RESUMEN
Foodborne pathogens remain a serious health issue in developed and developing countries. Safeness of food products has been assured for years with culture-based microbiological methods; however, these present several limitations such as turnaround time and extensive hands-on work, which have been typically address taking advantage of DNA-based methods such as real-time PCR (qPCR). These, and other similar techniques, are targeted assays, meaning that they are directed for the specific detection of one specific microbe. Even though reliable, this approach suffers from an important limitation that unless specific assays are design for every single pathogen potentially present, foods may be considered erroneously safe. To address this problem, next-generation sequencing (NGS) can be used as this is a nontargeted method; thus it has the capacity to detect every potential threat present. In this chapter, a protocol for the simultaneous detection and preliminary serotyping of Salmonella enterica serovar Enteritidis, Salmonella enterica serovar Typhimurium, Listeria monocytogenes, and Escherichia coli O157:H7 is described.
Asunto(s)
Microbiología de Alimentos , Enfermedades Transmitidas por los Alimentos , Secuenciación de Nucleótidos de Alto Rendimiento , Listeria monocytogenes , Microbiología de Alimentos/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Enfermedades Transmitidas por los Alimentos/microbiología , Enfermedades Transmitidas por los Alimentos/diagnóstico , Listeria monocytogenes/aislamiento & purificación , Listeria monocytogenes/genética , Escherichia coli O157/aislamiento & purificación , Escherichia coli O157/genética , Humanos , Serotipificación/métodos , ADN Bacteriano/genética , ADN Bacteriano/análisis , Salmonella typhimurium/aislamiento & purificación , Salmonella typhimurium/genéticaRESUMEN
Objective: To describe the profile of Streptococcus pneumoniae, identify research gaps, and provide in-depth insights into various aspects related to the pathogen. Methods: Google Scholar, PubMed, and ScienceDirect were searched for all studies on the pneumococcus in Ghana that reported on specimen collected, population and sample size, carriage prevalence, incidence of pneumococcal diseases, age of the study population, types of test performed, serotypes identified, antimicrobial susceptibilities, or molecular analysis on the pneumococci for data extraction. Results: Overall, a total of 7954 results were obtained from the three-database search, and of this, 24 articles were selected after screening. A total of 924 isolates were accounted for by serotyping/serogrouping. The prevalence of pneumococcal carriage in Ghana ranges from 11.0% to 51.4% in the population depending on the age (≤ 24-80 years), sickle cell disease (SCD), human immunodeficiency virus (HIV) status, or health of the study population, and penicillin (Pen)-nonsusceptible isolates ranged from 17% to 63%. The prevalence of pneumococci found as the etiologic agent of diseases among Ghanaians ranges from 3.4% for otitis media to 77.7% for meningitis. Overall, the 13-valent pneumococcal conjugate vaccine (PCV) (PCV-13) carriage serotypes accounted for 28.4% of the reported pneumococcal isolates. PCV-13 invasive serotypes accounted for 22.4% of the reported isolates. The non-PCV-13 carriage serotypes accounted for most (43.9%) of the reported isolates. In the pre-PCV-13 era, the nontypeable (NT) (5.5%) and other nonvaccine types (NVTs) (6.4%) were reported as being predominant. The non-PCV-13 serotypes accounted for 4.4% of the reported isolates in invasive pneumococcal disease (IPD) cases. Multidrug resistance (MDR) ranged from 7.8% to 100%. Conclusion: Predicting the invasiveness of pneumococci using molecular typing is the way to go in the future as this will provide answers to the extent to which capsular switching is contributing to the pneumococcal disease burden in Ghana almost a decade after introducing PCV-13. Continuous monitoring of antibiotic resistance patterns at both phenotypic and genotypic levels, along with serotyping and molecular typing, should be a standard practice in the surveillance of pneumococcal disease burden in Ghana.
Asunto(s)
Infecciones Neumocócicas , Vacunas Neumococicas , Streptococcus pneumoniae , Humanos , Ghana/epidemiología , Streptococcus pneumoniae/patogenicidad , Streptococcus pneumoniae/aislamiento & purificación , Infecciones Neumocócicas/epidemiología , Infecciones Neumocócicas/microbiología , Prevalencia , Serogrupo , Adulto , Anciano , Persona de Mediana Edad , Anciano de 80 o más Años , Serotipificación , Femenino , Antibacterianos/farmacología , Antibacterianos/uso terapéuticoRESUMEN
The emergence of EHDV in Europe during the autumn of 2022 reinforces the need for molecular tools (RT-PCR) for rapid detection of animals infected with this virus. Viral genome testing can be performed on whole blood under anticoagulant, spleen, and bloody organ homogenates from ruminants. It can also be performed on cell culture following viral isolation tests. Various so-called classical or end-point RT-PCRs will be described, which permit the amplification of a part of the viral genome (targeting segment 7) allowing the detection of EHDV whatever the serotype (pan-RT-PCR) and also to amplify a portion of the gene coding the viral protein (VP) 2 enabling serotyping. The PCR amplification products are visualized by agarose gel electrophoresis. Sequencing of the type-specific RT-PCR amplification products allows for the serotype of the virus to be determined.
