and simultaneously being used to identify AMR. The 3 main applications of high throughput sequencing in AMR include whole genome sequencing (WGS), targeted NGS (tNGS) and metagenomics NGS (mNGS). The sequencing platforms include the second sequencing platforms (Illumina, Ion Torrent, BGIseq) and the third sequencing platforms (Pacific Biosciences, Oxford Nonopore). The computational prediction of AMR depends largely on the maturation of well-curated gene databases of antimicrobial resistance. Generalized, specialized and hidden Markov model-based databases have been developed and updated continuously. We highlighted the high throughput sequencing technologies, computational methods, platforms and AMR databases used in antimicrobial resistance studies.

Prevention and control of antimicrobial resistance using CRISPR-Cas system: a review / 生物工程学报

Bacterial multi-drug resistance (MDR) is a global challenge in the fields of medicine and health, agriculture and fishery, ecology and environment. The cross-region spread of antibiotic resistance genes (ARGs) among different species is one of the main cause of bacterial MDR. However, there is no effective strategies for addressing the intensifying bacterial MDR. The CRISPR-Cas system, consisting of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated proteins, can targetedly degrade exogenous nucleic acids, thus exhibiting high application potential in preventing and controlling bacterial MDR caused by ARGs. This review briefly introduced the working mechanism of CRISPR-Cas systems, followed by discussing recent advances in reducing ARGs by CRISPR-Cas systems delivered through mediators (e.g. plasmids, bacteriophages and nanoparticle). Moreover, the trends of this research field were envisioned, providing a new perspective on preventing and controlling MDR.

Root canal microbiota as an augmented reservoir of antimicrobial resistance genes in type 2 diabetes mellitus patients

Abstract Antimicrobial resistance is a global public health problem. Root canal microbiota associated with apical periodontitis represents a well-known reservoir of antimicrobial resistance genes (ARGs). However, the effect of type 2 diabetes mellitus (T2DM) in this reservoir is unknown. This study aimed to establish if root canal microbiota associated with apical periodontitis in T2DM patients is an augmented reservoir by identifying the prevalence of nine common ARGs and comparing it with the prevalence in nondiabetic patients. Methodology This cross-sectional study included two groups: A T2DM group conformed of 20 patients with at least ten years of living with T2DM and a control group of 30 nondiabetic participants. Premolar or molar teeth with pulp necrosis and apical periodontitis were included. A sample was collected from each root canal before endodontic treatment. DNA was extracted, and ARGs were identified by polymerase chain reaction. Results tetW and tetM genes were the most frequent (93.3 and 91.6%, respectively), while ermA was the least frequent (8.3%) in the total population. The distribution of the ARGs was similar in both groups, but a significant difference (p<0.005) was present in ermB, ermC, cfxA, and tetQ genes, being more frequent in the T2DM group. A total of eighty percent of the T2DM patients presented a minimum of four ARGs, while 76.6% of the control group presented a maximum of three. Conclusions Root canal microbiota associated with apical periodontitis in T2DM patients carries more ARGs. Therefore, this pathological niche could be considered an augmented reservoir.

Genotypic evaluation of antimicrobial resistance in Staphylococcus spp. isolated from bovine clinical mastitis / [Avaliação genotípica da resistência antimicrobiana em Staphylococcus spp. isolados de mastite clínica bovina]

Bovine clinical mastitis caused by Staphylococcus spp. is a serious and widespread disease in the world of dairy farming. Antimicrobial therapy is of fundamental importance in the prevention and treatment of infectious mastitis, but the indiscriminate use of antimicrobials acts as a determining factor for the spread of the disease. The present study evaluated the resistance profiles of 57 Staphylococcus spp. isolated from bovine clinical mastitis to beta-lactams and gentamicin, relating characteristics of phenotype (in vitro susceptibility tests) and genotype (detection and expression of genes encoding resistance - mecA, mecALGA251, blaZ, femA, femB, and aacA-aphD - using PCR and RT-PCR, respectively). One or more genes coding for resistance to different antimicrobials were detected in 50 Staphylococcus spp. isolates. The femA and femB genes were the most frequent (75.4% for both). The observed expression of the genes was as follows: blaZ (60%), femA (39.5%), aacA-aphD (50%), femB (32.6%), mecA (8.3%), and mecALGA251 (0%). Considering the relevance of the genus Staphylococcus to bovine mastitis, this study aimed to elucidate aspects regarding the genotypic and phenotypic profiles of these microorganisms so as to contribute to the development of effective strategies for mastitis control.(AU)

