Population structure of Neisseria meningitidis ST-9493 identified in Colombian isolates

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.

Leading causes of excess mortality in Mexico during the COVID-19 pandemic 2020-2021: A death certificates study in a middle-income country

Background

The death toll after SARS-CoV-2 emergence includes deaths directly or indirectly associated with COVID-19. Mexico reported 325,415 excess deaths, 34.4% of them not directly related to COVID-19 in 2020. In this work, we aimed to analyse temporal changes in the distribution of the leading causes of mortality produced by COVID-19 pandemic in Mexico to understand excess mortality not directly related to the virus infection.

Methods

We did a longitudinal retrospective study of the leading causes of mortality and their variation with respect to cause-specific expected deaths in Mexico from January 2020 through December 2021 using death certificate information. We fitted a Poisson regression model to predict cause-specific mortality during the pandemic period, based on the 2015–2019 registered mortality. We estimated excess deaths as a weekly difference between expected and observed deaths and added up for the entire period. We expressed all-cause and cause-specific excess mortality as a percentage change with respect to predicted deaths by our model.

Findings

COVID-19 was the leading cause of death in 2020–2021 (439,582 deaths). All-cause total excess mortality was 600,590 deaths (38⋅2% [95% CI: 36·0 to 40·4] over expected). The largest increases in cause-specific mortality, occurred in diabetes (36·8% over expected), respiratory infections (33·3%), ischaemic heart diseases (32·5%) and hypertensive diseases (25·0%). The cause-groups that experienced significant decreases with respect to the expected pre-pandemic mortality were infectious and parasitic diseases (-20·8%), skin diseases (-17·5%), non-traffic related accidents (-16·7%) and malignant neoplasm (-5·3%).

Interpretation

Mortality from COVID-19 became the first cause of death in 2020–2021, the increase in other causes of death may be explained by changes in the health service utilization patterns caused by hospital conversion or fear of the population using them. Cause-misclassification cannot be ruled out.

Funding

This study was funded by Conacyt.

COVID-19 laboratory preparedness and response in the Americas Region: Lessons learned

By the time the etiologic agent of the COVID-19 was identified as a novel coronavirus, no country in the Americas Region had laboratory capacity for detecting this new virus. A strategic multilevel approach with specific reagent purchase and delivery, regional trainings, in-country missions, and the provision of technical support was established for timely preparedness of national reference laboratories for SARS-CoV-2 detection. All countries should be prepared to timely detect any potential pandemic emerging agent. The rapid SARS-CoV-2 molecular detection implementation throughout the Americas showed the importance of an efficient and coordinated laboratory response for preparedness. Here we present how in 25 days the Americas Region went from no SARS-CoV-2 diagnostic capacity, to molecular detection fully implemented in 28 Member States, under the coordinated strategy of the Pan American Health Organization and collaborative work at regional and country level with national authorities and public health laboratories.

Molecular characterization of Neisseria meningitidis isolates recovered from patients with invasive meningococcal disease in Colombia from 2013 to 2016

BACKGROUND

Neisseria meningitidis is a significant cause of morbidity and mortality worldwide. Meningococcal isolates have a highly dynamic population structure and can be phenotypically and genetically differentiated into serogroups and clonal complexes. The aim of this study was to describe the phenotypic and genotypic characteristics of invasive isolates recovered in Colombia from 2013 to 2016.

METHODOLOGY

A total of 193 invasive isolates were analyzed. Phenotypic and genotypic characteristics were determined by serotyping, antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing.

RESULTS

Based on the results, meningococcal serogroups C, B and Y were responsible for 47.9%, 41.7%, and 9.4% of cases, respectively, and the distribution of serogroups B and C changed over time. Fifteen clonal groups and 14 clonal complexes (cc) were identified by PFGE and genome sequencing. The main clonal group included serogroup B isolates with sequence type (ST)-9493 and its four single-locus variants, which has only been identified in Colombian isolates. The clonal population structure demonstrates that the isolates in this study mainly belong to four clonal complexes: ST-11 cc, ST-32 cc, ST-35 cc and ST-41/44 cc. Thirty-eight penA alleles were identified, but no correlation between MICs and specific sequences was observed.

CONCLUSION

This study shows that most meningococcal isolates recovered from patients with invasive meningococcal disease in Colombia are strains associated with distinct globally disseminated hyperinvasive clones.