Asunto(s)
Virus de la Enfermedad Hemorrágica Epizoótica , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Animales , Virus de la Enfermedad Hemorrágica Epizoótica/genética , Virus de la Enfermedad Hemorrágica Epizoótica/aislamiento & purificación , Virus de la Enfermedad Hemorrágica Epizoótica/clasificación , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/métodos , Infecciones por Reoviridae/veterinaria , Infecciones por Reoviridae/virología , Infecciones por Reoviridae/diagnóstico , ARN Viral/genética , Genoma Viral , Serotipificación/métodosRESUMEN
Molecular methods are routinely used for the differential diagnosis and genetic characterization of viral disease of livestock. Real-time, quantitative PCR (qPCR) allows RNA/DNA sequence detection and quantification and is considered the gold standard diagnostic method for most viruses. However, Sanger sequencing offers additional information and opportunity to differentiate closely related virus strains and/or serotypes, by providing the full sequence of a genetic region of interest. Therefore, to determine epizootic hemorrhagic disease virus (EHDV) serotype or identify additional genetic markers, end-point RT-PCR can be performed on EHDV-positive clinical samples, followed by Sanger sequencing and data analysis. Here we describe a detailed method for the molecular characterization of EHDV serotype using Sanger sequencing.
Asunto(s)
Virus de la Enfermedad Hemorrágica Epizoótica , Infecciones por Reoviridae , Serotipificación , Virus de la Enfermedad Hemorrágica Epizoótica/genética , Virus de la Enfermedad Hemorrágica Epizoótica/clasificación , Animales , Serotipificación/métodos , Infecciones por Reoviridae/virología , Infecciones por Reoviridae/veterinaria , ARN Viral/genética , Serogrupo , Análisis de Secuencia de ADN/métodos , Reacción en Cadena en Tiempo Real de la Polimerasa/métodosRESUMEN
Shiga toxin-producing and Enteropathogenic Escherichia coli are foodborne pathogens commonly associated with diarrheal disease in humans. This study investigated the presence of STEC and EPEC in 771 dairy cattle fecal samples which were collected from 5 abattoirs and 9 dairy farms in South Africa. STEC and EPEC were detected, isolated and identified using culture and PCR. Furthermore, 339 STEC and 136 EPEC isolates were characterized by serotype and major virulence genes including stx1, stx2, eaeA and hlyA and the presence of eaeA and bfpA in EPEC. PCR screening of bacterial sweeps which were grown from fecal samples revealed that 42.2% and 23.3% were STEC and EPEC positive, respectively. PCR serotyping of 339 STEC and 136 EPEC isolates revealed 53 different STEC and 19 EPEC serotypes, respectively. The three most frequent STEC serotypes were O82:H8, OgX18:H2, and O157:H7. Only 10% of the isolates were classified as "Top 7" STEC serotypes: O26:H2, 0.3%; O26:H11, 3.2%; O103:H8, 0.6%; and O157:H7, 5.9%. The three most frequent EPEC serotypes were O10:H2, OgN9:H28, and O26:H11. The distribution of major virulence genes among the 339 STEC isolates was as follows: stx1, 72.9%; stx2, 85.7%; eaeA, 13.6% and hlyA, 69.9%. All the 136 EPEC isolates were eaeA-positive but bfpA-negative, while 46.5% carried hlyA. This study revealed that dairy cattle are a major reservoir of STEC and EPEC in South Africa. Further comparative studies of cattle and human STEC and EPEC isolates will be needed to determine the role played by dairy cattle STEC and EPEC in the occurrence of foodborne disease in humans.Please kindly check and confirm the country and city name in affiliation [6].This affiliation is correct.Please kindly check and confirm the affiliationsConfirmed. All Affiliations are accurate.
Asunto(s)
Escherichia coli Enteropatógena , Infecciones por Escherichia coli , Proteínas de Escherichia coli , Heces , Serogrupo , Escherichia coli Shiga-Toxigénica , Factores de Virulencia , Animales , Bovinos , Sudáfrica , Escherichia coli Enteropatógena/genética , Escherichia coli Enteropatógena/aislamiento & purificación , Escherichia coli Enteropatógena/clasificación , Escherichia coli Enteropatógena/patogenicidad , Heces/microbiología , Escherichia coli Shiga-Toxigénica/genética , Escherichia coli Shiga-Toxigénica/patogenicidad , Escherichia coli Shiga-Toxigénica/aislamiento & purificación , Escherichia coli Shiga-Toxigénica/clasificación , Infecciones por Escherichia coli/microbiología , Infecciones por Escherichia coli/veterinaria , Factores de Virulencia/genética , Virulencia/genética , Proteínas de Escherichia coli/genética , Serotipificación , Enfermedades de los Bovinos/microbiología , Industria Lechera , Mataderos , Reacción en Cadena de la PolimerasaRESUMEN
Klebsiella pneumoniae has emerged as a global health threat due to its role in the spread of antimicrobial resistance and because it is a frequent cause of hospital-acquired infections and neonatal sepsis. Capsular and lipopolysaccharide (LPS) O-antigen polysaccharide surface antigens are major immunogens that are useful for strain classification and are candidates for vaccine development. We have developed real-time PCR reagents for molecular serotyping, subtyping, and quantitation of the most prevalent LPS O-antigen types (i.e., O1, O2, O3, and O5) of Klebsiella pneumoniae. We describe two applications for this O-typing assay: for screening culture isolates and for direct typing of Klebsiella pneumoniae present in stool samples. We find 100% concordance between the results of the O-typing assay and whole-genome sequencing of 81 culture isolates, and >90% agreement in O-typing performed directly on specimens of human stool, with disagreement arising primarily from a lack of sensitivity of the culture-based comparator method. Additionally, we find evidence for mixed O-type populations at varying levels of abundance in direct tests of stool from a hospitalized patient population. Taken together, these results demonstrate that this novel O-typing assay can be a useful tool for K. pneumoniae epidemiologic and vaccine studies.IMPORTANCEKlebsiella pneumoniae is an important opportunistic pathogen. The gastrointestinal (GI) tract is the primary reservoir of K. pneumoniae in humans, and GI carriage is believed to be a prerequisite for invasive infection. Knowledge about the dynamics and duration of GI carriage has been hampered by the lack of tools suitable for detection and strain discrimination. Real-time PCR is particularly suited to the higher-throughput workflows used in population-based studies, which are needed to improve our understanding of carriage dynamics and the factors influencing K. pneumoniae colonization.
