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Whole-genome sequencing identified three previously unidentified multilocus sequence types of Campylobacter jejuni (ST-12332) and Campylobacter coli (ST-12333 and ST-12663), harboring resistance genes for multiple antimicrobial classes. The sources of isolation highlight the circulation of resistance strains within animals and humans, emphasizing the need for preventive measures.
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BACKGROUND: Understanding the epidemiology of Streptococcus pneumoniae (S. pneumoniae) isolates is important for pneumonia treatment and prevention. This research aimed to explore the epidemiological characteristics of S. pneumoniae isolated from pediatric inpatients and outpatients during the same period. METHODS: S. pneumoniae were isolated from unsterile samples of inpatients and outpatients younger than five years old between March 2013 and February 2014. The serotypes were determined using diagnostic pneumococcal antisera. The resistance of each strain to 13 antibiotics was tested using either the E-test or the disc diffusion method. The Sequence Types (STs) were analyzed via Multilocus Sequence Typing (MLST). RESULTS: The dominant serotypes obtained from inpatients were 19F (32.9 %), 19A (20.7 %), 23F (10.7 %), 6A (10.0 %), and 14 (8.6 %), while those from outpatients were 19F (13.6 %), 23F (12.9 %), 6A (10.0 %), 6B (10.0 %), and 19A (7.9 %). The coverage rates of 13-valent Pneumococcal Conjugate Vaccine (PCV) formulations were high in both groups. The nonsusceptibility to penicillin, cefuroxime, imipenem, erythromycin, and trimethoprim-sulfamethoxazole among the inpatient isolates was 7.1 %, 92.8 %, 65.7 %, 100 %, and 85.0 %, respectively, while that among the outpatient isolates was 0.7 %, 50.0 %, 38.6 %, 96.4 %, and 65.7 %, respectively. There were 45 and 81 STs detected from the pneumococci isolated from inpatients and outpatients, respectively. CC271 was common among both inpatients and outpatients (43.6 % and 14.3 %). CONCLUSIONS: Pneumococcal vaccine-related serotypes are prevalent among both inpatients and outpatients, especially among inpatients, who exhibit more severe antibiotic resistance. Therefore, universal immunization with PCV13 would decrease the hospitalization rate due to S. pneumoniae and the antibiotic resistance rate of S. pneumoniae.
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Antibacterianos , Pacientes Internos , Pruebas de Sensibilidad Microbiana , Tipificación de Secuencias Multilocus , Pacientes Ambulatorios , Infecciones Neumocócicas , Serogrupo , Streptococcus pneumoniae , Humanos , Streptococcus pneumoniae/efectos de los fármacos , Streptococcus pneumoniae/clasificación , Streptococcus pneumoniae/aislamiento & purificación , Streptococcus pneumoniae/genética , Preescolar , Pacientes Ambulatorios/estadística & datos numéricos , Lactante , Antibacterianos/farmacología , Masculino , Femenino , Pacientes Internos/estadística & datos numéricos , Infecciones Neumocócicas/microbiología , Infecciones Neumocócicas/epidemiología , Hospitales Pediátricos , Farmacorresistencia Bacteriana , Beijing/epidemiología , Serotipificación , Vacunas Neumococicas/inmunologíaRESUMEN
Staphylococcus aureus is a common clinical pathogen that causes various human infections. The aim of this study was to investigate the antibiotic susceptibility pattern, molecular epidemiological characteristics, and biofilm formation ability of S. aureus isolates from clinical specimens in Xiangyang and to analyze the correlation among them. A total of 111 non-duplicate S. aureus isolates were collected from the Affiliated Hospital of Hubei University of Arts and Science. All isolates were tested for antibacterial susceptibility. Methicillin-resistant S. aureus (MRSA) was identified by the mecA gene PCR amplification. All isolates were analyzed to determine their biofilm-forming ability using the microplate method. The biofilm-related gene was determined using PCR. SCCmec, MLST, and spa types of MRSA strains were performed to ascertain the molecular characteristics. Among the 111 S. aureus isolates, 45 (40.5%) and 66 (59.5%) were MRSA and MSSA, respectively. The resistance of MRSA strains to the tested antibiotics was significantly stronger than that of MSSA strains. All isolates were able to produce biofilm with levels ranging from strong (28.9%, 18.2%), moderate (62.2%, 62.1%), to weak (8.9%, 19.7%). Strong biofilm formation was observed in MRSA strains than in MSSA strains, based on percentages. There were dynamic changes in molecular epidemic characteristics of MRSA isolates in Xiangyang. SCCmecIVa-ST22-t309, SCCmecIVa-ST59-t437, and SCCmecIVa-ST5-t2460 were currently the main epidemic clones in this region. SCCmecIVa-ST5-t2460 and SCCmecIVa/III-ST22-t309 have stronger antibiotic resistance than SCCmecIVa-ST59-t437 strains, with resistance to 6 ~ 8 detected non-ß-lactam antibiotics. The molecular epidemic and resistance attributes of S. aureus should be timely monitored, and effective measures should be adopted to control the clinical infection and spread of the bacteria.