Carriage of Neisseria meningitidis and other Neisseria species among children and young adults in Paraguay

Introduction. Colonization by Neisseria meningitidis is the pre-requisite for the development of disease. We present the findings of a cross-sectional investigation onto the oropharyngeal carriage of N. meningitidis and Neisseria species in the population aged 3 to 21 in Paraguay.Aim. Carriage prevalence by age groups, risk factors associated with carriage, and phenotypic and genotypic characteristics of strains are described.Methodology. We collected 2011 oropharyngeal swabs from consenting participants aged 3-21 years. Infants were recruited at immunization clinics, and older children and young adults were identified at schools and universities. A single oropharyngeal swab was collected and processed for the identification and isolation of Neisseria. Additionally, participants, or their legal guardian if these were minors, were requested to fill a standardized questionnaire.Results. N. meningitidis was isolated in 42/2011 (2.1 %) participants, while other Neisseria spp. were identified in 306/2011 (15.2 %) subjects: N. cinerea and N. lactamica were identified in 39/2011 (1.9 %) and 43/2011 (2.2 %), respectively. Meningococcal strains belonged to ten different clonal complexes, of which six are associated with invasive disease (ST-32/ET5 complex, ST-11/ET37 complex, ST-103 complex, ST-167 complex, ST-35 complex and ST-41/44 complex/lineage 3).Conclusion. Prevalence of N. meningitidis carriage was low compared to that reported from other settings, however, the overall carriage of Neisseria spp. (including N. meningitidis) was comparable to meningococcal carriage prevalence reported in the literature. This study is the first of its kind conducted in Paraguay, and one of the few known in the Southern Cone of Latin America.

Characterization of Carriage Isolates of Neisseria meningitides in the Adolescents and Young Adults Population of Bogota (Colombia)

Background

Meningococcal carriage studies are important to improve our understanding of the epidemiology of meningococcal disease. The aim of this study was to determine the prevalence of meningococcal carriage and the phenotypic and genotypic characteristics of isolates collected from a sample of students in the city of Bogotá, Colombia.

Materials and Methods

A total of 1459 oropharyngeal samples were collected from students aged 15–21 years attending secondary schools and universities. Swabs were plated on a Thayer Martin agar and N. meningitidis was identified by standard microbiology methods and PCR.

Results

The overall carriage prevalence was 6.85%. Carriage was associated with cohabitation with smokers, and oral sex practices. Non-groupable and serogroup Y isolates were the most common capsule types found. Isolates presented a high genetic diversity, and circulation of the hypervirulent clonal complexes ST-23, ST-32 and ST-41/44 were detected.

Conclusion

The meningococcal carriage rate was lower than those reported in Europe and Africa, but higher than in other Latin American countries. Our data also revealed antigenic and genetic diversity of the isolates and the circulation of strains belonging to clonal complexes commonly associated with meningococcal disease.

Where does human plague still persist in Latin America?

BACKGROUND

Plague is an epidemic-prone disease with a potential impact on public health, international trade, and tourism. It may emerge and re-emerge after decades of epidemiological silence. Today, in Latin America, human cases and foci are present in Bolivia, Brazil, Ecuador, and Peru.

AIMS

The objective of this study is to identify where cases of human plague still persist in Latin America and map areas that may be at risk for emergence or re-emergence. This analysis will provide evidence-based information for countries to prioritize areas for intervention.

METHODS

Evidence of the presence of plague was demonstrated using existing official information from WHO, PAHO, and Ministries of Health. A geo-referenced database was created to map the historical presence of plague by country between the first registered case in 1899 and 2012. Areas where plague still persists were mapped at the second level of the political/administrative divisions (counties). Selected demographic, socioeconomic, and environmental variables were described.

RESULTS

Plague was found to be present for one or more years in 14 out of 25 countries in Latin America (1899-2012). Foci persisted in six countries, two of which have no report of current cases. There is evidence that human cases of plague still persist in 18 counties. Demographic and poverty patterns were observed in 11/18 counties. Four types of biomes are most commonly found. 12/18 have an average altitude higher than 1,300 meters above sea level.

DISCUSSION

Even though human plague cases are very localized, the risk is present, and unexpected outbreaks could occur. Countries need to make the final push to eliminate plague as a public health problem for the Americas. A further disaggregated risk evaluation is recommended, including identification of foci and possible interactions among areas where plague could emerge or re-emerge. A closer geographical approach and environmental characterization are suggested.