A mastite clínica bovina causada por Staphylococcus spp. é uma doença grave e generalizada no mundo da pecuária leiteira. A terapia antimicrobiana é de fundamental importância na prevenção e no tratamento da mastite infecciosa, mas o uso indiscriminado de antimicrobianos atua como fator determinante para a disseminação da doença. O presente estudo avaliou os perfis de resistência de 57 Staphylococcus spp. isolados de mastite clínica bovina em relação ao uso de betalactâmicos e gentamicina, relacionando características do fenótipo (testes de suscetibilidade in vitro) e genótipo (detecção e expressão de genes que codificam resistência - mecA, mecALGA251, blaZ, femA, femB, e aacA-aphD - usando PCR e RT-PCR, respectivamente). Um ou mais genes que codificam resistência a diferentes antimicrobianos foram detectados em 50 Staphylococcus spp. isolados. Os genes femA e femB foram os mais frequentes (75,4% para ambos). A expressão observada dos genes foi a seguinte: blaZ (60%), femA (39,5%), aacA-aphD (50%), femB (32,6%), mecA (8,3%) e mecALGA251 (0%). Considerando-se a relevância do gênero Staphylococcus para a mastite bovina, este estudo teve como objetivo elucidar aspectos referentes aos perfis genotípico e fenotípico desses microrganismos, a fim de contribuir para o desenvolvimento de estratégias eficazes para o controle da mastite.(AU)

Environmental risks of antibiotics in soil and the related bioremediation technologies / 生物工程学报

Antibiotics are widely used and prevalently distributed in the environment. The issue of antibiotic resistance genes has posed a huge threat to the global public health. Soil is an important sink of antibiotics in the environment. Antibiotic exposure may introduce adverse effects on soil organisms, and bring indirect but potential risks to human health. Therefore, it is urgent to take actions to remediate antibiotics-contaminated soil. This review summarized effects of antibiotics on phenotype growth of plants, physiological characteristics and community structure of animals, composition and structure of microbial communities, and transmission of antibiotic resistance genes among organisms in soil. Additionally, the potential and prospects of employing antibiotic-resistant soil plants, animals, microorganisms, and their combinations to treat antibiotics-contaminated soil were illustrated. Last but not least, the unaddressed issues in this area were proposed, which may provide insights into relevant research directions in the future.

Expression of Pinellia ternata leaf agglutinin under rolC promoter confers resistance against a phytophagous sap sucking aphid, Myzus persicae

BACKGROUND: Piercing/sucking insect pests in the order Hemiptera causes substantial crop losses by removing photoassimilates and transmitting viruses to their host plants. Cloning and heterologous expression of plantderived insect resistance genes is a promising approach to control aphids and other sap-sucking insect pests. While expression from the constitutive 35S promoter provides broad protection, the phloem-specific rolC promoter provides better defense against sap sucking insects. The selection of plant-derived insect resistance genes for expression in crop species will minimize bio-safety concerns. RESULTS: Pinellia ternata leaf agglutinin gene (pta), encodes an insecticidal lectin, was isolated and cloned under the 35S and rolC promoters in the pGA482 plant transformation vector for Agrobacterium-mediated tobacco transformation. Integration and expression of the transgene was validated by Southern blotting and qRT-PCR, respectively. Insect bioassays data of transgenic tobacco plants showed that expression of pta under rolC promoter caused 100% aphid mortality and reduced aphid fecundity up to 70% in transgenic tobacco line LRP9. These results highlight the better effectivity of pta under rolC promoter to control phloem feeders, aphids. CONCLUSIONS: These findings suggested the potential of PTA against aphids and other sap sucking insect pests. Evaluation of gene in tobacco under two different promoters; 35S constitutive promoter and rolC phloemspecific promoter could be successfully use for other crop plants particularly in cotton. Development of transgenic cotton plants using plant-derived insecticidal, PTA, would be key step towards commercialization of environmentally safe insect-resistant crops.

