Linear Regression Equations To Predict ß-Lactam, Macrolide, Lincosamide, and Fluoroquinolone MICs from Molecular Antimicrobial Resistance Determinants in Streptococcus pneumoniae.

Antimicrobial resistance in Streptococcus pneumoniae represents a threat to public health, and monitoring the dissemination of resistant strains is essential to guiding health policy. Multiple-variable linear regression modeling was used to determine the contributions of molecular antimicrobial resistance determinants to antimicrobial MICs for penicillin, ceftriaxone, erythromycin, clarithromycin, clindamycin, levofloxacin, and trimethoprim-sulfamethoxazole. Training data sets consisting of Canadian S. pneumoniae isolates obtained from 1995 to 2019 were used to generate multiple-variable linear regression equations for each antimicrobial. The regression equations were then applied to validation data sets of Canadian (n = 439) and U.S. (n = 607 and n = 747) isolates. The MICs for ß-lactam antimicrobials were fully explained by amino acid substitutions in motif regions of the penicillin binding proteins PBP1a, PPB2b, and PBP2x. Accuracies of predicted MICs within 1 doubling dilution to phenotypically determined MICs were 97.4% for penicillin, 98.2% for ceftriaxone, 94.8% for erythromycin, 96.6% for clarithromycin, 98.2% for clindamycin, 100% for levofloxacin, and 98.8% for trimethoprim-sulfamethoxazole, with an overall sensitivity of 95.8% and specificity of 98.0%. Accuracies of predicted MICs to the phenotypically determined MICs were similar to those of phenotype-only MIC comparison studies. The ability to acquire detailed antimicrobial resistance information directly from molecular determinants will facilitate the transition from routine phenotypic testing to whole-genome sequencing analysis and can fill the surveillance gap in an era of increased reliance on nucleic acid assay diagnostics to better monitor the dynamics of S. pneumoniae.

Demographic patterns of exposure and transmission for a rural Canadian community outbreak of COVID-19, 2020.

Background: A coronavirus disease 2019 (COVID-19) community outbreak was declared October 5-December 3, 2020, in the Restigouche region of New Brunswick, Canada. This article describes the epidemiological characteristics of the outbreak and assesses factors associated with its transmission in rural communities, informing public health measures and programming. Methods: A provincial line list was developed from case and contact interviews. Descriptive epidemiological methods were used to characterize the outbreak. Incidence rates among contacts, and by gender for the regional population were estimated. Results: There were 83 laboratory-confirmed cases of COVID-19 identified during the observation period. The case ages ranged from 10-89 years of age (median age group was 40-59 years of age) and 51.2% of the cases were male. Symptom onset dates ranged from September 27-October 27, 2020, with 83% of cases being symptomatic. A cluster of early cases at a social event led to multiple workplace outbreaks, though the majority of cases were linked to household transmission. Complex and overlapping social networks resulted in multiple exposure events and that obscured transmission pathways. The incidence rate among men was higher than women, men were significantly more likely to have transmission exposure at their workplace than women, and men were the most common index cases within a household. No transmission in school settings among children was documented despite multiple exposures. Conclusion: This investigation highlighted the gendered nature and complexity of a COVID-19 outbreak in a rural Canadian community. Targeted action at workplaces and strategic messaging towards men are likely required to increase awareness and adherence to public health measures to reduce transmission in these settings.

Molecular characterization of predominant Streptococcus pneumoniae serotypes causing invasive infections in Canada: the SAVE study, 2011-15.

Objectives: This study characterized the 11 most predominant serotypes of invasive Streptococcus pneumoniae infections collected by the annual SAVE study in Canada, between 2011 and 2015. Methods: A subset of the 11 most predominant serotypes (7F, 19A, 22F, 3, 12F, 11A, 9N, 8, 33F, 15A and 6C) collected by the SAVE study was analysed using PFGE and MLST, as well as PCR to identify pilus-encoding genes. WGS analyses were performed on a subset of the above isolates plus a random selection of background strains. Results: Of the predominant serotypes analysed, 7F, 33F and 19A were obtained more commonly from children <6 years of age, whereas 15A, 6C, 22F and 11A were more common in adults >65 years of age. Pneumococcal pilus PI-1 was identified in antimicrobial-susceptible serotype 15A (61/212) and <10% of 6C isolates (16/188). PI-2 was found in serotype 7F (683/701) and two-thirds of 11A isolates (162/241). Only serotype 19A-ST320 possessed both pili. Molecular and phylogenetic analyses identified serotypes 19A, 15A, 6C, 9N and 33F as highly diverse, whereas 7F, 22F and 11A demonstrated clonality. Antimicrobial resistance determinants were common within diverse serotypes, and usually similar within a clonal complex. Conclusions: Despite successful use of conjugate vaccines, S. pneumoniae remains a highly diverse organism in Canada. Several predominant serotypes, both antimicrobial susceptible and MDR, have demonstrated rapid clonal expansion or an increase in diversity. As S. pneumoniae continues to evolve in Canada, WGS will be a necessary component in the ongoing surveillance of antimicrobial-resistant and expanding clones.