Deletion of the Correia element in the mtr gene complex of Neisseria meningitidis

The mtr gene complex in Neisseria meningitidis encodes an efflux pump that is responsible for export of antibacterial hydrophobic agents. The promoter region of the mtrCDE operon harbours an insertion sequence known as a Correia element, and a binding site for the integration host factor (IHF) is present at the centre of the Correia element. It has been suggested that the expression of the mtrCDE operon in meningococci is subject to transcriptional regulation by the IHF and post-transcriptional regulation by cleavage in the inverted repeat of the Correia element. The promoter region of the mtrCDE operon as well as the association of changes at that point with decreased susceptibility to antimicrobial drugs in 606 Neisseria meningitidis strains were analysed in this study. Two different deletions were present in the analysed region. The first one, found in seven strains, corresponded to absence of the Correia element. The second one, affecting the −10 region and first 100 bp of the mtrR gene and present in 57 isolates, was only found in ST-1624 isolates. None of the deletions were associated with decreased susceptibility to antimicrobial drugs. Although most of the meningococcal strains carry the Correia element at that position, its deletion is not an exception.

Molecular characterization of invasive serogroup Y Neisseria meningitidis strains isolated in the Latin America region

OBJECTIVES

To improve the understanding of serogroup Y invasive meningococcal disease (IMD) in Latin America, particularly IMD molecular epidemiology; 166 Y serogroup isolates received at the National Reference Laboratories of Argentina, Brazil, Chile, Colombia, and Costa Rica during 2000-2006 were characterized by their molecular markers.

METHODS

This analysis included serological assays to determine serogroup/serotype/serosubtype, DNA sequencing and genotyping of the porB and/or porA genes, multilocus sequence typing (MLST) and fetA allele determination.

RESULTS

Sixteen different antigenic combinations were observed. Sixty-two (37.3%) isolates were NT:P1.5 and 36 (21.7%) isolates were 14:NST. Thirty-two different STs appeared, but 3 STs (ST-1624, ST-23, and ST-5770) accounted for 69.9% (116) of the strains. Most of the IMD isolates belonged to the ST-23, ST-167 clonal complexes or the group composed by ST-5770 and related STs.

CONCLUSIONS

Isolates obtained in Colombia and Costa Rica were similar to that of the United States, in that most sequence types belonged to the ST-23 clonal complex. IMD isolates found in Argentina appear to be the result of an independent event and did not spread from nearby countries, being the sequence type ST-1624 (ST-167 clonal complex) the most frequently found. We were unable to correlate an antigenic shift of outer membrane proteins with an increase of serogroup Y meningococcal cases in our collection of isolates.

Pneumococcal disease and vaccination in the Americas: an agenda for accelerated vaccine introduction

This piece summarizes the presentations and discussions at a meeting on pneumococcal disease surveillance in the Americas that was held in Mexico City, Mexico, on 2 November 2004. This meeting was organized by the Pan American Health Organization (PAHO) and the Pneumococcal Vaccines Accelerated Development and Introduction Plan (PneumoADIP) of the Global Alliance for Vaccines and Immunization (GAVI). The meeting participants reviewed the status of pneumococcal disease surveillance in the Region of the Americas, estimates of the burden of pneumococcal disease, the distribution of Streptococcus pneumoniae serotypes that cause invasive disease, the status of pneumococcal vaccine introduction, health economic analyses, and financial issues related to vaccine introduction. The meeting participants also worked to identify the next steps for generating the critical information needed to help make decisions on pneumococcal vaccine introduction. Coordinated pneumococcal disease surveillance for the Region of the Americas dates back to the 1993 establishment by PAHO of the Regional System for Vaccines (RSV) project for surveillance of bacterial meningitis and pneumonia, including pneumococcal disease. Surveillance data from the RSV indicate that the distribution of major serotypes in the Americas has been stable over time (but that antibiotic resistance is increasing), with serotype 14 being the leading serotype isolated in most countries participating in RSV. Based on local serotype data from six of the RSV countries (Argentina, Brazil, Chile, Colombia, Mexico, and Uruguay), the 7-valent vaccine would cover 65% of serotypes, the 9-valent vaccine would cover 77%, and the 11-valent vaccine would cover 83%.