Asunto(s)
Heces , Infecciones por Klebsiella , Klebsiella pneumoniae , Antígenos O , Reacción en Cadena en Tiempo Real de la Polimerasa , Serogrupo , Serotipificación , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/aislamiento & purificación , Klebsiella pneumoniae/clasificación , Klebsiella pneumoniae/inmunología , Antígenos O/genética , Antígenos O/inmunología , Antígenos O/análisis , Humanos , Infecciones por Klebsiella/diagnóstico , Infecciones por Klebsiella/microbiología , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Heces/microbiología , Serotipificación/métodos , Reacción en Cadena de la Polimerasa Multiplex/métodos , Secuenciación Completa del GenomaRESUMEN
Limited data from Asia are available on long-term effects of pneumococcal conjugate vaccine introduction on pneumococcal carriage. Here we assess the impact of 13-valent pneumococcal conjugate vaccine (PCV13) introduction on nasopharyngeal pneumococcal carriage prevalence, density and antimicrobial resistance. Cross-sectional carriage surveys were conducted pre-PCV13 (2015) and post-PCV13 introduction (2017 and 2022). Pneumococci were detected and quantified by real-time PCR from nasopharyngeal swabs. DNA microarray was used for molecular serotyping and to infer genetic lineage (Global Pneumococcal Sequence Cluster). The study included 1461 infants (5-8 weeks old) and 1489 toddlers (12-23 months old) enrolled from family health clinics. We show a reduction in PCV13 serotype carriage (with non-PCV13 serotype replacement) and a reduction in the proportion of samples containing resistance genes in toddlers six years post-PCV13 introduction. We observed an increase in pneumococcal nasopharyngeal density. Serotype 15 A, the most prevalent non-vaccine-serotype in 2022, was comprised predominantly of GPSC904;9. Reductions in PCV13 serotype carriage will likely result in pneumococcal disease reduction. It is important for ongoing surveillance to monitor serotype changes to potentially inform new vaccine development.
Asunto(s)
Portador Sano , Nasofaringe , Infecciones Neumocócicas , Vacunas Neumococicas , Streptococcus pneumoniae , Vacunas Conjugadas , Vacunas Neumococicas/inmunología , Vacunas Neumococicas/administración & dosificación , Humanos , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/inmunología , Streptococcus pneumoniae/aislamiento & purificación , Streptococcus pneumoniae/clasificación , Lactante , Infecciones Neumocócicas/prevención & control , Infecciones Neumocócicas/microbiología , Infecciones Neumocócicas/epidemiología , Infecciones Neumocócicas/inmunología , Nasofaringe/microbiología , Portador Sano/epidemiología , Portador Sano/microbiología , Portador Sano/prevención & control , Mongolia/epidemiología , Estudios Transversales , Vacunas Conjugadas/inmunología , Femenino , Masculino , Serogrupo , Prevalencia , SerotipificaciónRESUMEN
Yersinia enterocolitica is a globally distributed food-borne gastrointestinal pathogen. The O-antigen variation-determined serotype is an important characteristic of Y. enterocolitica, allowing intraspecies classification for diagnosis and epidemiology purposes. Among the 11 serotypes associated with human yersiniosis, O:3, O:5,27, O:8, and O:9 are the most prevalent, and their O-antigen gene clusters have been well defined. In addition to the O-antigen, several virulence factors are involved in infection and pathogenesis of Y. enterocolitica strains, and these are closely related to their biotypes, reflecting pathogenic properties. In this study, we identified the O-AGC of a Y. enterocolitica strain WL-21 of serotype O:10, and confirmed its functionality in O-antigen synthesis. Furthermore, we analyzed in silico the putative O-AGCs of uncommon serotypes, and found that the O-AGCs of Y. enterocolitica were divided into two genetic patterns: (1) O-AGC within the hemH-gsk locus, possibly synthesizing the O-antigen via the Wzx/Wzy dependent pathway, and (2) O-AGC within the dcuC-galU-galF locus, very likely assembling the O-antigen via the ABC transporter dependent pathway. By screening the virulence genes against genomes from GenBank, we discovered that strains representing different serotypes were grouped according to different virulence gene profiles, indicating strong links between serotypes and virulence markers and implying an interaction between them and the synergistic effect in pathogenicity. Our study provides a framework for further research on the origin and evolution of O-AGCs from Y. enterocolitica, as well as on differences in virulent mechanisms among distinct serotypes.