Serotype distribution of invasive Streptococcus pneumoniae in adults 65 years of age and over after the introduction of childhood 13-valent pneumococcal conjugate vaccination programs in Canada, 2010-2016.

The 13-valent conjugate vaccine (PCV13) was recommended for childhood immunization programs in 2010 in Canada and has decreased the incidence of invasive pneumococcal disease (IPD) in children and changed the epidemiology of IPD in adults. This study investigated the epidemiology of IPD in adults 65 years of age and older in Canada. A total of 7282 invasive S. pneumoniae isolated from adults ≥65 years old were serotyped from 2010 to 2016 and antimicrobial susceptibility was performed on 2527 isolates. Serotyping was performed by Quellung reaction using commercial antisera and antimicrobial susceptibilities were determined by broth microdilution. PCV7 serotypes decreased non-significantly from 2010 to 2016 from 9.1% (n = 96) to 6.7% (n = 72) while the additional six PCV13 serotypes declined significantly from 39.5% (n = 418) to 18.6% (n = 201) (p < 0.05). The 23-valent pneumococcal polysaccharide vaccine (PPV23) and non-vaccine (NVT) serotypes increased from 26.3% (n = 278) to 36.2% (n = 393) (p < 0.05), and from 25.1% (n = 266) to 38.4% (n = 416) (p < 0.05), respectively. There were no significant changes in antimicrobial resistance rates from 2011 to 2016: 24.1% of the IPD from adults ≥65 years were resistant to clarithromycin (n = 609), 10.0% to doxycycline (n = 254), 11.8% to penicillin (n = 299), 5.2% to cefuroxime (n = 131), 6.6% to clindamycin (n = 168), 6.0% to trimethoprim-sulfamethoxazole (n = 152), and 0.5% (n = 12) to ceftriaxone. Although overall incidence of IPD in adults ≥65 years has remained relatively constant from 2010 to 2016, childhood PCV13 vaccination programs have been successful in indirectly reducing IPD caused by PCV13 serotypes in adults through herd immunity effects.

Antibiotic susceptibility and molecular analysis of invasive Haemophilus influenzae in Canada, 2007 to 2014.

Background: Previously we studied the antibiotic susceptibility of invasive Haemophilus influenzae collected in Canada from 1990 to 2006 and characterized isolates by serotype, MLST and ftsI gene sequencing for significant PBP3 mutations. Objectives: To provide an update based on isolates collected from 2007 to 2014. Methods: A total of 882 case isolates were characterized by serotype using slide agglutination and PCR. MLST was carried out to determine ST. Isolates were tested for ß-lactamase production, presence of significant PBP3 mutations and antibiotic susceptibility by disc diffusion against 14 antibiotics. MIC values of three antibiotics were determined for 316 isolates using microbroth dilution. Results: Non-typeable H. influenzae accounted for 54.6% of the isolates and 45.4% were serotypeable, predominantly type a (23.1%), type b (8.3%) and type f (10.8%). The overall rate of ampicillin resistance due to ß-lactamase production was 16.4% and increased from 13.5% in 2007-10 to 19% in 2011-14. Significant PBP3 mutations were identified in 129 isolates (14.6%) with 23 (2.6%) also producing ß-lactamase. MLST identified related STs (ST-136, ST-14 and ST-367) associated exclusively with genetically ß-lactamase-negative, ampicillin-resistant isolates and confirmed previously reported associations between significant PBP3 mutations and ST. Conclusions: A significant increase in ß-lactamase-producing isolates was observed from 2007 to 2014; the rate of significant PBP3 mutations has increased since previously reported and 52.5% of non-typeable H. influenzae now show resistance markers. Resistance to trimethoprim/sulfamethoxazole was common and no resistance to fluoroquinolones or third-generation cephalosporins was found.

Characterization of invasive Neisseria meningitidis from Atlantic Canada, 2009 to 2013: With special reference to the nonpolysaccharide vaccine targets (PorA, factor H binding protein, Neisseria heparin-binding antigen and Neisseria adhesin A).