Resistencia antibiótica: el papel del hombre, los animales y el medio ambiente / Antibiotic resistance: the role of man, animals and the environment

RESUMEN Los microorganismos, especialmente las bacterias, están distribuidos por todo el mundo, desde el suelo, los mares y los ríos hasta el sistema digestivo de los animales y los seres humanos; por lo tanto, las bacterias mantienen una interacción constante con los compuestos utilizados por los seres humanos y los animales como los antibióticos, y con otros microorganismos que pueden ser de la misma especie o de diferentes géneros taxonómicos; esta interacción podría dar lugar a una presión selectiva sobre las bacterias en el medio ambiente y promover el intercambio de material genético, lo que llevaría a una propagación global de la resistencia a los antibióticos y a una afectación mundial de la salud. En este contexto, esta revisión tiene por objeto ofrecer una visión general del papel de los seres humanos, los animales y el medio ambiente en la resistencia bacteriana, con énfasis en los procesos en el suelo y los medios acuáticos y los efectos sobre la salud humana.

ABSTRACT Microorganisms, especially bacteria, are distributed throughout the world, from the soil, seas and rivers to the digestive system of animals and humans. Therefore, the bacteria maintain a constant interaction with compounds used by humans and animals, such as antibiotics, and with other microorganisms that may be of the same species or of different taxonomic genera. In addition, this interaction could lead to selective pressure on bacteria in the environment and promote the exchange of genetic material, which would allow to a global spread of antibiotic resistance and thus a worldwide affectation on health. In this context, the present review aims to provide an overview of the role of humans, animals and the environment in bacterial resistance, with emphasis on soil and aquatic processes and effects on human health.

Characteristics of virulence, resistance and genetic diversity of strains of Salmonella Infantis isolated from broiler chicken in Brazil / Características de virulência, resistência e diversidade genética de estirpes de Salmonella Infantis isoladas de frangos de corte no Brasil