Asunto(s)
Familia de Multigenes , Antígenos O , Serogrupo , Factores de Virulencia , Yersiniosis , Yersinia enterocolitica , Yersinia enterocolitica/genética , Yersinia enterocolitica/patogenicidad , Yersinia enterocolitica/clasificación , Antígenos O/genética , Factores de Virulencia/genética , Virulencia/genética , Yersiniosis/microbiología , Humanos , Microbiología de Alimentos , Proteínas Bacterianas/genética , SerotipificaciónRESUMEN
Bangladesh experienced the largest and deadliest dengue outbreak in 2023, after the virus had reappeared in the country 2 decades earlier. A total of 1,705 people died in Bangladesh, representing the highest case fatality rate (0.5%) due to dengue in the world for that year. The severity of dengue infection is to some extent related to the emergence of new circulating serotypes. To identify the possible predominant serotype in 2023, the reverse transcription polymerase chain reaction-based identification technique was used on stored serum samples of suspected dengue patients during the period between July and December 2023. The overall result of molecular serotyping showed that dengue virus (DENV-2) reappeared as the predominant serotype (74.1%), followed by a moderate number of samples with DENV-1 (19.8%) and DENV-3 (6.1%), in 2023. However, DENV-1 was found to be dominant in a few rural areas of Cox's Bazar districts. During the 2019 outbreak, DENV-3 was the dominant serotype, which seemed to be replaced by the DENV-2 serotype; this may have impacted the increased case fatality in 2023.
Asunto(s)
Virus del Dengue , Dengue , Brotes de Enfermedades , Serogrupo , Bangladesh/epidemiología , Virus del Dengue/genética , Virus del Dengue/clasificación , Virus del Dengue/aislamiento & purificación , Humanos , Dengue/epidemiología , Dengue/virología , Masculino , Femenino , Adolescente , Serotipificación , Adulto , Adulto Joven , Niño , Preescolar , Persona de Mediana EdadRESUMEN
Salmonella is a zoonotic pathogen posing a serious risk to the farming industry and public health due to food animals serving as reservoirs for future contamination and spread of Salmonella. The present study is designed to monitor the contamination status of Salmonella in duck farms and the main control points during breeding. 160 strains of duck-derived Salmonella were isolated from the 736 samples (cloacal swabs, feces, water, feed, soil, air and dead duck embryos) collected in southwest Shandong Province and the province's surrounding area. The percentage of Salmonella-positive samples collected was 21.74 % (160/736), and the greatest prevalence from duck embryo samples (40.00 %, 36/90). These Salmonella were classified into 23 serotypes depending on their O and H antigens, in which S. Typhimurium (30.15 %), S. Kottbus (13.97 %) and S. Enteritidis (10.29 %) were the prevailing serotypes. Subsequently, the molecular subtyping was done. Clustered regularly interspaced short palindromic repeats (CRISPR) analysis showed that 41 strains of S. Typhimurium and 14 strains of S. Enteritidis were classified into 13 and 3 genotypes, respectively. 19 S. Kottbus isolates from different sources featured ST1546, ST198, ST321, and ST1690 by multilocus sequence typing (MLST) analysis, among which ST1546 belongs to S. Kottbus was a new ST. The minimum spanning tree analysis based on the two CRISPR loci and seven MLST loci from all S. Typhimurium, S. Enteritidis and S. Kottbus isolates revealed that duck embryos, feed and water were key control points to the spread of Salmonella along the breeding chain. Meanwhile, the emergence of S. Kottbus in duck flocks was considered a potential public health hazard.
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Patos , Granjas , Heces , Genotipo , Enfermedades de las Aves de Corral , Salmonelosis Animal , Salmonella , Serogrupo , Animales , Patos/microbiología , China/epidemiología , Salmonelosis Animal/microbiología , Salmonelosis Animal/epidemiología , Salmonella/genética , Salmonella/aislamiento & purificación , Salmonella/clasificación , Enfermedades de las Aves de Corral/microbiología , Enfermedades de las Aves de Corral/epidemiología , Heces/microbiología , Salmonella typhimurium/genética , Salmonella typhimurium/aislamiento & purificación , Salmonella typhimurium/clasificación , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/genética , Prevalencia , Filogenia , Salmonella enteritidis/genética , Salmonella enteritidis/aislamiento & purificación , Salmonella enteritidis/clasificación , Tipificación de Secuencias Multilocus , SerotipificaciónRESUMEN
INTRODUCTION: Vibrio parahaemolyticus is a common pathogen that can cause seafood-borne gastroenteritis in humans. We determined the prevalence and characteristics of V. parahaemolyticus isolated from clinical specimens and oysters in Thailand. METHODOLOGY: Isolates of V. parahaemolyticus from clinical specimens (n = 77) and oysters (n = 224) were identified by biochemical testing, polymerase chain reaction (PCR) assays, and serotyping. The toxin genes, antimicrobial resistance, and ß-lactamase production were determined. RESULTS: A total of 301 isolates were confirmed as V. parahaemolyticus by PCR using specific primers for the toxR gene. The majority of clinical isolates carried the tdh+/trh- genotype (82.1%), and one of each isolate was tdh-/trh+ and tdh+/trh+ genotypes. One isolate from oyster contained the tdh gene and another had the trh gene. Twenty-six serotypes were characterized among these isolates, and O3:K6 was the most common (37.7%), followed by OUT:KUT, and O4:K9. In 2010, most clinical and oyster isolates were susceptible to antibiotics, with the exception of ampicillin. In 2012, clinical isolates were not susceptible to cephalothin (52.4%), streptomycin (95.2%), amikacin (66.6%), kanamycin (61.9%), and erythromycin (95.2%), significantly more frequently than in 2010. More than 95% of isolates that were not susceptible to ampicillin produced ß-lactamase enzymes. CONCLUSIONS: We found toxin genes in two oyster isolates, and the clinical isolates that were initially determined to be resistant to several antibiotics. Toxin genes and antimicrobial susceptibility profiles of V. parahaemolyticus from seafood and environment should be continually monitored to determine the spread of toxin and antimicrobial resistance genes.
