Genomic characterization of invasive meningococcal X isolates from Brazil, 1992–2022 / Caracterización genómica de aislamientos invasivos de meningococo X de Brasil, 1992–2022

Introduction: Invasive meningococcal disease (IMD) is a major health problem. Given the post-COVID-19 pandemic scenario with the loosening of the non-pharmacological measures to control the virus transmission and considering the observed global reduction of meningococcal vaccination coverage, an increase in IMD cases can be expected. Methodology: Using whole-genome sequencing, we characterized six Neisseria meningitidis serogroup X (MenX) isolates recovered from IMD cases in Brazil in the last 30 years. Results: The predominance (66.6%, 4/6) of ST2888 presenting fHbp 160, NHBA 129, NadA 21, and PorA 19,15 was found on isolates. Two novel STs, 15458 and 15477, were described. Conclusion: This study describes the circulation of MenX lineage ST2888 in Brazil, previously reported only in Europe. Continuous universal surveillance is crucial to implement prompt public health measures aiming to prevent and control non-vaccine preventable serogroup X IMD cases.(AU)

Genomic characterization of invasive meningococcal X isolates from Brazil, 1992-2022.

INTRODUCTION: Invasive meningococcal disease (IMD) is a major health problem. Given the post-COVID-19 pandemic scenario with the loosening of the non-pharmacological measures to control the virus transmission and considering the observed global reduction of meningococcal vaccination coverage, an increase in IMD cases can be expected. METHODOLOGY: Using whole-genome sequencing, we characterized six Neisseria meningitidis serogroup X (MenX) isolates recovered from IMD cases in Brazil in the last 30 years. RESULTS: The predominance (66.6%, 4/6) of ST2888 presenting fHbp 160, NHBA 129, NadA 21, and PorA 19,15 was found on isolates. Two novel STs, 15458 and 15477, were described. CONCLUSION: This study describes the circulation of MenX lineage ST2888 in Brazil, previously reported only in Europe. Continuous universal surveillance is crucial to implement prompt public health measures aiming to prevent and control non-vaccine preventable serogroup X IMD cases.

Penicillin-resistant, ampicillin-susceptible Enterococcus faecalis isolates are uncommon in non-clinical sources.

This study aimed to investigate whether penicillin-resistant, ampicillin-susceptible E. faecalis (PRASEF) isolates are disseminated in non-clinical sources, and to compare the molecular characteristics and antimicrobial resistance (AMR) profile of clinical and non-clinical E. faecalis isolates. Non-clinical samples (n = 280) were collected and 101 E. faecalis isolates were recovered from food (n = 18), faeces of healthy animals (n = 24), water (n = 28) and sewage (n = 31). PRASEF (n = 68) and penicillin-susceptible, ampicillin-susceptible E. faecalis (n = 77) isolates of clinical origin were also evaluated. A significant variety of AMR profiles was observed among non-clinical isolates according to the source. No food isolate exhibited a multidrug resistance (MDR) phenotype different from those of isolates from animal faeces (50.0%) and sewage (38.7%). Overall, the MDR phenotype was more frequent among clinical (56.6%) than non-clinical isolates (22.8%) (p < 0.01). Non-clinical PRASEF isolates (n = 3) were only recovered from hospital sewage. Note that representative clinical and non-clinical PRASEF isolates were grouped in pulsotype A, and belonged to CC9 (clonal complex). In conclusion, E. faecalis isolates exhibiting the unusual penicillin-resistant but ampicillin-susceptible phenotype appeared to be restricted to the hospital environment. Our findings highlight the ability of PRASEF isolates to survive in sewage, which could enable these hospital-adapted lineages to spread to new ecological niches.

Genomic surveillance of invasive Streptococcus pneumoniae isolates in the period pre-PCV10 and post-PCV10 introduction in Brazil.