Salmonella Infantis is frequently associated with human infections worldwide and is transmitted by consumption of contaminated foods, particularly those of animal origin, especially the chicken meat. We aimed to evaluate virulence characteristics, antimicrobial resistance and the genetic similarity of 51 strains of S. Infantis isolated from samples of poultry origin. The strains were isolated from 2009 to 2010 in a company with full cycle of broiler's production in the state of São Paulo, Brazil. The antimicrobial susceptibility test was performed and, by PCR, we evaluated the presence of the genes lpfA (hem-adhesion), agfA (hem-biofilm) and sefA (hem-adhesion) and resistance genes to beta-lactams (blaTEM, blaSHV, bla CTX-M and blaAmpC ). The phylogenetic relationship was determined by RAPD-PCR method. Among the drugs tested, the highest percentages of resistance were to amoxicillin (35.3%) and to sulfonamide (15.7%). Eleven antimicrobial resistance patterns were identified (A1 to A11), none of them presented a multiresistance profile (> 3 antimicrobials classes). There was 100% of positivity for the agfA gene, 92.2% for the lpfA gene, and no strain presented the sefA gene. Most of the isolates showed similarities in virulence potential, since they were simultaneously positive for two studied genes, agfA and lpfA (92.2%, 47/51). Of the 18 (35.3%) strains resistant to antimicrobials of the β-lactam class, 10 (55.5%) were positive to blaAmpC gene, five (27.8%) for blaCTX-M , two (11.1%) to blaSHV and no strain presented the blaTEM gene. The phylogenetic evaluation has shown the presence of five clusters (A, B, C, D and E) with similarity greatSalmonella Infantis is frequently associated with human infections worldwide and is transmitted by consumption of contaminated foods, particularly those of animal origin, especially the chicken meat. We aimed to evaluate virulence characteristics, antimicrobial resistance and the genetic similarity of 51 strains of S. Infantis isolated from samples of poultry origin. The strains were isolated from 2009 to 2010 in a company with full cycle of broiler's production in the state of São Paulo, Brazil. The antimicrobial susceptibility test was performed and, by PCR, we evaluated the presence of the genes lpfA (hem-adhesion), agfA (hem-biofilm) and sefA (hem-adhesion) and resistance genes to beta-lactams (blaTEM, blaSHV, bla CTX-M and blaAmpC ). The phylogenetic relationship was determined by RAPD-PCR method. Among the drugs tested, the highest percentages of resistance were to amoxicillin (35.3%) and to sulfonamide (15.7%). Eleven antimicrobial resistance patterns were identified (A1 to A11), none of them presented a multiresistance profile (> 3 antimicrobials classes). There was 100% of positivity for the agfA gene, 92.2% for the lpfA gene, and no strain presented the sefA gene. Most of the isolates showed similarities in virulence potential, since they were simultaneously positive for two studied genes, agfA and lpfA (92.2%, 47/51). Of the 18 (35.3%) strains resistant to antimicrobials of the ß-lactam class, 10 (55.5%) were positive to blaAmpC gene, five (27.8%) for blaCTX-M , two (11.1%) to blaSHV and no strain presented the blaTEM gene. The phylogenetic evaluation has shown the presence of five clusters (A, B, C, D and E) with similarity greater than 80%, and three distinct strains which were not grouped in any cluster. Cluster B grouped 33 strains, all positive for lpfA and agfA genes, from both, the broiler farming facility and the slaughterhouse, persistent throughout all the study period. This cluster also grouped 18 strains clones with genetic similarity greater than 99%, all isolated in the slaughterhouse. The presence of virulence genes associated with persistent strains clones for a long period, warns to the possibility of S. Infantis to form biofilm, and should be constantly monitored in broilers' production chain, in order to know the profile of the strains that may contaminate the final product and evaluate the hazards that represents to public health.er than 80%, and three distinct strains which were not grouped in any cluster. Cluster B grouped 33 strains, all positive for lpfA and agfA genes, from both, the broiler farming facility and the slaughterhouse, persistent throughout all the study period. This cluster also grouped 18 strains clones with genetic similarity greater than 99%, all isolated in the slaughterhouse. The presence of virulence genes associated with persistent strains clones for a long period, warns to the possibility of S. Infantis to form biofilm, and should be constantly monitored in broilers' production chain, in order to know the profile of the strains that may contaminate the final product and evaluate the hazards that represents to public health.(AU)