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Ostreidae , Vibriosis , Vibrio parahaemolyticus , Vibrio parahaemolyticus/genética , Vibrio parahaemolyticus/aislamiento & purificación , Vibrio parahaemolyticus/efectos de los fármacos , Vibrio parahaemolyticus/clasificación , Tailandia/epidemiología , Ostreidae/microbiología , Humanos , Animales , Vibriosis/microbiología , Vibriosis/epidemiología , beta-Lactamasas/genética , Antibacterianos/farmacología , Pruebas de Sensibilidad Microbiana , Serotipificación , Reacción en Cadena de la Polimerasa , Prevalencia , Genotipo , Farmacorresistencia Bacteriana/genética , Toxinas Bacterianas/genética , Masculino , Adulto , Femenino , Persona de Mediana EdadRESUMEN
An outbreak of Salmonella Stanley in the United States associated with dried wood ear mushrooms imported from China prompted us to conduct serotyping of Salmonella isolated from dried wood ear mushrooms in voluntary testing, and quantitative test for Salmonella along with enumeration of hygienic indicator bacteria in positive samples in order to evaluate the risk of Salmonella outbreak from dried wood ear mushrooms. The major serovars of Salmonella isolates obtained from 20 samples were as follows: O3,10 group-London (n=3) and Weltevreden (n=5) etc, totaling 9 strains; O4 serogroup-Saintpaul (n=2), Stanley (n=1), Typhimurium (including monophasic variant; n=3), totaling 6 strains. O7 serogroup (Potsdam) and O8 serogroup (Newport) were one strain each. Qualitative and quantitative tests for Salmonella were conducted on 10 samples with remaining amounts. As a result, one sample was 220 MPN/g, six samples were<0.6 MPN/g, and three samples were negative for Salmonella per 25 g. The mean aerobic bacterial counts and coliforms in these samples were 7.8 and 6.1 log10 CFU/g, respectively. Furthermore, qualitative test for Salmonella and enumeration of hygienic indicator bacteria were conducted on dried wood ear mushroom products (33 domestic and 30 imported products) retailed in Japan. No samples showed positive for Salmonella per 25 g, and the mean aerobic bacterial counts and coliforms were approximately 2 log10 CFU/g lower than those in the 10 samples where Salmonella was isolated during voluntary testing. While no Salmonella was detected in domestically retailed wood ear mushrooms products, the serovars associated with foodborne diseases were isolated from voluntary testing samples. It indicates that potential for consumption of Salmonella contaminated wood ear mushrooms, which is at risk of causing food poisoning.
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Agaricales , Microbiología de Alimentos , Salmonella , Salmonella/aislamiento & purificación , Agaricales/clasificación , Serotipificación , Carga Bacteriana , Brotes de Enfermedades , Intoxicación Alimentaria por Salmonella/prevención & control , Intoxicación Alimentaria por Salmonella/microbiología , ChinaRESUMEN
This study focuses on the genomic characterization of a multidrug-resistant Escherichia coli strain responsible for a severe gastrointestinal infection in a 33-year-old male. The patient initially received sulfamethoxazole/trimethoprim treatment, which proved ineffective. Fecal culture confirmed the presence of E. coli displaying a MDR profile to ampicillin, nalidixic acid, ciprofloxacin, sulfamethoxazole, trimethoprim, and tetracycline. Serotyping identified the strain as ONT:H19. Virulence analysis indicated a highly virulent profile with numerous virulence markers. Plasmid analysis uncovered various plasmids carrying both antimicrobial resistance and virulence genes. MLST assigned the strain to ST10955. Phylogenomic analysis revealed similarity to an older Brazilian isolate, suggesting the persistence of a common lineage with evolving antimicrobial resistance. This report highlights the first identification of a multidrug-resistant ST10955 E. coli strain with a wide resistome and virulence potential, emphasizing the importance of ongoing surveillance of E. coli strains due to their potential for severe infections, resistance development, and virulence.