An outbreak of plague including cases with probable pneumonic infection, Ecuador, 1998

During February and March of 1998, 12 sudden deaths were reported among residents of a high-Andean community in Ecuador. All 12 fatalities were members of the same extended family and some had apparent exposure to sick guinea-pigs. Following an initial investigation by public health officials, an additional death was reported in a nearby community in April, also associated with exposure to sick guinea-pigs. Blood samples from humans, dogs, and a rodent were tested for antibody to the F1 antigen of Yersinia pestis by passive haemagglutination assay. Tissue from rodents was subjected to direct fluorescent antibody staining using fluorescein-labelled monoclonal antibody to Y. pestis F1 antigen. Formalin-fixed specimens from the 2 autopsies were evaluated using a 2-step alkaline phosphatase immunoassay with a monoclonal antibody to Y. pestis F1 antigen, and tissues that had not been embedded in paraffin were tested for the presence of DNA encoding the F1 structural antigen by polymerase chain reaction. Serological evaluation of close contacts of the fatalities revealed positive titres to F1 antigen of Y. pestis, the aetiological agent of plague, in 3 contacts from the first community and 1 from the second. Immunohistochemical staining of tissues collected from 2 of the fatalities provided evidence that both had pneumonic plague. Five of 14 dogs found in the communities were seropositive for plague antibody, providing evidence of a recent epizootic plague in the area.

[Multidrug resistant bacteria in a psychiatric milieu]

Isolation rates of multiple-drug resistant (MDR) bacteria were evaluated retrospectively in a psychiatric care facility. Over the six-year study period, 66 MDR bacterial strains were found. Methicillin-resistant Staphylococcus aureus contributed half of all MDR strains and 31% of all S. aureus strains. Among Pseudomonas aeruginosa strains, 22% were resistant to ticarcillin or imipenem, and among Enterobacteriaceae, 4.1% were MDR strains (production of a derepressed cephalosporinase or of an extended-spectrum beta-lactamase). Although most MDR strains were probably acquired during hospitalizations in short-term care facilities outside our institution, patient-to-patient transmission, either direct or via other individuals, cannot be ruled out. These data indicate that psychiatric care facilities should adopt the MDR strain monitoring strategies already used in other hospitals.

[Digestive amines of bacterial origin and behavior disorders. Apropos of a case]

Implication of amines in central nervous system diseases such as migraine, Parkinson disease, epilepsy and depressive illness, is well established. On an other hand, intestinal flora is responsible for the production of specific metabolites such as amines, particularly histamine, tyramine, putrescine and cadaverine. These amines can be absorbed in situ and, through unknown mechanisms, may affect the host's behavior. Most of the data about the pathological activities of bacterial amines concern animals. The concentrations of histamine, tyramine, putrescine and cadaverine in the feces of the studied "controls" appeared steady over time. For the patient presenting clastic crisis without any starting factor, variations appear to overcome the "controls" values, with a great variability. At least tyramine, putrescine and cadaverine concentrations variations are striking by superposed and seem associated to the arising hyper agressivity crisis.

Two stages of enteropathogenic Escherichia coli intestinal pathogenicity are up and down-regulated by the epithelial cell differentiation

Pathogens and eucaryotic cells are active partners during the process of pathogenicity. To gain access to enterocytes and to cross the epithelial membrane, many enterovirulent microorganisms interact with the brush border membrane-associated components as receptors. Recent reports provide evidence that intestinal cell differentiation plays a role in microbial pathogenesis. Human enteropathogenic Escherichia coli (EPEC) develop their pathogenicity upon infecting enterocytes. To determine if intestinal epithelial cell differentiation influences EPEC pathogenicity, we examined the infection of human intestinal epithelial cells by JPN 15 (pMAR7) [EAF+ eae+] EPEC strain as a function of the cell differentiation. The human embryonic intestinal INT407 cells, the human colonic T84 cells, the human undifferentiated HT-29 cells (HT-29 Std) and two enterocytic cell lines, HT-29 glc-/+ and Caco-2 cells, were used as cellular models. Cells were infected apically with the EPEC strain and the cell-association and cell-entry were examined by quantitative determination using metabolically radiolabeled bacteria, as well as by light, scanning and transmission electron microscopy. [EAF+ eae+] EPEC bacteria efficiently colonized the cultured human intestinal cells. Diffuse bacterial adhesion occurred to undifferentiated HT-29 Std and INT407 cells, whereas characteristic EPEC cell clusters were observed on fully differentiated enterocytic HT-29 glc-/+ cells and on colonic crypt T84 cells. As shown using the Caco-2 cell line, which spontaneously differentiates in culture, the formation of EPEC clusters increased as a function of the epithelial cell differentiation. In contrast, efficient cell-entry of [EAF+ eae+] EPEC bacteria occurred in recently differentiated Caco-2 cells and decreased when the cells were fully differentiated.(ABSTRACT TRUNCATED AT 250 WORDS)