Salmonella Infantis é frequentemente associada a infecções humanas no mundo todo sendo transmitida pelo consumo de alimentos contaminados, principalmente aqueles de origem animal, com destaque para a carne de frango. Objetivou-se avaliar características de virulência, resistência antimicrobiana e a similaridade genética de 51 estirpes de S. Infantis isoladas em amostras de origem avícola. As estirpes foram isoladas no período de 2009 a 2010 em uma empresa com ciclo completo de produção de frango de corte, localizada no estado de São Paulo, Brasil. Foi realizado o teste de susceptibilidade antimicrobiana e pela técnica de PCR, foi avaliada a presença dos genes lpfA (fímbria-adesão), agfA (fímbria-biofilme) e sefA (fímbria-adesão) e os genes de resistência aos beta-lactâmicos (bla TEM, blaSHV, blaCTX-M e blaAmpC ). A relação filogenética foi determinada pelo método de RAPD-PCR. Dentre as drogas testadas, os maiores percentuais de resistência foram para amoxacilina com 35,3% e sulfonamida com 15,7%. Onze perfis de resistência aos antimicrobianos foram identificados (A1 a A11), sendo que nenhum deles apresentou perfil de multirresistência (>3 classes de antimicrobianos). Houve 100% de positividade para o gene agfA, 92,2% para o gene lpfA e nenhuma estirpe apresentou o gene sefA. A maioria dos isolados apresentaram semelhanças no potencial de virulência, pois foram positivos simultaneamente para dois genes estudados, agfA e lpfA (92,2% - 47/51). Das 18 (35,3%) estirpes resistentes aos antimicrobianos da classe dos ß-lactâmicos, 10 (55,5%) foram positivas para o gene blaAmpC , cinco (27,8%) para blaCTX-M , duas (11,1%) para blaSHV e nenhuma estirpe apresentou o gene bla TEM . A avaliação filogenética demonstrou a presença de cinco clusters (A, B, C, D e E) com similaridade superior a 80%, e três estirpes distintas que não foram agrupadas em nenhum dos clusters. O cluster B agrupou 33 estirpes, todas positivas para os genes lpfA e agfA, provenientes tanto do aviário quanto do matadouro frigorífico, persistentes durante todo o período do estudo. Este cluster ainda agrupou 18 estirpes clones com similaridade genética superior a 99%, todas isoladas no matadouro frigorífico. A presença dos genes de virulência, associada à persistência das estirpes clones durante um longo período do estudo, alertam para a possibilidade de S. Infantis em formar biofilme, devendo ser constantemente monitorada na cadeia de produção avícola, especialmente no ambiente de abate, de forma a conhecer o perfil das estirpes que podem contaminar o produto final e assim avaliar os perigos que representam para a saúde pública.(AU)

Overview of antibiotic resistance genes database / 生物工程学报

The discovery of antibiotics is a big revolution in human history, and its clinical application has saved countless lives. However, with the widespread and abuse of antibiotics, many pathogens have developed resistance, and even "Super Bacteria" resistance to multiple drugs have evolved. In the arms race between humans and pathogens, humans are about to face a situation where no medicine is available. Research on microbial antibiotic resistance genes, resistance mechanisms, and the spread of resistance has attracted the attention of many scientific researchers, and various antibiotic resistance gene databases and analysis tools have emerged. In this review, we collect the current databases that focus on antibiotics resistance genes, and discuss these databases in terms of database types, data characteristics, antibiotics resistance gene prediction models and the types of analyzable sequences. In addition, a few gene databases of anti-metal ions and anti-biocides are also involved. It is believed that this summary will provide a reference for how to select and use antibiotic resistance gene databases.

Antibiotic resistance of Enterococcus faecalis from persistent endodontic infections / Resistencia antibiótica de Enterococcus faecalis provenientes de infecciones endodónticas persistentes

Enterococci are important nosocomial pathogens due to their intrinsic multiresistance and the acquisition of new antibiotic resistance genes (ARG). Enterococcus faecalis has been shown to be one of the main pathogens in persistent endodontic infections, therefore, the main objective of this study was to evaluate the phenotype and resistance genotype of strains of E. faecalis isolated from teeth with persistent endodontic lesions, to the most commonly prescribed antibiotics in dentistry. Thirteen strains of E. faecalis of different pulsotype were analyzed to evaluate the susceptibility to antibiotics, amoxicillin, amoxicillin/clavulanic acid, tetracycline, erythromycin and metronidazole, using the Epsilometer test (E- test) and the presence of beta-lactamases with nitrocefin test. Finally, the detection of ARG was performed with a molecular polymerase chain reaction (PCR) technique and confirmed by the sequencing of the amplification products. Fisher's exact test was used, using 95 % confidence. Regarding the phenotype of resistance, the evaluated strains, independent of the pulsotype, were totally resistant to the action of metronidazole. Antibiotics with higher minimum inhibitory concentration (MIC) after metronidazole include tetracycline and erythromycin. In contrast, lower MIC are applied to the combination of amoxicillin with clavulanic acid. The nitrocefin test was positive only in one strain. Genotypically, two genetically distant strains isolated from a single patient, presented a genotype of resistance to erythromycin, determined by the presence of the ermB gene. No statistically significant relationship was found between phenotypic resistance and the presence of ARG in relation to erythromycin (p> 0.05). It was concluded that isolates of E. faecalis from persistent endodontic infections showed phenotypes of resistance to several antimicrobial agents, all of which were susceptible to amoxicillin/clavulanic acid. Periodic evaluation of susceptibility to antibiotics is suggested as an important practice for the surveillance of antibiotic resistance in oral strains.