BACKGROUND: Serogroup B Neisseria meningitidis (MenB) has always been a major cause of invasive meningococcal disease (IMD) in Canada. With the successful implementation of a meningitis C conjugate vaccine, the majority of IMD in Canada is now caused by MenB. OBJECTIVE: To investigate IMD case isolates in Atlantic Canada from 2009 to 2013. Data were analyzed to determine the potential coverage of the newly licensed MenB vaccine. METHODS: Serogroup, serotype and serosubtype antigens were determined from IMD case isolates. Clonal analysis was performed using multilocus sequence typing. The protein-based vaccine antigen genes were sequenced and the predicted peptides were investigated. RESULTS: The majority of the IMD isolates were MenB (82.5%, 33 of 40) and, in particular, sequence type (ST)-154 B:4:P1.4 was responsible for 47.5% (19 of 40) of all IMD case isolates in Atlantic Canada. Isolates of this clone expressed the PorA antigen P1.4 and possessed the nhba genes encoding for Neisseria heparin-binding antigen peptide 2, which together matched exactly with two of the four components of the new four-component meningococcal B vaccine. Nineteen MenB isolates had two antigenic matches, another five MenB and one meningitis Y isolate had one antigenic match. This provided 75.8% (25 of 33) potential coverage for MenB, or a 62.5% (25 of 40) overall potential coverage for IMD. CONCLUSION: From 2009 to 2013, IMD in Atlantic Canada was mainly caused by MenB and, in particular, the B:4:P1.4 ST-154 clone, which accounted for 47.5% of all IMD case isolates. The new four-component meningococcal B vaccine appeared to offer adequate coverage against MenB in Atlantic Canada.

HISTORIQUE: Le Neisseria meningitidis du sérogroupe B (MenB) a toujours été une cause importante de méningococcie invasive (MI) au Canada. Depuis l'adoption d'un vaccin conjugué contre le méningocoque du groupe C, la majorité des MI au Canada sont désormais attribuables au MenB. OBJECTIF: Examiner les isolats de cas de MI dans les Maritimes entre 2009 et 2013. Analyser les données pour déterminer la couverture potentielle du vaccin nouvellement homologué contre le MenB. MÉTHODOLOGIE: Les chercheurs ont déterminé le sérogroupe, le sérotype et les antigènes des sous-types sérologiques des isolats de cas de MI. Ils ont effectué l'analyse clonale au moyen du typage génomique multilocus. Ils ont séquencé les gènes des antigènes du vaccin à base de protéines et examiné les peptides prédits. RÉSULTATS: La majorité des isolats de MI étaient des MenB (82,5 %, 33 sur 40). Notamment, le type séquentiel (TS)-154 B:4:P1,4 était responsable de 47,5 % (19 sur 40) de tous les isolats de cas de MI dans les Maritimes. Les isolats de ce clone ont exprimé l'antigène porA P1.4 et étaient dotés des gènes nhba codant pour le peptide 2 de l'antigène de liaison à l'héparine de Neisseria. Ensemble, ces antigènes correspondaient exactement à deux des quatre composants du nouveau vaccin contre le méningocoque du groupe B à quatre composants. Dix-neuf isolats du MenB étaient dotés de deux correspondances antigéniques, tandis que cinq autres MenB et un isolat de la méningite Y étaient dotés d'une correspondance antigénique. Ces résultats assuraient une couverture potentielle du MenB de 72,7 % (24 sur 33) ou une couverture potentielle globale de la MI de 62,5 % (25 sur 40). CONCLUSION: De 2009 à 2013, dans les Maritimes, la MI était surtout causée par le MenB, en particulier le clone B:4:P1.4 ST-154, responsable de 47,5 % de tous les isolats de cas de MI. Le nouveau vaccin contre le méningocoque du groupe B à quatre composants semble offrir une couverture pertinente contre le MenB dans cette région.

Development of a checklist of quality indicators for clinical trials in resource-limited countries: the French National Agency for Research on AIDS and Viral Hepatitis (ANRS) experience.