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Antibacterianos , Biopelículas , Pruebas de Sensibilidad Microbiana , Epidemiología Molecular , Infecciones Estafilocócicas , Staphylococcus aureus , Centros de Atención Terciaria , Biopelículas/crecimiento & desarrollo , Biopelículas/efectos de los fármacos , Humanos , China/epidemiología , Infecciones Estafilocócicas/microbiología , Infecciones Estafilocócicas/epidemiología , Antibacterianos/farmacología , Staphylococcus aureus/efectos de los fármacos , Staphylococcus aureus/genética , Staphylococcus aureus/fisiología , Staphylococcus aureus/aislamiento & purificación , Staphylococcus aureus/clasificación , Staphylococcus aureus Resistente a Meticilina/genética , Staphylococcus aureus Resistente a Meticilina/efectos de los fármacos , Staphylococcus aureus Resistente a Meticilina/aislamiento & purificación , Staphylococcus aureus Resistente a Meticilina/clasificación , Staphylococcus aureus Resistente a Meticilina/fisiología , Femenino , Masculino , Proteínas Bacterianas/genética , Adulto , Farmacorresistencia Bacteriana , Persona de Mediana Edad , Adulto Joven , Adolescente , Tipificación de Secuencias Multilocus , Niño , Anciano , Proteínas de Unión a las PenicilinasRESUMEN
Abstract Background Understanding the epidemiology of Streptococcus pneumoniae (S. pneumoniae) isolates is important for pneumonia treatment and prevention. This research aimed to explore the epidemiological characteristics of S. pneumoniae isolated from pediatric inpatients and outpatients during the same period. Methods S. pneumoniae were isolated from unsterile samples of inpatients and outpatients younger than five years old between March 2013 and February 2014. The serotypes were determined using diagnostic pneumococcal antisera. The resistance of each strain to 13 antibiotics was tested using either the E-test or the disc diffusion method. The Sequence Types (STs) were analyzed via Multilocus Sequence Typing (MLST). Results The dominant serotypes obtained from inpatients were 19F (32.9 %), 19A (20.7 %), 23F (10.7 %), 6A (10.0 %), and 14 (8.6 %), while those from outpatients were 19F (13.6 %), 23F (12.9 %), 6A (10.0 %), 6B (10.0 %), and 19A (7.9 %). The coverage rates of 13-valent Pneumococcal Conjugate Vaccine (PCV) formulations were high in both groups. The nonsusceptibility to penicillin, cefuroxime, imipenem, erythromycin, and trimethoprim-sulfamethoxazole among the inpatient isolates was 7.1 %, 92.8 %, 65.7 %, 100 %, and 85.0 %, respectively, while that among the outpatient isolates was 0.7 %, 50.0 %, 38.6 %, 96.4 %, and 65.7 %, respectively. There were 45 and 81 STs detected from the pneumococci isolated from inpatients and outpatients, respectively. CC271 was common among both inpatients and outpatients (43.6 % and 14.3 %). Conclusions Pneumococcal vaccine-related serotypes are prevalent among both inpatients and outpatients, especially among inpatients, who exhibit more severe antibiotic resistance. Therefore, universal immunization with PCV13 would decrease the hospitalization rate due to S. pneumoniae and the antibiotic resistance rate of S. pneumoniae.