Los enterococos son importantes patógenos nosocomiales debido a su multi resistencia intrínseca y la adquisición de nuevos genes de resistencia a los antibióticos (ARG). Enterococcus faecalis es uno de los principales patógenos en infecciones endodónticas persistentes, por lo tanto, el objetivo principal de este estudio fue evaluar el fenotipo y el genotipo de resistencia de cepas de E. faecalis aisladas de dientes con lesiones endodóncicas persistentes, a los antibióticos comúnmente recetados en odontología. Se analizaron 13 cepas de E. faecalis de diferentes pulsotipos para evaluar la susceptibilidad a los antibióticos, amoxicilina, amoxicilina / ácido clavulánico, tetraciclina, eritromicina y metronidazol, utilizando la prueba de Epsilometría (E-test) y la presencia de beta-lactamasas con prueba de nitrocefina. Finalmente, la detección de ARG se realizó con una técnica molecular de reacción en cadena de la polimerasa (PCR) y se confirmó mediante la secuenciación de los productos de amplificación. Se utilizó la prueba exacta de Fisher, con un 95 % de confianza. En cuanto al fenotipo de resistencia, las cepas evaluadas, independientes del pulsotipo, fueron totalmente resistentes a la acción del metronidazol. Los antibióticos con los valores más altos de concentración mínima inibitoria (CMI) después del metronidazol incluyen tetraciclina y eritromicina. En contraste, las CMI mas bajas se aplican a la combinación de amoxicilina con ácido clavulánico. La prueba de nitrocefina fue positiva solo en una cepa. Genotípicamente, dos cepas distantes genéticamente, aisladas de un mismo paciente fueron positivas para el gen ermB. No se encontró una relación estadísticamente significativa entre la resistencia fenotípica y la presencia de ARG en relación con la eritromicina (p> 0,05). Se concluyó que los aislamientos de E. faecalis de infecciones endodónticas persistentes mostraron fenotipos de resistencia a varios agentes antimicrobianos, todos los cuales fueron susceptibles a amoxicilina / ácido clavulánico. Se sugiere una evaluación periódica de la susceptibilidad a los antibióticos como una práctica importante para la vigilancia de la resistencia a los antibióticos en las cepas orales.

Resistance profile to antimicrobials agents in methicillin-resistant Staphylococcus aureus isolated from hospitals in South Brazil between 2014-2019

