Historical, current, and emerging tools for identification and serotyping of Shigella.

The Shigella genus includes serious foodborne disease etiologic agents, with 4 species and 54 serotypes. Identification at species and serotype levels is a crucial task in microbiological laboratories. Nevertheless, the genetic similarity between Shigella spp. and Escherichia coli challenges the correct identification and serotyping of Shigella spp., with subsequent negative repercussions on surveillance, epidemiological investigations, and selection of appropriate treatments. For this purpose, multiple techniques have been developed historically ranging from phenotype-based methods and single or multilocus molecular techniques to whole-genome sequencing (WGS). To facilitate the selection of the most relevant method, we herein provide a global overview of historical and emerging identification and serotyping techniques with a particular focus on the WGS-based approaches. This review highlights the excellent discriminatory power of WGS to more accurately elucidate the epidemiology of Shigella spp., disclose novel promising genomic targets for surveillance methods, and validate previous well-established methods.

Increase in Streptococcus pneumoniae serotype 3 associated parapneumonic pleural effusion/empyema after the introduction of PCV13 in Germany.

INTRODUCTION: Pediatric pneumococcal pneumonia complicated by parapneumonic pleural effusion/empyema (PPE/PE) remains a major concern despite general immunization with pneumococcal conjugate vaccines (PCVs). METHODS: In a nationwide pediatric hospital surveillance study in Germany we identified 584 children <18 years of age with bacteriologically confirmed PPE/PE from October 2010 to June 2018. Streptococcus pneumoniae was identified by culture and/or PCR of blood samples and/or pleural fluid and serotyped. RESULTS: S. pneumoniae was identified in 256 of 584 (43.8%) children by culture (n = 122) and/or PCR (n = 207). The following pneumococcal serotypes were detected in 114 children: serotype 3 (42.1%), 1 (25.4%), 7F (12.3%), 19A (7.9%), other PCV13 serotypes (4.4%) and non-PCV13 serotypes (7.9%). Between October 2010 and June 2014 serotype 1 (38.1%) and serotype 3 (25.4%) were most prevalent, whereas between July 2014 and June 2018 serotype 3 (62.7%) and non-PCV13 serotypes (15.7%) were dominant. Compared to children with other pneumococcal serotypes, children with serotype 3 associated PPE/PE were younger (median 3.2 years [IQR 2.1-4.3 years] vs. median 5.6 years [IQR 3.8-8.2 years]; p < 0.001) and more frequently admitted to intensive care (43 [89.6%] vs. 48 [73.8%]; p = 0.04). Seventy-six of 114 (66.7%) children with pneumococcal PPE/PE had been vaccinated with pneumococcal vaccines. Thirty-nine of 76 (51.3%) had received a vaccine covering the serotype detected. Thirty of these 39 breakthrough cases were age-appropriately vaccinated with PCV13 and considered vaccine failures, including 26 children with serotype 3, three children with serotype 19A and one child with serotype 1. CONCLUSION: Following the introduction of PCV13 in general childhood vaccination we observed a strong emergence of serotype 3 associated PPE/PE in the German pediatric population, including a considerable number of younger children with serotype 3 vaccine breakthrough cases and failures. Future PCVs should not only cover newly emerging serotypes, but also include a more effective component against serotype 3.

Native trees of the Northeast Argentine: natural hosts of the Cryptococcus neoformans-Cryptococcus gattii species complex / Árboles autóctonos del nordeste argentino. Huéspedes naturales de las especies del complejo Cryptococcus neoformans-Cryptococcus gattii

Background. In Argentina, information about epidemiology and environmental distribution of Cryptococcus is scarce. The city of Resistencia borders with Brazil and Paraguay where this fungus is endemic. All these supported the need to investigate the ecology of the genus and the epidemiology of cryptococcosis in this area. Aims. The aim was to investigate the presence of species of Cryptococcus neoformans-Cryptococcus gattii complex and their genotypes in trees of the city of Resistencia. Methods. One hundred and five trees were sampled by swabbing technique. The isolates were identified using conventional and commercial methods and genotyped by PCR-RFLP (Restriction Fragment Length Polymorphism). Results. Cryptococcus was found in 7 out of the total trees. 6 out of 7 Cryptococcus isolates were identified as C. neoformans and one as C. gattii. C. gattii was isolated from Grevillea robusta. C. neoformans strains were isolated from Tabebuia avellanedae and Peltophorum dubium. Genotyping showed that all C. neoformans belonged to the VNI type and C. gattii belonged to the VGI type. Conclusions. This represents the first study on the ecology of Cryptococcus spp. associated to trees from northeastern Argentina, and the first report describing Grevillea robusta as a host of members of this fungal genus. Another finding is the isolation of C. neoformans from Tabebuia avellanedae and Peltophorum dubium, both tree species native to northeastern Argentina (AU)

Antecedentes. En Argentina la información sobre la epidemiología y la distribución ambiental de Cryptococcus es escasa.. Resistencia es una ciudad que limita con Brasil y Paraguay, donde este hongo es endémico. Esto apoya la necesidad de investigar la ecología de este género y la epidemiología de la criptococosis en la región. Objetivos. El objetivo del presente estudio fue investigar la presencia de especies del complejo Cryptococcus neoformans - Cryptococcus gattii y sus genotipos en árboles de la ciudad de Resistencia, situada en el nordeste argentino. Métodos. Mediante la técnica del hisopo se tomaron muestras de 105 árboles. Los aislamientos se identificaron utilizando métodos convencionales y comerciales, y se genotipificaron mediante la prueba PCR-RFLP (Restriction Fragment Length Polimorphism). Resultados. Se aisló Cryptococcus en 7 árboles. Se identificaron 6 aislamientos como Cryptococcus neoformans y uno como Cryptococcus gattii. Este último se aisló de Grevillea robusta. Cryptococcus neoformans se aisló de Tabebuia avellanedae y Peltophorum dubium. La genotipificación mostró que todos los aislamientos de C. neoformans pertenecían al tipo molecular VNI, y C. gattii al tipo molecular VGI. Conclusiones. El presente estudio es la primera investigación sobre la ecología del género Cryptococcus asociado a árboles del nordeste argentino, y la primera que describe Grevillea robusta como nicho ecológico de este género fúngico. Otro hallazgo es el aislamiento de C. neoformans de Tabebuia avellanedae y Peltophorum dubium, ambas especies de árboles originarias del nordeste argentino (AU)