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Acinetobacter baumannii is an opportunistic pathogen responsible for healthcare-associated infections (HAIs) and outbreaks. Antimicrobial resistance mechanisms and virulence factors allow it to survive and spread in the hospital environment. However, the molecular mechanisms of these traits and their association with international clones are frequently unknown in low- and middle-income countries. Here, we analyze the phenotype and genotype of seventy-six HAIs and outbreak-causing A. baumannii isolates from a Mexican hospital over ten years, with special attention to the carbapenem resistome and biofilm formation. The isolates belonged to the global international clone (IC) 2 and the Latin America endemic IC5 and were predominantly extensively drug-resistant (XDR). Oxacillinases were identified as a common source of carbapenem resistance. We noted the presence of the blaOXA-143-like family (not previously described in Mexico), the blaOXA-72 and the blaOXA-398 found in both ICs. A low prevalence of efflux pump overexpression activity associated with carbapenem resistance was observed. Finally, strong biofilm formation was found, and significant biofilm-related genes were identified, including bfmRS, csuA/BABCDE, pgaABCD and ompA. This study provides a comprehensive profile of the carbapenem resistome of A. baumannii isolates belonging to the same pulse type, along with their significant biofilm formation capacity. Furthermore, it contributes to a better understanding of their role in the recurrence of infection and the endemicity of these isolates in a Mexican hospital.
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Dermatophytes are fungi included in the genera Trichophyton, Microsporum, Epidermophyton, Nannizzia, Paraphyton, Lophophyton, and Arthroderma. Molecular techniques have contributed to faster and more precise identification, allowing significant advances in phylogenetic studies. This work aimed to identify clinical isolates of dermatophytes through phenotypic (macro- and micromorphology and conidia size) and genotypic methods (sequences of ITS regions, genes of ß tubulin (BT2), and elongation factor α (Tef-1α)) and determine the phylogenetic relationships between isolates. Ninety-four dermatophyte isolates from Costa Rica, Guatemala, Honduras, Mexico, and the Dominican Republic were studied. The isolates presented macro- and micromorphology and conidia size described for the genera Trichophyton, Microsporum, and Epidermophyton. Genotypic analysis classified the isolates into the genera Trichophyton (63.8%), Nannizzia (25.5%), Arthroderma (9.6%), and Epidermophyton (1.1%). The most frequent species were T. rubrum (26 isolates, 27.6%), T. interdigitale (26 isolates, 27.6%), and N. incurvata (11 isolates, 11.7%), N. gypsea and A. otae (nine isolates, 9.6%), among others. The genotypic methods clarified the taxonomic status of closely related species. For instance, the ITS and BT2 markers of T. rubrum/T. violaceum did not differ but the Tef-1α gene did. On the other hand, the three markers differed in T. equinum/T. tonsurans. Therefore, the ITS, BT2, and Tef-1α genes are useful for typing in phylogenetic analyses of dermatophytes, with Tef-1α being the most informative locus. It should be noted that isolate MM-474 was identified as T. tonsurans when using ITS and Tef-1α, but when using BT2, it was identified as T. rubrum. On the other hand, no significant difference was found when comparing the methods for constructing phylogenies, as the topologies were similar.
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Salmonella Gallinarum (SG) is the causative agent of fowl typhoid (FT), a disease that is harmful to the poultry industry. Despite sanitation and prophylactic measures, this pathogen is associated with frequent disease outbreaks in developing countries, causing high morbidity and mortality. We characterized the complete genome sequence of Colombian SG strains and then performed a comparative genome analysis with other SG strains found in different regions worldwide. Eight field strains of SG plus a 9R-derived vaccine were subjected to whole-genome sequencing (WGS) and bioinformatics analysis, and the results were used for subsequent molecular typing; virulome, resistome, and mobilome characterization; and a comparative genome study. We identified 26 chromosome-located resistance genes that mostly encode efflux pumps, and point mutations were found in gyrase genes (gyrA and gyrB), with the gyrB mutation S464T frequently found in the Colombian strains. Moreover, we detected 135 virulence genes, mainly in 15 different Salmonella pathogenicity islands (SPIs). We generated an SPI profile for SG, including C63PI, CS54, ssaD, SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-6, SPI-9, SPI-10, SPI-11, SPI-12, SPI-13, and SPI-14. Regarding mobile genetic elements, we found the plasmids Col(pHAD28) and IncFII(S) in most of the strains and 13 different prophage sequences, indicating a frequently obtained profile that included the complete phage Gifsy_2 and incomplete phage sequences resembling Escher_500465_2, Shigel_SfIV, Entero_mEp237, and Salmon_SJ46. This study presents, for the first time, the genomic content of Colombian SG strains and a profile of the genetic elements frequently found in SG, which can be further studied to clarify the pathogenicity and evolutionary characteristics of this serotype.