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Farmacorresistencia Bacteriana Múltiple , Infecciones por Escherichia coli , Escherichia coli , Genoma Bacteriano , Filogenia , Humanos , Escherichia coli/genética , Escherichia coli/efectos de los fármacos , Escherichia coli/aislamiento & purificación , Escherichia coli/patogenicidad , Escherichia coli/clasificación , Infecciones por Escherichia coli/microbiología , Infecciones por Escherichia coli/diagnóstico , Adulto , Masculino , Farmacorresistencia Bacteriana Múltiple/genética , Genoma Bacteriano/genética , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Heces/microbiología , Plásmidos/genética , Tipificación de Secuencias Multilocus , Factores de Virulencia/genética , Enfermedades Gastrointestinales/microbiología , Enfermedades Gastrointestinales/diagnóstico , Virulencia/genética , Serotipificación , BrasilRESUMEN
BACKGROUND: Streptococcus agalactiae is a recognized pathogen that primarily affects infants and pregnant women. However, its increasingly important role in causing invasive infections among non-pregnant adults has become a significant health concern due to the severity and variety of its clinical impacts. METHODS: Nonduplicate S. agalactiae clinical strains associated with clinical infections (n = 139) were isolated from non-pregnant adults in Shandong, China. Antibiotic susceptibility testing, whole-genome sequencing and genomic analyses were conducted to characterize the genome and identify resistance features of these strains. RESULTS: The strains exhibited universal susceptibility to penicillin, ampicillin, cefotaxime, meropenem, linezolid and vancomycin. Notably, high resistance rates were observed for erythromycin (91.4%), clindamycin (89.2%), levofloxacin (84.2%), tetracycline (54.0%) and, to a lesser extent, chloramphenicol (12.9%). Serotyping revealed seven serotypes and one non-typeable strain. Serotypes Ia, Ib, III and V predominated, representing 95.7% of the strains. Nineteen sequence types were categorized into seven clonal complexes, with CC10 being the most prevalent at 48.9%. The resistance genes mreA (100%), ermB (70.5%) and tetM (46.0%) were commonly detected. All the isolates carried at least one pilus backbone determinant and one alpha-like protein gene, with the PI-1+PI-2a and the bca gene being the most frequent at 84.2% and 54.7%, respectively. CONCLUSIONS: While S. agalactiae strains in non-pregnant adults retain sensitivity to ß-lactam antibiotics, the elevated resistance to erythromycin, clindamycin, levofloxacin and tetracycline is concerning. Given the growing elderly population worldwide, the burden of S. agalactiae infections is significant. Continuous surveillance of serotype distribution and antibiotic resistance patterns is imperative for targeted prevention and therapeutic strategies.
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Antibacterianos , Genoma Bacteriano , Pruebas de Sensibilidad Microbiana , Infecciones Estreptocócicas , Streptococcus agalactiae , Secuenciación Completa del Genoma , Streptococcus agalactiae/efectos de los fármacos , Streptococcus agalactiae/genética , Streptococcus agalactiae/aislamiento & purificación , Streptococcus agalactiae/clasificación , Humanos , China , Antibacterianos/farmacología , Adulto , Infecciones Estreptocócicas/microbiología , Femenino , Masculino , Serogrupo , Farmacorresistencia Bacteriana Múltiple/genética , Serotipificación , Persona de Mediana Edad , Farmacorresistencia Bacteriana/genética , Adulto Joven , GenómicaRESUMEN
Dengue, a mosquito-borne viral disease, poses a significant public health challenge in Pakistan, with a significant outbreak in 2023, prompting our investigation into the serotype and genomic diversity of the dengue virus (DENV). NS-1 positive blood samples from 153 patients were referred to the National Institute of Health, Pakistan, between July and October 2023. Among these, 98 (64.1%) tested positive using multiplex real-time PCR, with higher prevalence among males (65.8%) and individuals aged 31-40. Serotyping revealed DENV-1 as the predominant serotype (84.7%), followed by DENV-2 (15.3%). Whole-genome sequencing of 18 samples (DENV-1 = 17, DENV-2 = 01) showed that DENV-1 (genotype III) samples were closely related (>99%) to Pakistan outbreak samples (2022), and approx. > 98% with USA (2022), Singapore and China (2016), Bangladesh (2017), and Pakistan (2019). The DENV-2 sequence (cosmopolitan genotype; clade IVA) shared genetic similarity with Pakistan outbreak sequences (2022), approx. > 99% with China and Singapore (2018-2019) and showed divergence from Pakistan sequences (2008-2013). No coinfection with dengue serotypes or other viruses were observed. Comparisons with previous DENV-1 sequences highlighted genetic variations affecting viral replication efficiency (NS2B:K55R) and infectivity (E:M272T). These findings contribute to dengue epidemiology understanding and underscore the importance of ongoing genomic surveillance for future outbreak responses in Pakistan.
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Virus del Dengue , Dengue , Brotes de Enfermedades , Variación Genética , Genoma Viral , Genotipo , Filogenia , Serogrupo , Secuenciación Completa del Genoma , Humanos , Pakistán/epidemiología , Virus del Dengue/genética , Virus del Dengue/clasificación , Virus del Dengue/aislamiento & purificación , Dengue/epidemiología , Dengue/virología , Masculino , Adulto , Femenino , Adulto Joven , Persona de Mediana Edad , Adolescente , Niño , Genoma Viral/genética , Preescolar , Anciano , Lactante , Serotipificación , ARN Viral/genéticaRESUMEN
Streptococcus suis is an important zoonotic pathogen causing severe infections in pigs and humans. Serotyping of S. suis strains is crucial for epidemiological surveillance, outbreak investigations, and understanding the pathogenesis of this bacterium. Here, we describe a step-by-step approach that enhances a previously developed pipeline by utilizing a computational script for efficient and accurate typing of S. suis strains. The pipeline is implemented in Perl programming language and leverages the Short Read Sequence Typing for Bacterial Pathogens (SRST2) tool. It integrates various bioinformatics techniques and utilizes multiple databases, including a serotype database, cpsH confirmation database, multi-locus sequence typing (MLST) database, recN species-specific gene database, and virulence gene database. These databases contain comprehensive information on S. suis serotypes, genetic markers, and virulence factors. The script can utilize paired-end or single-end fastq files as input and first confirms the species by sequence read data aligning to the recN gene, ensuring the accurate identification of S. suis strains. The pipeline next performs MLST typing and virulence factor identification using SRST2 while in a parallel processes it performs in silico serotyping of the strains. The pipeline offers a streamlined and semiautomated approach to serotyping S. suis strains, facilitating large-scale studies and reducing the manual effort required for data analysis.