[Phenotypes of resistance to antibiotics of the most frequently isolated strains in five specialized hospital centers. Multicenter study]

Antibiotic susceptibility of 948 bacterial strains isolated from varied samples essentially proceeding from urinary infections in five Paris psychiatric Hospitals was determined by disk diffusion method. E. coli, P. mirabilis, Klebsiella spp., P. aeruginosa et S. aureus are the predominant bacteria. 40% of S. aureus are methicilline resistant. Enterobacteriaceae are progressively becoming resistant to aminopenicillines, but remain sensitive to third generation cephalosporines. They are still susceptible to first generation quinolones. At least, if no resistance of P. aeruginosa to imipeneme has been reported, 30% of strains are resistant to ciprofloxacine. Resistance phenotypes to antibiotics of the strains isolated in patients from psychiatric Hospitals are located between those observed in out patients and in patients from general Hospitals. However, we noticed a worrying evolution of resistance to those encontered in psychiatric Hospitals. Therefore, a multiresistant strains emergence monitoring must be carried out regulary.

Human cultured intestinal cells express attachment sites for uropathogenic Escherichia coli bearing adhesins of the Dr adhesin family

We have recently demonstrated that cultured human intestinal HT-29 and Caco-2 cell lines express receptors for the F1845 fimbrial adhesin harbored by the diarrheagenic C1845 Escherichia coli (Kernéis et al., Infect. Immun. 59 (1991) 4013-4018). This adhesin belongs to a family of adhesins including the Dr hemagglutinin and the afimbrial adhesin AFA-I harbored by uropathogenic E. coli. Here we investigated the cell association of laboratory E. coli strains expressing the Dr hemagglutinin and the afimbrial adhesin AFA-I with human cultured enterocyte-like or mucosecreting cells. We observed that the E. coli strains bearing these adhesins adhere both to human intestinal undifferentiated and differentiated fluid-transporting cells, and to mucus-secreting cells. This result strongly suggests a high capacity of intestinal colonization for the uropathogenic E. coli harboring adhesive factors belonging to the Dr adhesin family. These results further corroborate the intestinal colonization by uropathogenic E. coli of the Dr family related to the fecal-perineal-urethral hypothesis of urinary tract infection pathogenesis.

Influence of age, sex and ABO blood group on activated partial thromboplastin time

To evaluate the influence of age, sex and ABO blood group on the activated partial thromboplastin time (APTT), we performed this test in 642 preoperative ambulant adult subjects. There was a significant negative correlation (R = 0.31, p < 0.001) between age and APTT. Sex and ABO blood group had a significant influence on APTT, with lower mean in females (30.9 s) and non-O subjects (30.7 s) than in males (31.6 s) and O subjects (32.0 s) (p = 0.015 and < 0.001, respectively). The largest difference between the upper cut-off values of APTT determined in patient subgroups defined on age, sex and ABO blood group is observed for non-O females over 40 years (36.9 s) and O males under 40 years (41.1 s). These results emphasize the laboratory's difficulties to define valid APTT normal range and thus to detect true mild coagulation disorders in preoperative asymptomatic patients.

Urinary alanine aminopeptidase assay improved as result of multivariate response-surface analysis

Optimization of determination of alanine aminopeptidase in urine by univariate study led to a method involving pretreatment of urine with Sephadex G50. Re-examination of the optimization by multivariate study led us to recommend higher optimal concentrations: 5.8 mmol/L for the substrate and 300 mmol/L for the Tris buffer. Under these new conditions, pretreatment of urine was no longer necessary and the assay could be completely automated.

Urinary alanine aminopeptidase assay improved as result of multivariate response-surface analysis

Optimization of determination of alanine aminopeptidase in urine by univariate study led to a method involving pretreatment of urine with Sephadex G50. Re-examination of the optimization by multivariate study led us to recommend higher optimal concentrations: 5.8 mmol/L for the substrate and 300 mmol/L for the Tris buffer. Under these new conditions, pretreatment of urine was no longer necessary and the assay could be completely automated.