In 2010, Brazil introduced the 10-valent pneumococcal conjugate vaccine (PCV10) into the national children's immunization programme. This study describes the genetic characteristics of invasive Streptococcus pneumoniae isolates before and after PCV10 introduction. A subset of 466 [pre-PCV10 (2008-2009): n=232, post-PCV10 (2012-2013): n=234;<5 years old: n=310, ≥5 years old: n=156] pneumococcal isolates, collected through national laboratory surveillance, were whole-genome sequenced (WGS) to determine serotype, pilus locus, antimicrobial resistance and genetic lineages. Following PCV10 introduction, in the <5 years age group, non-vaccine serotypes (NVT) serotype 3 and serotype 19A were the most frequent, and serotypes 12F, 8 and 9 N in the ≥5 years old group. The study identified 65 Global Pneumococcal Sequence Clusters (GPSCs): 49 (88 %) were GPSCs previously described and 16 (12 %) were Brazilian clusters. In total, 36 GPSCs (55 %) were NVT lineages, 18 (28 %) vaccine serotypes (VT) and 11 (17 %) were both VT and NVT lineages. In both sampling periods, the most frequent lineage was GPSC6 (CC156, serotypes 14/9V). In the <5 years old group, a decrease in penicillin (P=0.0123) and cotrimoxazole (P<0.0001) resistance and an increase in tetracycline (P=0.019) were observed. Penicillin nonsusceptibility was predicted in 40 % of the isolates; 127 PBP combinations were identified (51 predicted MIC≥0.125 mg l-1); cotrimoxazole (folA and/or folP alterations), macrolide (mef and/or ermB) and tetracycline (tetM, tetO or tetS/M) resistance were predicted in 63, 13 and 21.6 % of pneumococci studied, respectively. The main lineages associated with multidrug resistance in the post-PCV10 period were composed of NVT, GPSC1 (CC320, serotype 19A), and GPSC47 (ST386, serotype 6C). The study provides a baseline for future comparisons and identified important NVT lineages in the post-PCV10 period in Brazil.

Molecular characterization of Latin American invasive Streptococcus pneumoniae serotype 19A isolates.

Streptococcus pneumoniae is a major cause of morbidity and mortality worldwide, especially among children and the elderly. S. pneumoniae serotype 19A has emerged as a major cause of invasive disease in many countries, regardless of whether pneumococcal conjugate vaccines are used. The aim of this study was molecular characterization of invasive S. pneumoniae serotype 19A isolates recovered between 2000 and 2015 from 13 National Laboratories through the laboratory-based surveillance of invasive S. pneumoniae program SIREVA II in Latin American countries. The isolates were submitted with antimicrobial susceptibility tests and were genotyped by a combination of pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Of the 185 isolates assayed, notable rates of resistance to penicillin (MIC ≥ 0.125 µg/mL; 68.6%), tetracycline (63.7%), trimethoprim-sulfamethoxazole (63.2%), and erythromycin (43.2%) were observed, while 44.3% of isolates were multidrug resistant. The most frequently observed sequence types (ST) were ST320 (32.4%), ST199 (14.1%), ST172 (10.8%) and ST5204 (7.1%). The distribution of STs indicated regional differences in the epidemiology of the clonal groups. The present study showed a diverse genetic background of the pneumococcal population in Latin American countries. Continuous surveillance of the pneumococcal serotype 19A population in the region will be necessary to obtain information about geographical differences and changes in the spread and the establishment of particular clones.

Long-term effect of 10-valent pneumococcal conjugate vaccine on nasopharyngeal carriage of Streptococcus pneumoniae in children in Brazil.

Brazil introduced the 10-valent pneumococcal vaccine (PCV10) to the routine national immunization program (NIP) in March 2010. In 2017, we investigated the effects of PCV10 on nasopharyngeal carriage of vaccine-types (VT) and non-vaccine-types (NVT) of Streptococcus pneumoniae (Spn) among children living in São Paulo city. We also compared the prevalence of VT and NVT with previous carriage surveys performed in 2010 (baseline) and 2013. METHOD: The carriage survey was conducted among 531 children, aged 12 months to <24 months, recruited from public Primary Health Units during the immunization campaign, using previous surveys methodology, except for qPCR, which was performed in the 2017 survey only. RESULTS: No statistical difference was found in the prevalence of Spn either by culture (59.7%) or by qPCR (61.2%). Spn carriage increased from 40.3% (baseline) to 59.7% (2017 survey) (p < 0.001). Colonization by VT isolates significantly decreased by 90.9% (19.8-1.8%) and 95.5% (19.8-0.9%) in the 2013 and 2017 surveys, respectively, compared to that at baseline. NVT isolates increased significantly by 128% (19.6-44.8%) and 185% (19.6-55.9%) in the respective post-PCV10 surveys, most led to high prevalence of serotypes 6C (27%), 15B (9.8%), 19A (9.2%), 15A (6.0%), and 16F (5.7%). In 2017, reduction in serotype 6A (4.2-0.6%, p < 0.001) and increase in serotype 19A (1.8-6.0%, p = 0.001) were found; serotype 3 isolate was not detected in the present survey. We identified the emergence of 19A isolates CC320, associated with high penicillin (MIC ≥ 2.0 mg/L) and cefotaxime (MIC ≥ 1.0 mg/L) values. CONCLUSION: After 7 years of PCV10 introduction in the NIP, colonization by VT among toddlers decreased substantially to a residual level, along with substantial serotype replacement by novel serotypes not present in any current conjugated pneumococcal vaccine and serotype 19A. The present findings can assist policy decisions in Brazil.