BACKGROUND: Since 1994, the French National Agency for Research on AIDS and Viral Hepatitis (ANRS) has funded research sites in resource-limited countries (RLCs). These sites implement research on human immunodeficiency virus (HIV) infection and Hepatitis C. In parallel, international regulations and recommendations for clinical trials have evolved and proliferated. However, little guidance exists on how these should be interpreted and applied within academic trials and in the context of RLCs. After developing a specific Ethical Charter for research in developing countries in 2002, ANRS developed a set of quality indicators (QIs) as a monitoring tool for assessing compliance to international guidelines. PURPOSE: We describe here the development process, QIs adopted, and areas for improvement. METHODS: In 2008, a group of experts was convened that included a researcher representing each ANRS site (Cote d'Ivoire, Senegal, Cameroun, Burkina Faso, Egypt, and Cambodia). Our structuring interaction development process combined evidence and expert opinion in two nominal group meetings to identify (1) clinical trial processes involved, (2) issues specific to RLCs in terms of Good Clinical Practice (GCP) and the application of ethical recommendations, and (3) checklists of QIs adapted to clinical trials conducted in RLCs. RESULTS: The trial process reviewed and proposed for RLCs was mostly similar to the one produced in wealthier countries. The scheme generated by our work group added two further processes: 'drug management' and 'biological investigations'. Specific issues regarding trial management in RLCs were therefore described for eight trial steps (1) protocol conception and seeking authorizations, (2) participant enrollment and follow-up, (3) site monitoring, (4) drug management, (5) biological investigations, (6) record management, (7) data management, and (8) site closeout. A total of 58 indicators were identified with at least one indicator for each trial process. LIMITATIONS: Some trial activities require further consideration, that is, in the case of vulnerable participants (children, pregnant women). Proposed indicators are the result of expert consensus and reflect their experience in the HIV field. Relevance to existing trials and extrapolation to other fields must be assessed. CONCLUSIONS: This innovative program allowed ANRS sites located in RLCs to share their GCP implementation experiences in order to build a list of relevant indicators for clinical trials. The next step is to collect data from ongoing HIV and hepatitis C trials in these settings and will assess the relevance of these indicators to document current quality of performance among trials in resource-limited settings.

Risk perception and priority setting for intervention among hepatitis C virus and environmental risks: a cross-sectional survey in the Cairo community.

BACKGROUND: Hepatitis C virus (HCV) recently emerged as a major public health hazard in Egypt. However, dramatic healthcare budget constraints limit access to the costly treatment. We assessed risk perception and priority setting for intervention among HCV, unsafe water, and outdoor air pollution in Cairo city. METHODS: A survey was conducted in the homes of a representative sample of household heads in Cairo city. Risk perception was assessed using the "psychometric paradigm" where health hazards are evaluated according to several attributes and then summarized by principal component analysis. Priority setting was assessed by individual ranking of interventions reducing health hazards by 50% over five years. The Condorcet method was used to aggregate individual rankings of the three interventions (main study) or two of three interventions (validation study). Explanatory factors of priority setting were explored in multivariate generalized logistic models. RESULTS: HCV was perceived as having the most severe consequences in terms of illness and out-of-pocket costs, while outdoor air pollution was perceived as the most uncontrollable risk. In the main study (n = 2,603), improved water supply received higher priority than both improved outdoor air quality (60.1%, P < .0001) and screening and treatment of chronic hepatitis C (66.3%, P < .0001), as confirmed in the validation study (n = 1,019). Higher education, report of HCV-related diseases in the household, and perception of HCV as the most severe risk were significantly associated to setting HCV treatment as the first priority. CONCLUSIONS: The Cairo community prefers to further improving water supply as compared to improved outdoor air quality and screening and treatment of chronic hepatitis C.

Response to pegylated interferon alfa-2a and ribavirin in chronic hepatitis C genotype 4.

The safety and efficacy of pegylated interferon (PEG-IFN) alfa-2a and ribavirin were studied among patients treated for genotype 4 chronic hepatitis C. Ninety-five patients with chronic hepatitis C genotype 4 were treated with PEG-IFN alfa-2a (180 microg/week) plus ribavirin (> or =11 mg/kg/day) for 48 weeks. The primary end point was sustained virological response, defined as non-detectable levels of HCV RNA at the end of follow up (week 72). The proportion with sustained virological response was 58/95 = 61.1% (95% CI = 50.5-70.9%). Side effects were generally mild, well managed by dose reductions (in 62% of patients); in only two patients were side effects sufficiently severe to require treatment interruption. Ninety percent of patients adhered to treatment up to week 12, and their sustained virological response rate was higher compared to non-adherent (65% vs. 22%, respectively, P = 0.012). None of the patients who failed to achieve 1 log reduction of viral load by week 8 (n = 15), or 2 log reduction by week 12 (n = 17), had a sustained virological response. In conclusion, sustained virological response in genotype 4 Egyptian patients treated with PEG-IFN alfa-2a and ribavirin was estimated around 60%, intermediate between sustained virological response observed in genotype 1 and genotype 2-3 patients in Western countries. The early virological response (week 4 or week 8) should be investigated as a criterion to decide whether the patient may benefit from a shorter duration of therapy.