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Biología Computacional , Tipificación de Secuencias Multilocus , Programas Informáticos , Streptococcus suis , Streptococcus suis/genética , Streptococcus suis/clasificación , Streptococcus suis/patogenicidad , Streptococcus suis/aislamiento & purificación , Tipificación de Secuencias Multilocus/métodos , Biología Computacional/métodos , Animales , Factores de Virulencia/genética , Humanos , Porcinos , Serotipificación/métodos , Técnicas de Tipificación Bacteriana/métodos , Simulación por Computador , Bases de Datos Genéticas , Infecciones Estreptocócicas/microbiologíaRESUMEN
This research attempted to clarify the clinical diagnostic value of combined detection of gastric function and Helicobacter pylori (Hp) serotyping in chronic gastritis and gastric cancer (GC). The 80 chronic non atrophic gastritis (CNAG) patients treated in our hospital from October 2021 to October 2022 received selection as the CNAG group. The 96 chronic atrophic gastritis (CAG) patients diagnosed by gastroscopy and pathology in the same period received selection as CAG group. During the same period, 50 patients diagnosed with GC received inclusion in GC group. Pepsin I (PG I), PG II (PG II), gastrin-17 (G-17) and Hp serotyping received detection and comparison in three groups. The diagnostic efficacy of PG â , PG â ¡, G-17, the ratio of serum PG I to PG II (PGR), and Hp serotyping in chronic gastritis and GC received evaluation by receiver operating characteristic (ROC). Relative to in the CNAG group, PG I and PGR levels in the other two groups exhibited depletion (P < 0.05); no statistical significance was observed in the PG II level among the three groups (P > 0.05); relative to the CNAG group, the G-17 level in the other two groups exhibited elevation (P < 0.05). Total Hp positive rate was 61.06 %, among which GC group exhibited the highest positive rate (72.00 %), and type I Hp positive rate also exhibited the highest in GC group (60.00 %). The type II Hp positive rate exhibited the highest in CNAG group (15.00 %). The PG I and PGR levels in type I Hp positive patients exhibited depletion relative to those in type II Hp positive patients, whereas PG II and G-17 levels exhibited elevation. When testing each indicator alone, the area under the curve (AUC) of PG I exhibited the highest in CNAG group, which was 0.874. When testing each indicator alone, AUC of Hp typing exhibited the highest in CAG group, which was 0.515. When testing each indicator alone, AUC of G-17 exhibited the highest in GC group, which was 0.787. The performance of combined detection was better than that of individual detection, with AUCs greater than 0.9 in three groups. In conclusion, changes in PG I, PG II, PGR and G-17 levels and Hp serotyping can receive application as screening indicators for chronic gastritis and GC, which can reflect relevant status of gastric mucosa to varying degrees. Combined detection of indicators has higher diagnostic performance and can receive application as an auxiliary diagnostic indicator in addition to gastroscopy biopsy, providing a reference basis for the formulation of clinical diagnosis and treatment plans.
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Gastritis , Infecciones por Helicobacter , Helicobacter pylori , Neoplasias Gástricas , Humanos , Neoplasias Gástricas/diagnóstico , Neoplasias Gástricas/microbiología , Gastritis/diagnóstico , Gastritis/microbiología , Masculino , Femenino , Infecciones por Helicobacter/diagnóstico , Infecciones por Helicobacter/microbiología , Persona de Mediana Edad , Adulto , Enfermedad Crónica , Gastrinas/sangre , Anciano , Curva ROC , Serotipificación/métodosRESUMEN
According to the 2020 CDC criteria, multisystem inflammatory syndrome in children (MIS-C) due to Coronavirus disease-19 (COVID-19) is diagnosed when all of the following criteria are met: fever for+≥+24 hours, laboratory evidence of inflammation, multisystem (+≥+2) organ involvement, evidence of SARS-CoV-2 infection or exposure, and no alternative plausible diagnoses (CDC, 2020). Alternative diagnosis need to be excluded before coming upon an MIS-C diagnosis since there are plenty of infectious diseases that may mimic MIS-C (Dworsky et al., Pediatr Infect Dis J 2021; 40; e159-e161; Yalçinkaya et al., Pediatr Infect Dis J 2021; 40; e524-e525; Kaneta et al., Pediatr Infect Dis J 2023; 42; 590-593; Stanzelova et al., Pediatr Infect Dis J 2023; 42; e201-e203; Kolsi et al., Arch Pediatr 2023; 30; 521-523). Herein, we present a 6-year-old girl who was preliminarily diagnosed with MIS-C and received intravenous immunoglobulin (IVIG) treatment before referral to our center. She was diagnosed with acute pneumococcal meningitis due to serotype 19 F and ultimately suffered from sensorineural hearing loss (SNHL) as a sequela. We present this case to remind physicians that MIS-C should not be diagnosed unless other infectious causes are excluded.