Long-term effect of 10-valent pneumococcal conjugate vaccine on nasopharyngeal carriage of Streptococcus pneumoniae in children in Brazil

Brazil introduced the 10-valent pneumococcal vaccine (PCV10) to the routine national immunization program (NIP) in March 2010. In 2017, we investigated the effects of PCV10 on nasopharyngeal carriage of vaccine-types (VT) and non-vaccine-types (NVT) of Streptococcus pneumoniae (Spn) among children living in São Paulo city. We also compared the prevalence of VT and NVT with previous carriage surveys performed in 2010 (baseline) and 2013. Method: The carriage survey was conducted among 531 children, aged 12 months to <24 months, recruited from public Primary Health Units during the immunization campaign, using previous surveys methodology, except for qPCR, which was performed in the 2017 survey only. Results: No statistical difference was found in the prevalence of Spn either by culture (59.7%) or by qPCR (61.2%). Spn carriage increased from 40.3% (baseline) to 59.7% (2017 survey) (p < 0.001). Colonization by VT isolates significantly decreased by 90.9% (19.8­1.8%) and 95.5% (19.8­0.9%) in the 2013 and 2017 surveys, respectively, compared to that at baseline. NVT isolates increased significantly by 128% (19.6­44.8%) and 185% (19.6­55.9%) in the respective post-PCV10 surveys, most led to high prevalence of serotypes 6C (27%), 15B (9.8%), 19A (9.2%), 15A (6.0%), and 16F (5.7%). In 2017, reduction in serotype 6A (4.2­0.6%, p < 0.001) and increase in serotype 19A (1.8­6.0%, p = 0.001) were found; serotype 3 isolate was not detected in the present survey. We identified the emergence of 19A isolates CC320, associated with high penicillin (MIC 2.0 mg/L) and cefotaxime (MIC 1.0 mg/L) values. Conclusion: After 7 years of PCV10 introduction in the NIP, colonization by VT among toddlers decreased substantially to a residual level, along with substantial serotype replacement by novel serotypes not present in any current conjugated pneumococcal vaccine and serotype 19A. The present findings can assist policy decisions in Brazil

Características fenotípicas e moleculares de cepas de Streptococcus pneumoniae do sorotipo 19A isoladas de doenças invasivas e de portadores antes e após a introdução da vacina conjugada 10-valente no Brasil / Phenotypic and molecular characteristics of Streptococcus pneumoniae serotype 19A strains isolated from invasive diseases and from carriers before and after the introduction of the 10-valent conjugate vaccine in Brazil

Introdução: Com a introdução das vacinas pneumocócicas conjugadas 7-valente (PCV7) e 10-valente (PCV10), diversos países reportaram o aumento de Streptococcus pneumoniae do sorotipo 19A (Spn19A) como principal causa de doenças pneumocócicas invasivas (DPI) e em portadores da nasofaringe. Objetivo: O objetivo deste estudo foi avaliar as características fenotípicas e moleculares de cepas de Spn19A no Brasil. Metodologia: A totalidade das cepas de DPI de Spn19A recebidas pelo Instituto Adolfo Lutz nos anos de 2014 a 2017 (n=446) foram analisadas quanto à prevalência e a resistência antimicrobiana, e todas as cepas dos grupos etários <5 anos e ≥50 anos (n=265) foram selecionadas para caracterização molecular por ¨Multilocus Sequence Type¨; para portadores, foram selecionadas todas as cepas Spn19A (n=32) de crianças <2 anos de um estudo realizado em São Paulo no ano de 2017. Para o sequenciamento de genoma completo (WGS), 50 cepas de Spn19A isoladas de DPI (2005-2015) e de portadores (2010 e 2013) foram selecionadas. Resultados: De acordo com os dados de...(AU)

Expansion of the multidrug-resistant clonal complex 320 among invasive Streptococcus pneumoniae serotype 19A after the introduction of a ten-valent pneumococcal conjugate vaccine in Brazil.