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Salmonelosis Animal , Fiebre Tifoidea , Animales , Colombia/epidemiología , Perfil Genético , Salmonelosis Animal/epidemiología , Salmonella/genética , GenómicaRESUMEN
Salmonella Gallinarum (SG) is a host-restricted enterobacteria and the causative agent of fowl typhoid in poultry. Here, we report the complete genomes of two strains belonging to this serotype. SA68 is a field strain isolated from the livers of dead hen carcasses of a commercial layer farm presenting high mortality located in São Paulo city, Brazil, in 1990. Strain 9R corresponds to a live attenuated SG commercial vaccine. DNA was extracted from pure cultures and subjected to whole genome sequencing (WGS) using the Ion Torrent PGM System. The assemblies reached lengths of 4,657,435 (SA68) and 4,657,471 (9R) base pairs. Complete genomes were deposited in GenBank under the accession numbers CP110192 (SA68) and CP110508 (9R). Both genomes were analyzed and compared in terms of molecular typing, antibiotic resistance genes, virulence genes, Salmonella pathogenic islands (SPIs), insertion sequences and prophages. The data obtained show many similarities in the genetic content, with the exception of the SPI-12 and CS54 pathogenic islands, which are exclusive to the field strain. The information generated will help to understand the virulence differences of field and vaccinal SG strains and can be used to perform evolutionary and epidemiologic studies.
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INTRODUCTION: Neisseria meningitidis is associated with invasive infections causing high mortality rates. The objective of this study was to describe the population structure of Colombian invasive isolates with ST-9493, a potentially emerging clonal group in the country. METHODS: The complete genomes of 34 invasive isolates of serogroup B with ST-9493 and its variants at one or two loci were sequenced by Illumina to describe the phenotypic and genotypic characteristics of these isolates. RESULTS: The relationship of a clonal group associated with ST-136 CC41/44 was phylogenetically established, identifying two main clades composed of isolates from an outbreak or endemic. The most frequent alleles and peptides included porA 17, porB 44, fHbp 2.24, NHBA 10, and the FetA F5-17 variant. Most of the isolates were susceptible to the antibiotics evaluated. CONCLUSION: This study shows that meningococcal isolates with ST-9493 are an autochthonous clonal group with population dynamics and the capacity to cause endemic and epidemic meningococcal disease in Colombia.
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Infecciones Meningocócicas , Neisseria meningitidis , Humanos , Neisseria meningitidis/genética , Colombia/epidemiología , Infecciones Meningocócicas/epidemiología , Serogrupo , GenotipoRESUMEN
Introduction: Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae are on the WHO priority pathogens list because they are associated with high mortality, health-care burden, and antimicrobial resistance (AMR), a serious problem that threatens global public health and should be addressed through the One Health approach. Non-human primates (NHP) have a high risk of acquiring these antibiotic-resistant bacteria due to their close phylogenetic relationship with humans and increased anthropogenic activities in their natural environments. This study aimed to detect and analyze the genomes of ESBL-producing Escherichia coli (ESBL-producing E. coli) in NHP from the Peruvian Amazon. Materials and methods: We collected a total of 119 fecal samples from semi-captive Saguinus labiatus, Saguinus mystax, and Saimiri boliviensis, and captive Ateles chamek, Cebus unicolor, Lagothrix lagothricha, and Sapajus apella in the Loreto and Ucayali regions, respectively. Subsequently, we isolated and identified E. coli strains by microbiological methods, detected ESBL-producing E. coli through antimicrobial susceptibility tests following CLSI guidelines, and analyzed their genomes using previously described genomic methods. Results: We detected that 7.07% (7/99) of E. coli strains: 5.45% (3/55) from Loreto and 9.09% (4/44) from Ucayali, expressed ESBL phenotype. Genomic analysis revealed the presence of high-risk pandemic clones, such as ST10 and ST117, carrying a broad resistome to relevant antibiotics, including three blaCTX-M variants: blaCTX-M-15, blaCTX-M-55, and blaCTX-M-65. Phylogenomic analysis confirmed the clonal relatedness of high-risk lineages circulating at the human-NHP interface. Additionally, two ESBL-producing E. coli strains were identified as EPEC (eae) and ExPEC according to their virulence profiles, and one more presented a hypermucoviscous phenotype. Discussion: We report the detection and genomic analysis of seven ESBL-producing E. coli strains carrying broad resistome and virulence factors in NHP from two regions of the Peruvian Amazon. Some of these strains are closely related to high-risk pandemic lineages previously reported in humans and domestic animals, highlighting the negative impact of anthropogenic activities on Amazonian wildlife. To our knowledge, this is the first documentation of ESBL-producing E. coli in NHP from the Amazon, underscoring the importance of adopting the One Health approach to AMR surveillance and minimizing the potential transmission risk of antibiotic-resistant bacteria at the human-NHP interface.