Bacteriemia neumocócica durante el año 2009 en un hospital pediátrico de nivel 2: características clínicas y microbiológicas / Bacteremia pneumococcal throughout 2009 in a level 2 children's hospital: clinical and microbiological characteristics

Objetivo: Estudiar las características clínicas y microbiológicas de los pacientes con hemocultivo positivo a Streptococcus pneumoniae durante el año 2009 en un hospital pediátrico de nivel 2. Material y métodos: Estudio observacional descriptivo de los pacientes pediátricos con hemocultivo positivo a neumococo desde el 1 de enero hasta el 31 de diciembre de 2009. Se analizaron las siguientes variables: edad, vacunación antineumocócica conjugada heptavalente, antibioterapia previa, diagnóstico clínico, serotipo y sensibilidad antibiótica, así como la necesidad de ingreso hospitalario. Resultados: Se detectaron 15 pacientes con hemocultivo positivo a S. pneumoniae. El 60% de los aislamientos se obtuvo en niños entre 3 y 36 meses de edad. El diagnóstico clínico más frecuente fue neumonía, con o sin derrame pleural (67%). El serotipo aislado más frecuentemente fue el 1 (40%). Todos los pacientes infectados por el serotipo 1 presentaban como manifestaciónclínica la neumonía. Todas las cepas aisladas fueronsensibles a penicilina y cefotaxima según los nuevos criterios del Clinical Laboratory Standards Institute (2008). El 80%de los serotipos aislados están incluidos en la vacuna antineumocócica conjugada 13-valente, el 67% en la 10-valente y ninguno en la 7-valente.Conclusión: Los serotipos más frecuentemente aislados productores de enfermedad neumocócica invasiva durante el año2009 en nuestro centro son serotipos no incluidos en la vacuna antineumocócica conjugada heptavalente. Todos los serotipos aislados fueron sensibles a penicilina y cefotaxima(AU)

Objective: To study the clinical and microbiological characteristics of patients with positive blood culture for Streptococcus pneumoniae in 2009 in a pediatric level 2 hospital. Material and methods: Retrospective observational study of pediatric patients with positive blood culture for Streptococcus pneumoniae from January 1st to December 31st 2009. We analyzed the following variables: age, heptavalent pneumococcal conjugate vaccine (PCV7), previous antibiotic therapy, clinical diagnosis, serotype and antibiotic sensitivity and need for hospitalization. Results: We identified 15 patients with positive blood culture for S. pneumoniae (60%) and were obtained in children aged between 3 and 36 months of age. The most common clinical diagnosis was pneumonia with or without pleural effusion(67%). Serotype 1 was the most frequently isolated serotype(40%). All serotype 1-infected patients had pneumonia as a clinical manifestation. All isolates were susceptible to penicillin and cefotaxime under the new criteria of the Clinical Laboratory Standards Institute (2008). 80% of the isolated serotypes are included in pneumococcal conjugate vaccine13-valent, 67% in 10-valent and none in 7-valent.Conclusion: The most frequently isolated invasive pneumococcal disease producing serotypes in our center in 2009 were serotypes not included in PCV7 and were sensitive to penicillin and cefotaxime(AU)

Basic rationale, current methods and future directions for molecular typing of human enterovirus.

Enterovirus is a genus of the Picornaviridae family including more than 80 serotypes belonging to four species designed Human enterovirus A to D. The antigens of the structural proteins support the subdivision of enteroviruses into multiple serotypes. Comparative phylogeny based on molecular typing methods has been of great help to classify former and new types of enterovirus, and to investigate the diversity of enteroviruses and the evolutionary mechanisms involved in their diversity. By now, molecular typing methods of enterovirus rely mainly on the sequencing of an amplicon targeting a variable part of the region coding for the capsid proteins (VP1 and, alternatively, VP2 or VP4), either from a strain recovered by cell culture or, more recently, by direct amplification of a clinical or environmental specimen. In the future, microarrays are thought to play a major role in enterovirus typing and in the analysis of the determinants of virulence that support the puzzling diversity of the pathological conditions associated with human infection by these viruses.

Trends in serotypes and antimicrobial susceptibility of group B streptococci isolated in Korea.

Studies of group B streptococci (GBS) have been limited in Korea, despite the necessity for such studies because of the increase in serious adult infections, the emergence of new serotypes, and the increase of resistance to certain antibiotics. In this study, trends in serotypes of GBS isolated in Korea were compared to determine any changes and emergence of new types, while antimicrobial susceptibility was tested and compared with that of group A streptococci (GAS). It was found that the most frequent infections caused by GBS were of the urinary tract, but other severe infections also occurred not only in newborns but also in adults. The prevalent serotypes were still Ia, Ib, and III, while new serotypes, VI and VIII, also emerged. GBS were susceptible to beta-lactam antibiotics, but were much less so than GAS. The resistance rates to erythromycin and tetracycline were much higher than those in other countries, suggesting that these antibiotics are no longer very useful in Korea for the treatment of GBS infections.