BACKGROUND: In 2010, a ten-valent pneumococcal conjugate vaccine (PCV10) was introduced in the routine infant national immunization program in Brazil. Invasive pneumococcal disease (IPD) caused by serotype 19A (Spn19A) increased after the introduction of PCVs in several countries. We compared the frequency, antimicrobial resistance and molecular patterns of invasive Spn19A strains before and after PCV10 introduction in Brazil using data from the national laboratory-based surveillance. METHODS: We analyzed invasive Spn19A strains isolated from 2005-2009 (pre-PCV10 period), 2011-2015 and 2016-2017 (post-PCV10 periods). Antimicrobial susceptibility was performed for all Spn19A strains, and multilocus sequence typing (MLST) was performed for strains isolated in the age groups <5 years and ≥50 years. RESULTS: Among the study period, a total of 9,852 invasive Spn strains were analyzed, and 673 (6.8%) belonged to serotype 19A. Overall, the proportion of Spn19A among the total number of IPD strains increased from 2.8% in 2005-2009 to 7.0% and 16.4% in 2011-2015 and 2016-2017, respectively. The relative increase in Spn19A was observed especially in children <5 years old (2005-2009: 3.2%; 2011-2015: 15.5%; 2016-2017: 31.2%). The percentage of penicillin resistance (MIC 2.0-4.0 µg/mL), erythromycin resistance and multidrug resistance (MDR) increased after PCV10 introduction due to the expansion of the MDR clonal complex CC320 (2005-2009: 8.6%; 2011-2015: 56.1%; 2016-2017: 66.5%). CONCLUSION: We observed an expansion of MDR-CC320 among invasive Spn19A strains after PCV10 introduction in Brazil, probably related to a combination of factors, such as vaccination and antimicrobial pressure. Continued surveillance of Spn19A strains is necessary to monitor the sustainability of this clonal complex in the Brazilian population.

Emergence of resistance to ciprofloxacin in Neisseria meningitidis in Brazil.

To prevent secondary invasive meningococcal disease (IMD) cases and outbreaks, antimicrobial prophylaxis of high-risk contacts is indicated. This study reports two ciprofloxacin-resistant Neisseria meningitidis strains in Brazil. The 3523 N. meningitidis isolates collected throughout Brazil from 2009 to 2016 were evaluated for antimicrobial resistance. Meningococcal isolates showing minimal inhibitory concentrations, MICs≥0.125µg ml-1 to ciprofloxacin, were analysed to determine the presence of mutations in the quinolone resistance-determining regions (QRDRs) of gyrA and parC genes. Two ciprofloxacin-resistant N. meningitidis isolates were found, both presenting a single mutation in the quinolone resistance-determining region of the gyrA gene. These results confirmed that ciprofloxacin is still a first-line drug for chemoprophylaxis. However, we highlight the importance of continued surveillance to monitor the trends of N. meningitidis susceptibility profiles to the antimicrobials recommended for chemoprophylaxis and IMD treatment.

Avaliação do teste de aglutinação microscópica utilizando-se como antígeno leptospiras saprófitas para o diagnóstico da leptospirose humana / Evaluation of microscopic agglutination test using saprophytic leptospires for diagnosis of human leptospirosis

O objetivo deste trabalho foi avaliar a capacidade de efetuar o diagnóstico precoce do teste de aglutinação microscópica (MAT) utilizando-se como antígeno leptospiras saprófitas sorovar Patoc (MAT-Patoc). Neste contexto, os resultados obtidos em amostras de soro de casos confirmados de leptospirose foram comparados com aqueles obtidos no teste ELISA IgM. Cento e cinquenta e oito amostras colhidas na fase aguda da doença foram analisadas pelo MAT-Patoc. Os soros com títulos ≥ 50 foram considerados reagentes. A sensibilidade do MAT-Patoc e do ELISA-IgM foi de 13,29% e 28,48%, respectivamente. Nos sete primeiros dias da doença, o MAT-Patoc foi capaz de detectar 12,29% dos casos, enquanto o ELISA-IgM detectou 24,59%. O MAT-Patoc foi reagente em amostras de casos cujos prováveis sorogrupos infectantes foram Icterohaemorrhagiae, Cynopteri e Ballum. Em conclusão, a utilização do teste MAT-Patoc apresentou menor sensibilidade no diagnóstico quando comparado ao ELISA-IgM, embora tenha sido reagente em algumas amostras com resultado não reagente. O MAT-Patoc deve ser utilizado em combinação com ELISA-IgM para melhorar a sensibilidade do diagnóstico de leptospirose na primeira fase da doença, com subsequente confirmação pelo MAT de referência.