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Background and Aim: One of the most significant public health concerns is multidrug-resistant (MDR) microorganisms. Klebsiella spp. have been at the forefront of causing different types of infections such as bacteremia, urinary tract infections, pneumonia, enteritis, and sepsis in humans as well as animals. This study aimed to determine the genomic similarity between Klebsiella spp. isolated from wild animal samples and those described in the Institut Pasteur genomic database to verify the spread of resistant clones regionally in the state of Mato Grosso, and to compare the epidemiological data in different regions of Brazil and the world. Materials and Methods: Isolates from various sites of injury in wild animals were identified by sequencing the 16S rRNA gene. Antimicrobial susceptibility testing was performed using the disk diffusion method to verify the resistance profile, and then, multilocus sequence typing was performed to verify the population structure and compare the isolates from other regions of Brazil and the world. Results: Twenty-three sequence types (STs) were observed; of these, 11 were new STs, as new alleles were detected. There was no predominant ST among the isolates. All isolates were MDR, with high rates of resistance to sulfonamides, ampicillin, amoxicillin, and nitrofurantoin and low resistance to meropenem, imipenem, and amikacin. Conclusion: Improving our understanding of the population structure of Klebsiella spp. in wild animals may help determine the source of infection during outbreaks in humans or animals, as the One Health concept emphasizes the interlinks between humans, animals, and environmental health.
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Clostridium perfringens is the causative agent of many enterotoxic diseases in humans and animals, and it is present in diverse environments (soil, food, sewage, and water). Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) have provided a general approach about genetic diversity of C. perfringens; however, those studies are limited to specific locations and often include a reduced number of genomes. In this study, 372 C. perfringens genomes from multiple locations and sources were used to assess the genetic diversity and phylogenetic relatedness of this pathogen. In silico MLST was used for typing the isolates, and the resulting sequence types (ST) were assigned to clonal complexes (CC) based on allelic profiles that differ from its founder by up to double-locus variants. A pangenome analysis was conducted, and a core genome-based phylogenetic tree was created to define phylogenetic groups. Additionally, key virulence factors, toxinotypes, and antibiotic resistance genes were identified using ABRicate against Virulence Factor Database (VFDB), TOXiper, and Resfinder, respectively. The majority of the C. perfringens genomes found in publicly available databases were derived from food (n = 85) and bird (n = 85) isolates. A total of 195 STs, some of them shared between sources such as food and human, horses and dogs, and environment and birds, were grouped in 25 CC and distributed along five phylogenetic groups. Fifty-three percent of the genomes were allocated to toxinotype A, followed by F (32%) and G (7%). The most frequently found virulence factors based on > 70% coverage and 99.95% identity were plc (100%), nanH (99%), ccp (99%), and colA (98%), which encode an alpha-toxin, a sialidase, an alpha-clostripain, and a collagenase, respectively, while tetA (39.5%) and tetB (36.2%), which mediate tetracycline resistance determinants, were the most common antibiotic resistance genes detected. The analyses conducted here showed a better view of the presence of this pathogen across several host species. They also confirm that the genetic diversity of C. perfringens is based on a large number of virulence factors that vary among phylogroups, and antibiotic resistance markers, especially to tetracyclines, aminoglycosides, and macrolides. Those characteristics highlight the importance of C. perfringens as a one of the most common causes of foodborne illness.
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Despite several reports worldwide documenting the presence of Rickettsia asembonensis in samples derived from ectoparasites, animals and more recently humans, genomic information of these specimens remains scarce, and when available, is usually limited to small genomic fragments of limited value. We generated complete sequences for two conserved (17-kDa antigen gene and gltA) and three variable (sca4, ompB and ompA) genes in five R. asembonensis DNA samples detected in cat and dog fleas in Peru. Complete gene sequences were used to conduct multi-locus sequence typing and phylogenetic analyses to assess diversity and infer relationships among strains and other reference sequences. The 17-kDa antigen gene was highly conserved across Rickettsia species. Of the variable genes ompB was the most variable, but this diversity was not captured through phylogenetics alone even when efforts were made to maximize potential diversity in terms of flea species, animal host and location. Through a combination of de novo and reference-based genome assembly we identified a 75 bp insertion in ompA that encodes a 25 aa repetitive motif found in other Rickettsia species, but not present in the original prototype strain from Kenya. R. asembonensis has only recently been shown to be a bona-fide human pathogen. As such, and compounded by a lack of available genomic information, it remains understudied. Our work directly addresses the lack of genomic information available worldwide for the study of these novel Rickettsia species and specifically contributes to our understanding of the diversity and molecular epidemiology of R. asembonensis in Peru.