Abstract INTRODUCTION: Methicillin-resistant Staphylococcus aureus (MRSA) is a common pathogen causing healthcare-associated infections. Owing to the restricted use of beta-lactams in MRSA infections, non-beta-lactam antimicrobials are required for treatment. However, MRSA can develop resistance mechanisms to non-beta-lactam antimicrobials, which reduces viable treatment options. Here, we evaluated the antimicrobial susceptibility and resistance genes of MRSA isolated from hospitalized patients in South Brazil. METHODS: The antimicrobial susceptibilities of hospital MRSA (217) isolates were determined by disk diffusion or microdilution methods. Additionally, the presence of 14 resistance genes and SCCmec typing was performed by PCR. RESULTS: Among the antimicrobials tested, we observed high erythromycin (74.2%), ciprofloxacin (64.5%), and clindamycin (46.1%) resistance rates and complete susceptibility to linezolid and vancomycin. Seventeen different patterns of MRSA antimicrobial resistance were observed, of which 42.9% represented multidrug resistance. Among erythromycin-resistant MRSA, 53.4%, 45.3%, 37.9%, 13.0%, and 6.8% carried ermA, msrA, msrB, ermC, and ermB genes, respectively. Among clindamycin-resistant MRSA, 83%, 17%, 10%, 4%, and 2% carried ermA, ermC, ermB, linA, and linB genes, respectively. Among gentamicin-resistant MRSA, 96.8%, 83.9%, and 9.7% carried aac(6')/aph(2''), aph(3')-IIIa, and ant(4')-Ia genes, respectively. Among tetracycline-resistant MRSA, 6.5% and 93.5% carried tetK and tetM genes, respectively. Lastly, among trimethoprim/sulfamethoxazole-resistant MRSA, 13.3% and 100% carried dfrA and dfrG genes, respectively. The SCCmec type IV isolates were detected more frequently, whereas the SCCmec type III isolates exhibited higher multidrug resistance. CONCLUSIONS: The study data provides information regarding the MRSA resistance profile in South Brazil that is associated with the clinical conditions of patients and can contribute to clinical decision-making.

Comparison of Treponema pallidum genomes for the prediction of resistance genes

Syphilis is a sexually transmitted infection caused by Treponema pallidum, which is highly prevalent in several countries,including Brazil. The use of bioinformatics’ tools for the identification of resistance genes is an important practice for thestudy of microorganisms, such as T. pallidum. In this study, the complete genomes of 43 strains of T. pallidum, isolatedfrom different countries, were analyzed. A total of 41,514 sequences were obtained, and compared against prokaryoteresistance gene databases using BLASTn, BLASTx and RGI for gene alignment and prediction. From the alignments, itwas possible to identify antibiotic resistance genes for each strain. The genes identified in each comparison were groupedaccording to the antibiotic category in which they show resistance to. The antibiotic-resistant genes related to drugs used totreat syphilis were grouped separately. The in silico tools used have shown to be effective in identifying resistance genes ingenomes of T. pallidum strains. Due to the lack of research and accurate information regarding the antibiotic resistancegenes in T. pallidum, this study serves as a basis for studies in molecular biology whose aim is the identification of thesegenes, besides being a reference to help in the control and treatment of this infection.

Transcriptome profiling of coriander: a dual purpose crop unravels stem gall resistance genes

Stem gall (Protomyces macrosporus Unger), a serious disease that affects leaves, petioles, stems and fruits of coriander (Coriandrum sativum L.) causing heavy loss in yield. Genetic improvement of coriander for stem gall disease is indispensable. Coriander cultivars of stem gall resistance (ACr-1) and susceptible (CS-6) leaf samples were utilized and transcriptome sequenced using Illumina NextSeq500 platform. After trimming low-quality reads and adapter sequences, a total of 49,163,108 and 43,746,120 high-quality reads were retained and further assembly resulted validated transcripts of 59,933 and 56,861. We have predicted 52,506 and 48,858 coding sequences (CDS) of which 50,506 and 46,945 were annotated using NCBInr database. Gene ontology analysis annotated 19,099 and 17,625 terms; pathway analysis obtained 24 different functional pathway categories; signal transduction, transport, catabolism, translation and carbohydrate metabolism pathways etc. were dominated. Differentially expressed genes analysis predicted 13,123 CDS commonly expressed of which 431 and 400 genes were significantly upregulated and downregulated, respectively, in which Rgenes, stress inducible transcription factors such as ERF, NAC, bZIP, MYB, DREB and WRKY and antifungal related genes were predicted. The real-time PCR analysis of HSP20 gene expression in resistance showed upregulation by 10-fold over susceptible sample and 18s used as a housekeeping gene for normalization. The present results provide an insights into various aspects underlying the development of resistance to stem gall in coriander.