Predictors of a sustained virological response in patients with genotype 4 chronic hepatitis C.

OBJECTIVES: To determine the clinical, biological, virological and histological predictive factors associated with a sustained virological response (SVR) to combined interferon therapy among Egyptian patients infected by genotype 4 hepatitis C virus (HCV). PATIENTS AND METHODS: Individual data from 250 patients with genotype 4 chronic hepatitis C, treated with different regimens of combined interferon, were analysed. The primary end point was SVR defined as undetectable HCV RNA by polymerase chain reaction (PCR) 24 weeks after the end of treatment. Multivariate logistic regression analysis was performed to select the independent prognostic parameters associated with SVR. RESULTS: A sustained virological response was achieved among 137/250 (54.8%) patients. Baseline factors independently and negatively associated with SVR were serum alpha-fetoprotein (AFP) level (above 0.3 upper limit of normal) [odds ratio (OR)=0.5, 95% confidence interval (CI): 0.2-0.8], severe fibrosis (Metavir score >F2) (OR=0.4, 95% CI: 0.2-0.8), presence of steatosis (OR=0.5, 95% CI: 0.3-0.97) and standard interferon treatment (OR=0.4, 95% CI: 0.2-0.8). CONCLUSIONS: Among genotype 4 chronic hepatitis C patients, severe fibrosis, severe steatosis, treatment with standard interferon and a high serum AFP level were all negatively associated with SVR. Pretreatment serum AFP level should be considered in the routine assessment of factors predictive of a treatment response.

Serum alpha-foetoprotein level predicts treatment outcome in chronic hepatitis C.

OBJECTIVES: To analyse the association between serum alpha-foetoprotein (AFP) levels and sustained virological response (SVR) in treated patients. METHODS: One-hundred patients with chronic hepatitis C were treated with pegylated interferon alpha-2a plus ribavirin for 48 weeks. The primary endpoint was SVR. Linear regression analysis was performed to identify clinical, biological, and histological factors affecting baseline AFP levels. The association between pretreatment serum AFP and SVR was assessed by multivariate logistic regression analysis. RESULTS: Of 100 patients, 95 were infected with genotype 4, one with genotype 1, and four with undetermined genotype. The median serum AFP level was 4.5 ng/ml and AFP values ranged from 1.2 to 49.8 ng/ml. In multivariate analysis, higher fibrosis stage and higher steatosis score were independently associated with higher serum AFP levels. SVR rate was 61.0% (61/100), and was lower for patients with AFP levels above rather than below the median value (40.8% versus 80.4%, respectively, P < 0.001). In multivariate analysis, including adjustment for age, gender, body mass index, steatosis score, fibrosis stage, ALT level, haemoglobin level, clotting time, HCV RNA viral load, and treatment dose received, a baseline serum AFP level above the median value was associated with a lower SVR rate (OR [95% CI]=0.10 [0.03-0.42], P < 0.001). None of the seven patients with increased (above 15 ng/ml) pretreatment AFP achieved SVR. CONCLUSIONS: In this study, higher baseline serum AFP levels independently predicted a lower SVR rate among patients with chronic hepatitis C. If confirmed with genotypes other than 4, these findings would suggest adding serum AFP to the list of factors predictive of treatment response.

Nicotine dependance among adult male smokers in rural Egypt.

Nicotine dependence is a significant public health problem. This study describes the nicotine dependence status among male adults in rural communities in Egypt. A survey was carried out in five rural villages in Egypt to study the smoking prevalence. A total of 938 current smokers were identified and their nicotine dependence status was studied. About 9% of all smokers in the studied villages were found to have heavy dependence to nicotine. Heavy dependence was associated with younger age of smoking initiation (p<0.05) and more smoking in the first hours of the day (p<0.001). Heavy dependent smokers are less likely to quit smoking (p<0.001), lack the confidence to quit by themselves (p<0.001) and less likely to have tried to quit earlier (p<0.001). Dependent smokers are more likely to smoke in the presence of their children (p<0.001). Reasons for smoking included the habit of smoking helping them to keep them going when tired, to make them alert and not knowing what to do with their hands without a cigarette. The main reasons they identified for restarting smoking after quitting were the signs of withdrawal namely headaches, irritability and difficulty in concentration. Nicotine dependence status and attributes were comparable to studies reported in other countries around the world. Enhanced behavioral and medical intervention strategies are needed to motivate helping both low and heavy nicotine dependent smokers to increase the number and effectiveness of quit attempts.