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COVID-19 , Errores Diagnósticos , Meningitis Neumocócica , SARS-CoV-2 , Síndrome de Respuesta Inflamatoria Sistémica , Humanos , COVID-19/diagnóstico , COVID-19/complicaciones , Síndrome de Respuesta Inflamatoria Sistémica/diagnóstico , Meningitis Neumocócica/diagnóstico , Meningitis Neumocócica/tratamiento farmacológico , Diagnóstico Diferencial , Femenino , Streptococcus pneumoniae , Niño , SerotipificaciónRESUMEN
BACKGROUND: In 2012, Botswana introduced 13-valent pneumococcal conjugate vaccine (PCV-13) to its childhood immunization program in a 3+0 schedule, achieving coverage rates of above 90% by 2014. In other settings, PCV introduction has been followed by an increase in carriage or disease caused by non-vaccine serotypes, including some serotypes with a high prevalence of antibiotic resistance. METHODS: We characterized the serotype epidemiology and antibiotic resistance of pneumococcal isolates cultured from nasopharyngeal samples collected from infants (≤12 months) in southeastern Botswana between 2016 and 2019. Capsular serotyping was performed using the Quellung reaction. E-tests were used to determine minimum inhibitory concentrations for common antibiotics. RESULTS: We cultured 264 pneumococcal isolates from samples collected from 150 infants. At the time of sample collection, 81% of infants had received at least one dose of PCV-13 and 53% had completed the three-dose series. PCV-13 serotypes accounted for 27% of isolates, with the most prevalent vaccine serotypes being 19F (n = 20, 8%), 19A (n = 16, 6%), and 6A (n = 10, 4%). The most frequently identified non-vaccine serotypes were 23B (n = 29, 11%), 21 (n = 12, 5%), and 16F (n = 11, 4%). Only three (1%) pneumococcal isolates were resistant to amoxicillin; however, we observed an increasing prevalence of penicillin resistance using the meningitis breakpoint (2016: 41%, 2019: 71%; Cochran-Armitage test for trend, p = 0.0003) and non-susceptibility to trimethoprim-sulfamethoxazole (2016: 55%, 2019: 79%; p = 0.04). Three (1%) isolates were multi-drug resistant. CONCLUSIONS: PCV-13 serotypes accounted for a substantial proportion of isolates colonizing infants in Botswana during a four-year period starting four years after vaccine introduction. A low prevalence of amoxicillin resistance supports its continued use as the first-line agent for non-meningeal pneumococcal infections. The observed increase in penicillin resistance at the meningitis breakpoint and the low prevalence of resistance to ceftriaxone supports use of third-generation cephalosporins for empirical treatment of suspected bacterial meningitis.
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Antibacterianos , Pruebas de Sensibilidad Microbiana , Infecciones Neumocócicas , Vacunas Neumococicas , Serogrupo , Streptococcus pneumoniae , Humanos , Streptococcus pneumoniae/efectos de los fármacos , Streptococcus pneumoniae/aislamiento & purificación , Streptococcus pneumoniae/clasificación , Botswana/epidemiología , Lactante , Infecciones Neumocócicas/microbiología , Infecciones Neumocócicas/epidemiología , Infecciones Neumocócicas/prevención & control , Infecciones Neumocócicas/tratamiento farmacológico , Vacunas Neumococicas/inmunología , Femenino , Antibacterianos/farmacología , Masculino , Farmacorresistencia Bacteriana , Serotipificación , Nasofaringe/microbiología , PrevalenciaRESUMEN
INTRODUCTION: Streptococcus pneumoniae cause a significant global health challenge. We aimed to determine nasopharyngeal carriage, serotypes distribution, and antimicrobial profile of pneumococci among the children of Aden. METHODOLOGY: A total of 385 children, aged 2-17 years, were included. Asymptomatic samples were randomly collected from children in selected schools and vaccination centers. Symptomatic samples were obtained from selected pediatric clinics. The nasopharyngeal swabs were tested for pneumococci using culture and real time polymerase chain reaction (RT-PCR). Serotyping was done with a pneumotest-latex kit and antimicrobial susceptibility was tested by disc diffusion and Epsilometer test. RESULTS: The total pneumococcal carriage was 44.4% and 57.1% by culture and RT-PCR, respectively. There was a statistically significant association between carriage rate and living in single room (OR = 7.9; p = 0.00001), sharing a sleeping space (OR = 15.1; p = 0.00001), and low monthly income (OR = 2.02; p = 0.007). The common serotypes were 19, 1, 4, 5, 2, and 23. The proportion of non-pneumococcal conjugate vaccine (non-PCV13) serotypes was 24%. Pneumococci were resistant to penicillin (96.5%), cefepime (15.8%), ceftriaxone (16.4%), and amoxicillin-clavulanate (0%). Erythromycin, azithromycin, and doxycycline had resistance rates of 48%, 31%, and 53.3%, respectively. CONCLUSIONS: A high pneumococcal carriage rate was observed in Yemeni children, particularly in low-income households and shared living conditions. There was significant penicillin resistance at meningitis breakpoint. Furthermore, non-PCV13 serotypes were gradually replacing PCV13 serotypes. The findings underscore the urgent need for enhanced surveillance and stewardship to improve vaccination and antibiotic policies in Yemen.