Isolation, Incidence and Molecular Characterization of Drug-resistant Escherichia coli of Goat Milk

Background: Goat milk is recognized for its high nutritive profile. The practise of antimicrobials in feeding of animals produces resistance in bacteria. Therefore, the present study was proposed to study the incidence of drug-resistant E. coli from raw goat milk samples and investigate the genes responsible for the resistance. Methods: A total of 250 raw milk samples were obtained from different farms of Taif province, Saudi Arabia. Collected samples were cultured on MacConkey agar. Morphological and biochemical tests were achieved for the identification of isolates. Antimicrobial resistance pattern of E. coli was estimated by the disk diffusion method. The resistance genes tet(A) and tet(B), ere(A), aadA1, blaSHV, aac(3)-IV, sul1, catA1 and cmlA, were examined by PCR. Results: Results of the present study showed that out of the 250 samples examined, 100 (40%) were found to be infected with E. coli. Antimicrobial resistance profile evaluated showed a higher resistance against ceftriaxone (90 %) and ticarcillin (86%), followed by amikacin and cefotaxime (87%), and augmentin and penicillin (85%). Lower percentage was observed for gentamicin (58%), ampicillin (66%), bacitracin (75%) and imipenem (32%). Furthermore, multi-drug resistance was observed in most of the isolates. Among E. coli isolates, 86% gave positive amplicons for the blaSHV gene followed by tet(A) and tet(B) genes (85%). Conclusion: The results suggested a probability of possible public health risk of multi-drug resistance of E. coli strains collecting from raw goat milk samples. Consequently, appropriate handling of goat milk processing is significant to prevent E. coli infection.

Characteristics of etiology and drug and disinfectant resistant genes of Yersinia pestis in natural plague foci of Haixi Prefecture, Qinghai Province / 中华地方病学杂志

Objective To analyze the biological characteristics of Yersinia pestis strains in Haixi Prefecture,Qinghai Province,in order to provide a scientific basis for plague prevention and control in future.Methods Totally 181 strains were separated from variety kinds of host in Haixi Prefecture,Qinghai Province from 1957 to 2011,and these strains were conducted biochemical test,virulence factor evaluation,plasmid analysis,different region (DFR) genotyping,drug and disinfectant resistant genes detection;79 of the 181 strains were examined by toxicity test and classified according to the criteria (minimum lethal dose:MLD≤ 10 000 was velogenic strain,10 000 ＜ MLD ＜ 100 000 was moderate virulence strain,MLD ≥ 100 000 was hypovirulent strain).Results According to six biochemical typing about gelatin candy,rhamnose,maltose,melibiose,glycerin and denitrification,the 181 strains of Yersinia pestis were antique biovar and Qing-Tibet Plateau ecotype.Aproportion of 81.22％ (147/181) of Yersiniapestis strains contained all the four virulence factors (F1,Pst Ⅰ,VW,Pgm).Totally 63.54％ (115/181) of the strains contained 3 kinds of plasmid-6 × 106,45 × 106,and 52 × 106;31.49％ (57/181) of the strains contained 3 kinds of plasmid-6 × 106,45 × 106,and 65 × 106.The strains had 8 genomovars,and were given priority to genomovar 8 (109 strains),secondly,genomovar 32 (33 strains),genomovar 5 (20 strains),genomovar 1b(i4 strains),genomovar 44 (2 strains),genomovar 7 (1 strain),genomovar 37 (1 strain),and genomovar 49 (1 strain).Among the 181 Yersinia pestis strains,strains with genes related to streptomycin resistance,sulfanilamide resistance,beta lactam resistance and disinfectant resistance were not found;and 75 of 79 strains were velogenic strains by toxicity test (MLD ≤ 10 000),accounted for 94.94％ (75/79).Conclusion The strains separated in Haixi Prefecture,Qinghai Province have the characteristics of Qinghai-Tibet Plateau plague's pathogen and have strong toxicity;all strains don't have the characteristics of drug and disinfectant resistance genes.