The aim of this study was to evaluate the early detection of antibodies by the microscopic agglutination test (MAT) using saprophytic leptospira serovar Patoc (MAT-Patoc), in serum samples from patients with confirmed leptospirosis. The obtained results were compared with those found in ELISA-IgM. A hundred fifty-eight serum samples collected from patients in acute phase of illness were analysed by MAT-Patoc. Samples with titers ≥ 50 were considered positive. The sensitivity of MAT-Patoc and IgM-ELISA was 13.29 % and 28.48 %, respectively. In the first seven days of the disease, MAT-Patoc was positive in 12.29 % of the cases, while the IgM-ELISA was positive in 24.59 %. The MAT-Patoc was positive in sera from confirmed cases, and the infecting serogroups were Icterohaemorrhagiae, Cynopteri and Ballum. In conclusion, the use of MAT-Patoc test showed lower sensitivity for diagnosing leptospirosis when compared with ELISA-IgM, although positive reactivity was found in some samples with negative results. The MAT-Patoc should be used in combination with ELISA-IgM to improve the sensitivity of the diagnosis of leptospirosis in the first phase of the disease, with subsequent confirmation by standard MAT.

Importância de Streptococcus pneumoniae do sorotipo 19A isolados de doenças invasivas e de portadores antes e após a introdução da vacina conjugada 10-valente no Brasil

Em 2010 foi introduzida a vacina pneumocócica conjugada 10-valente (PCV10) no calendário de imunização infantil no Brasil. Com a introdução das vacinas conjugadas diversos países reportaram o aumento de Streptococcus pneumoniae do sorotipo 19A (Spn19A) em portadores e como principal causa de doenças pneumocócicas invasivas (DPI). O objetivo deste estudo foi avaliar o efeito da introdução da PCV10 nas características fenotípicas e moleculares de Spn19A isolados de DPI e de portadores. Do banco de dados do Núcleo de Meningites, Pneumonias e Infecções Pneumocócicas do Instituto Adolfo Lutz foram selecionadas todas as cepas de Spn19A do período de 2005 a 2013 para as análises de prevalência e resistência antimicrobiana, e, destas, foram selecionadas todos os isolados de DPI (n=155) de pacientes das faixas etárias mais afetadas pela DPI (<5 anos e ≥50 anos) para caracterização molecular por Multi Locus Sequence Type. Também foram selecionados isolados (n=22) de portadores dos anos de 2010 e 2013. De acordo com os dados de vigilância laboratorial passiva, pode-se notar que apesar do aumento no numero de cepas invasivas de Spn19A, este aumento não foi significativo, variando de 2,8% no período pré-vacinal para 4,4% no período pós-vacinal. Foi observada uma diminuição nos percentuais de resistência à penicilina nas cepas isoladas de DPI, porém não significativo, de 39,5% para 30,5% nos períodos pré- e pós-vacinal respectivamente, porém houve aumento significativo da multirresistência nestes períodos (18,5% - 43,5%). Das 155 cepas invasivas, no período pré-vacinal foi observada prevalência do CC62 (55,2%), principalmente relacionado à ST1118; neste período este CC apresentava-se disseminado nas cinco regiões geográficas do Brasil. No período pós-PCV10, o CC320 (53,1%) foi o mais frequente, principalmente relacionado à ST320, que também foi observada nas cinco regiões...

In 2010, it was introduced a 10-valent pneumococcal conjugate vaccine (PCV10) in Brazil. Since the introduction of conjugate vaccines, many countries have reported an increase in Streptococcus pneumoniae serotype 19A (Spn19A) in invasive pneumococcal disease (IPD) and carriage.The aim of this study was to evaluate the effect of PCV10 introduction in phenotypic and molecular characteristics of Spn19A isolated from IPD and carriers. From database of Meningitis, Pneumonia and Pneumococcal Infections Laboratory, Center of Bacteriology, Institute Adolfo Lutz were selected all Spn19A strains collected in 2005 to 2013 for analysis of prevalence and antimicrobial resistance. Of these, all invasive isolates of most affected age groups patients by IPD (<5 and ≥50 years) were selected (n=155) to molecular characterization by Multi Locus Sequence Type. Were also selected isolates (n=22) of nasopharyngeal carriages from 2010 and 2013. According to the passive laboratory surveillance data it can be noted that despite the increase in number of invasive strains of Spn19A, this increase was not significant, ranging from 2.8% in the pre-vaccine period to 4.4% in the post-vaccination period. There was no significant decrease in penicillin resistance in strains isolated from IPD (39.5% pré- to 30.5% post-vaccination), but there was a significant increase in multidrug resistance in these periods (18.5% - 43.5%). Of the 155 invasive strains in the pre-vaccine period it was observed prevalence of CC62 (55.2%), mainly related to ST1118; this CC had become widespread in the five geographical regions of Brazil in this period. In the post-PCV... .