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Rickettsia , Animales , Gatos , ADN Bacteriano/genética , Perros , Tipificación de Secuencias Multilocus/veterinaria , Perú/epidemiología , Filogenia , Rickettsia/genéticaRESUMEN
The aim of this study was to evaluate genetic diversity, distribution, evolution and population structure of Brazilian Brachyspira hyodysenteriae strains isolated from swine. Multilocus Sequence Typing (MLST) analysis using seven housekeeping genes was applied to 46 isolates obtained from outbreaks of swine dysentery that occurred between 2011 and 2015 in the states of Minas Gerais, São Paulo, Mato Grosso, Rio Grande do Sul and Santa Catarina. Historical isolates from Rio Grande do Sul obtained in 1998 were also included in the study. An independent international profile of the global sequences deposited in the B. hyodysenteriae database was used for comparisons with the Brazilian strains. All isolates from 2011 to 2015 were classified into nine sequence type (STs) and divided into four clonal complexes. These findings indicated genetic relationships among the B. hyodysenteriae from different Brazilian states, among historical strains isolated in 1998 and from recent outbreaks, and relatedness with global isolates. Seven STs were unique and, to date, only reported in Brazil.
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Brachyspira hyodysenteriae , Brachyspira , Disentería , Infecciones por Bacterias Gramnegativas , Enfermedades de los Porcinos , Animales , Brachyspira/genética , Brachyspira hyodysenteriae/genética , Brasil/epidemiología , Disentería/epidemiología , Disentería/veterinaria , Infecciones por Bacterias Gramnegativas/epidemiología , Infecciones por Bacterias Gramnegativas/veterinaria , Tipificación de Secuencias Multilocus/veterinaria , Porcinos , Enfermedades de los Porcinos/epidemiologíaRESUMEN
AIMS: To characterize the genetic relatedness, phenotypic and genotypic antimicrobial resistance and plasmid content of 80 Salmonella Infantis strains isolated from food, humans and veterinary sources from 2013 to 2018 in Brazil. METHODS AND RESULTS: Pulsed-field gel electrophoresis and single-nucleotide polymorphism analysis showed major clusters containing 50% and 38.8% of the strains studied respectively. Multilocus sequence typing assigned all strains to ST32. Disk-diffusion revealed that 90% of the strains presented resistant or intermediate resistant profiles and 38.8% displayed multidrug resistance. Resistance genes for aminoglycosides (aac(6')-Iaa; aadA12; aph(3â³-Ib; aph(6)-Id), ß-lactams (blaTEM-1 ; blaCTX-M-8 ; blaCMY-2 ), trimethoprim (dfrA8), tetracycline (tet(A)), amphenicols (floR), sulfonamide (sul2), efflux pumps (mdsA; mdsB), chromosomal point mutations in gyrB, parC, acrB and pmrA were detected. Strains harboured IncI, IncF, IncX, IncQ, IncN and IncR plasmids. CONCLUSIONS: The presence of a prevalent S. Infantis subtype in Brazil and the high antimicrobial resistance rates reinforced the potential hazard of this serovar for the public health and food safety fields. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study characterizing a large set of S. Infantis from Brazil by whole-genome sequencing, which provided a better local and global comprehension about the distribution and characteristics of this serovar of importance in the food, human and veterinary fields.
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Antibacterianos , Salmonella enterica , Antibacterianos/farmacología , Brasil , Farmacorresistencia Bacteriana/genética , Farmacorresistencia Bacteriana Múltiple/genética , Genómica , Humanos , Pruebas de Sensibilidad Microbiana , Plásmidos/genética , Salmonella , SerogrupoRESUMEN
This study was conducted to determine the molecular epidemiology of blaKPC-encoding Klebsiella pneumoniae recovered from three public hospitals in Brazil. Molecular investigation of blaOXA-48, blaKPC, blaNDM, blaCTX-M, blaSHV, blaTEM, blaIMP, and blaVIM resistance genes was performed in 99 K. pneumoniae isolates from inpatients of intensive care units. Antimicrobial susceptibility was determined with a Vitek-2 System, except for polymyxin B, which was evaluated by the microbroth dilution test. Clonal relatedness was established by pulsed-field gel electrophoresis and multilocus sequence typing. Screening resistance genes showed that K. pneumoniae isolates carried the blaKPC (88.9%), blaSHV (73.5%), blaTEM (72.2%), and blaCTX-M (43.9%) genes. The most frequent sequence types (STs) were ST273, ST11, ST 1298, ST13, ST2687, and ST37. We report new STs in K. pneumoniae that have not been detected previously in Brazil. K. pneumoniae belonging to the same clone is present in different hospitals in the same region, showing the spread of multidrug-resistant K. pneumoniae.
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Antibacterianos/farmacología , Farmacorresistencia Bacteriana Múltiple/genética , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/genética , Brasil , Genes Bacterianos , Hospitales Públicos , Humanos , Pruebas de Sensibilidad Microbiana , Epidemiología Molecular , beta-Lactamasas/genéticaRESUMEN
Background: ß-lactamase-producing Escherichia coli are a widely distributed source of antimicrobial resistance for animals and humans. Little is known about the susceptibility profile and genetic characteristics of E. coli strains isolated from domestic dogs in Latin America. Methods: We report on a cross-sectional study that evaluated E. coli strains isolated from fecal samples of domestic dogs in central Panama. The extended-spectrum ß-lactamase (ESBL), AmpC genes, and plasmid-mediated quinolone resistance were investigated. Molecular typing using Pasteur's multilocus sequence typing (MLST) was conducted. Results: A total of 40 E. coli isolates were obtained, of which 80% (32/40) were resistant to at least one of the antibiotics tested, while 20% (8/40) were sensitive to all antibiotics analyzed in this study (p < 0.001). Forty percent of the strains were resistant to three or more antibiotics. The most common resistance was to tetracycline (45%) and ampicillin (30%) while 2.5% showed an ESBL phenotype. Antibiotic resistance genes were detected for one ß-lactamase (blaTEM-1) and two plasmid-mediated quinolone resistance (PMQR) enzymes (qnrS and qnrB). In addition, mutations in the chromosomal AmpC gene were observed at positions −35, −28, −18, −1, and +58. Fourteen different sequence types (STs) were identified; the most frequent were ST399 and ST425 (12% each). ST3 and ST88, which have been previously identified in human clinical isolates, were also evidenced. Three new STs were found for the first time: ST1015, ST1016 (carrier of the blaTEM-1 gene), and ST1017 (carrier of the blaTEM-1, qnrS, and qnrB genes). Conclusions: In the intestinal strains of E. coli isolated from domestic dogs, there was a high frequency of resistance to antibiotics. The presence of genes from plasmids and chromosomal mutations that conferred antibiotic resistance, the identification of isolates previously reported in humans, and the genetic diversity of STs (including three that were newly identified) confirmed the determinants of resistance to antibiotics in the domestic dogs from central Panama.
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Escherichia coli , Quinolonas , Humanos , Perros , Animales , beta-Lactamasas/genética , Quinolonas/farmacología , Tipificación de Secuencias Multilocus , Estudios Transversales , Antibacterianos/farmacología , Plásmidos/genética , Variación Genética/genéticaRESUMEN
INTRODUCCIÓN. Staphylococcus aureus es parte de la microbiota nasal en 20-30% de la población general, colonización que constituye un reservorio para su transmisión, lo que es preocupante en cepas resistentes a meticilina (SARM). OBJETIVO: Determinar la prevalencia de S. aureus en estudiantes de Medicina y Enfermería del Campus San Felipe y caracterizar sus aislamientos. MATERIAL Y MÉTODOS: El 2017 se midió la portación nasal a 225 estudiantes, a las cepas aisladas se le analizó su antibiotipo por difusión en agar, la relación clonal por electroforesis de campo pulsado y MLST. En SARM se determinó el cassette SCCmec y gen de la leucocidina de Panton-Valentine. RESULTADOS: 61 estudiantes portaron S. aureus (27,1%) incluyendo dos cepas SARM (0,9%). Staphylococcus aureus mostró resistencia a penicilina (75%), eritromicina (14%) y clindamicina (10%), cloranfenicol (1,6%) y levofloxacina, oxacilina, cefoxitina (3,3%). Se diferenciaron diecinueve pulsotipos y el secuenciotipo coincidió con complejos clonales descritos a nivel mundial en portadores de S. aureus: CC30, CC8, CC97, CC15, CC22 y CC1. Las dos cepas SARM correspondieron con los clones chileno/cordobés y USA100NY/J, ambas del CC5. CONCLUSIÓN: La portación nasal de S. aureus y SARM en los estudiantes coincidió con la portación en la población general y las cepas sensibles a meticilina mostraron diversidad clonal y alta susceptibilidad antimicrobiana, exceptuando a penicilina.
BACKGROUND: Staphylococcus aureus is part of the nasal microbiota in 20-30% of the population. This colonization is also a reservoir for its dissemination, which is worrying in the case of strains with resistance to methicillin (MRSA). AIM: To determine S. aureus nasal carriage in nursing and medical students of San Felipe Campus and characterize theirs isolates. METHODS: During 2017, nasal swabs were taken from 225 students and seeded in salt manitol agar. Antibiotypes were determined by agar diffusion and the genetic clonality was assessed by PFGE and MLST in isolated S. aureus. SCCmec cassette and Panton-Valentine leukocidin gene (pvl) presence were determined in the MRSA isolates. RESULTS: 61 students carried S. aureus (27.1%) including two MRSA strains (0.9%). S. aureus showed resistance to penicillin (75%), erythromycin (14%) and clindamycin (10%), chloramphenicol (1.6%) and levofloxacin, oxacillin, cefoxitin (3.3%). Nineteen PFGE-types were differentiated, and their sequence-types coincided with main clonal complexes described in S. aureus carriers from different places worldwide: CC30, CC8, CC97, CC15, CC22 and CC1. MRSA strains belonged to CC5 and they corresponded to the Chilean/Cordobes and USA100NY/J clones. CONCLUSION: Nasal carriage of S. aureus and MRSA in students, coincided with the general population and sensitive-methicillin strains showed clonal diversity and high antimicrobial susceptibility except for penicillin.
Asunto(s)
Humanos , Infecciones Estafilocócicas/epidemiología , Estudiantes de Enfermería , Staphylococcus aureus Resistente a Meticilina/genética , Staphylococcus aureus/genética , Pruebas de Sensibilidad Microbiana , Chile , Agar , Tipificación de Secuencias Multilocus , Genotipo , Meticilina , Antibacterianos/farmacologíaRESUMEN
Acinetobacter baumannii is an important Gram-negative opportunistic pathogen that is responsible for many nosocomial infections. This etiologic agent has acquired, over the years, multiple mechanisms of resistance to a wide range of antimicrobials and the ability to survive in different environments. In this context, our study aims to elucidate the resistome from the A. baumannii strains based on phylogenetic, phylogenomic, and comparative genomics analyses. In silico analysis of the complete genomes of A. baumannii strains was carried out to identify genes involved in the resistance mechanisms and the phylogenetic relationships and grouping of the strains based on the sequence type. The presence of genomic islands containing most of the resistance gene repertoire indicated high genomic plasticity, which probably enabled the acquisition of resistance genes and the formation of a robust resistome. A. baumannii displayed an open pan-genome and revealed a still constant genetic permutation among their strains. Furthermore, the resistance genes suggest a specific profile within the species throughout its evolutionary history. Moreover, the current study performed screening and characterization of the main genes present in the resistome, which can be used in applied research to develop new therapeutic methods to control this important bacterial pathogen.
RESUMEN
RESUMO: The Klebsiella pneumoniae (K. pneumoniae) bacterium is responsible for many opportunistic infections such as sepsis, and a multidrug-resistant (MDR) clone sequence type (ST) 307 has recently begun to spread. The objective of this study was to report the first occurrence of this virulent genotype, which was found in the context of a urinary infection in a domestic feline in Brazil. The K. pneumoniae isolate was identified from the urine of a 6-month-old male crossbreed cat using 16S rRNA sequencing. It was then subjected to antimicrobial susceptibility testing, followed by multilocus sequence typing analysis, and PCR detection of virulence and resistance genes. The antimicrobial susceptibility profile demonstrated that the isolate was MDR and associated with the presence of the colistin resistance gene (mcr-1). Genotyping allowed us to classify the isolate as K. pneumoniae ST307 with the presence of wabG, uge, and entB genes. MDR K. pneumoniae is important in human and veterinary medicine because it causes many types of infections. Clonal propagation of virulent or MDR genotypes such as K. pneumoniae ST307 is a global concern. This report of ST307 isolation from a urine sample in a domestic feline is the first in Brazil.