Nasopharyngeal carriage and antimicrobial susceptibility pattern of Streptococcus pneumoniae among pediatric outpatients at Gondar University Hospital, North West Ethiopia

Prevalence, Antimicrobial Drug Resistance and Associated Risk Factors of Streptococcus Pneumoniae Bacteria Infection Among Under-Five Children With Acute Lower Respiratory Tract Infection Attending Sheik Hassan Yebere Referral Hospital, Jig-Jiga, Ethiopia

Background

Pneumonia is inflammation of the lung. The Streptococcus pneumoniae (S. pneumoniae) is commensal in the upper airway and can cause infection to under-five children. The bacteria is gram-positive diplococci, catalase negative, and optochin sensitive. The bacteria is the leading cause of bacterial pneumonia among under-five children. No similar data is reported from the current study area.

Objective

To determine prevalence, antimicrobial drug resistance and associated factors of S. pneumoniae infection among under-five children with acute lower respiratory tract infection attending Sheck Hassan Yebere Referral Hospital from March 1 to April 30, 2021 Jig-Jiga, Ethiopia.

Methods

A cross-sectional study was conducted among 374 study participants selected by convenience sampling method. A structured questionnaire was used to collect child data. Nasopharyngeal/oropharyngeal swabs were collected and diagnosed to isolate S. pneumoniae by using culture then identified by biochemical examination. Later antimicrobial drug resistance testing was performed by Kirby-Bauer disk diffusion method. All data were entered on epi-data 3.1 then exported to SPSS version 22 to calculate analysis. Statistically significant value was found by calculating an adjusted odds ratio with p-value ≤ 0.05 in a multivariate logistic regression model.

Results

Among 374 under-five children, 180 (48.1%) were males and 109 (29.2%) were from low income families. The overall prevalence of S. pneumoniae infection in the study was 18% (95% CI 14.4-22.2). No window (AOR=2.8 CI 1.1-7.6), no/non-exclusive breast-feeding (AOR= 2.1 CI 1.1-4.1), and previous URTI (AOR= 3.2 CI 1.7-6.1) were significantly associated with S. pneumoniae infection. The isolated organism showed drug resistance for Cotrimoxazole (35%), and Tetracycline (34%).

Conclusion

The prevalence and antimicrobial resistance in this study were comparatively high. No window, non-exclusive breast-feeding and previous URTI were associated with S. pneumoniae infection. The isolated S. pneumoniae showed high drug resistance to cotrimoxazole and tetracycline.

Nasopharyngeal colonization by Streptococcus pneumoniae in children and adults before the introduction of the 10-valent conjugate vaccine, Paraguay

Streptococcus pneumoniae is a cause of invasive diseases such as pneumonia, meningitis, and other serious infections among children and adults in Paraguay. This study was conducted to establish S. pneumoniae baseline prevalence, serotype distribution, and antibiotic resistance patterns in healthy children aged 2 to 59 months and adults ≥60 years of age prior to the introduction of PCV10 in the national childhood immunization program in Paraguay. Between April and July 2012, a total of 1444 nasopharyngeal swabs were collected, 718 from children aged 2 to 59 months and 726 from adults ≥60 years of age. The pneumococcal isolation, serotyping, and antibiotic susceptibility testing were performed using standard tests. Pneumococcal colonization prevalence was 34.1% (245/718) in children and 3.3% (24/726) in adults. The most frequent pneumococcal vaccine-types (VT) detected in the children were 6B (42/245), 19F (32/245), 14 (17/245), and 23F (20/245). Carriage prevalence with PCV10 serotypes was 50.6% (124/245) and PCV13 was 59.5% (146/245). Among colonized adults, prevalence of PCV10 and PCV13 serotypes were 29.1% (7/24) and 41.6% (10/24), respectively. Colonized children were more likely to share a bedroom, have a history of respiratory infection or pneumococcal infection compared to non-colonized children. no associations were found in adults. However, no significant associations were found in children and neither in adults. Vaccine-type pneumococcal colonization was highly prevalent in children and rare in adults in Paraguay prior to vaccine introduction, supporting the introduction of PCV10 in the country in 2012. These data will be useful to evaluate the impact of PCV introduction in the country.

High Prevalence of Asymptomatic Nasopharyngeal Carriage Rate and Multidrug Resistance Pattern of Streptococcus pneumoniae Among Pre-School Children in North Showa Ethiopia

Background

Streptococcus pneumoniae infection is still the world’s most serious public health problem among children under the age of five. Nasopharyngeal carriage rate of Streptococcus pneumoniae has been identified as an important risk factor for the acquisition of community acquired respiratory tract infection. To date, little is known about the nasopharyngeal infection and antimicrobial susceptibility pattern of Streptococcus pneumoniae among preschool children in Ethiopia.

Objective

The aim of this study was to assess the prevalence of nasopharyngeal carriage and antimicrobial susceptibility pattern of Streptococcus pneumoniae among preschool children.

Methods

A cross-sectional study was conducted from September 2021 to April 2022. A total of 418 preschool children were enrolled using a multistage sampling technique. Nasopharyngeal swab was collected and transported to Medical Microbiology Laboratory at Debre Berhan comprehensive specialized hospital using skim-milk tryptone glucose glycerol transport media. The swab was inoculated on blood agar plates supplemented with 5µg/mL gentamycin and incubated at 37°C for 24–48 hours under 5% CO2 using a candle jar. Identification of Streptococcus pneumoniae was performed using Gram stain, catalase test, optochin test and bile solubility test. Antimicrobial sensitivity tests were done using a modified Kirby-Bauer disk diffusion method. Data were entered into the statistical package Epi data 4.0.0.6 and transferred to and analyzed using SPSS software version-23. A P-value ≤0.05 with 95% CI was considered to be statistically significant.

Results

The prevalence of Streptococcus pneumoniae nasopharyngeal carriage was 29.9% (125/418). The overall rate of multidrug resistance was 86 (68.8%), with tetracycline (68.8%) and TMP-SMX (68%). Among risk factors, young age and passive smoking were associated with pneumococcal carriage.

Conclusion

The present study revealed a substantially lower prevalence of Streptococcus pneumoniae nasopharyngeal carriage. High antimicrobial resistance was observed for most antimicrobial drugs tested. Younger age groups and passive smokers were at risk of Streptococcus pneumoniae nasopharyngeal carriage.

Impact of Pneumococcal Vaccination on Nasopharyngeal Carriage of Streptococcus pneumoniae and Microbiota Profiles in Preschool Children in South East Poland

In 2017, Poland introduced the 10-valent pneumococcal conjugate vaccine (PCV) into its national immunization schedule. This prospective study was conducted between March and June 2020 to determine the impact of vaccination on prevalence of the nasopharyngeal carriage of S. pneumoniae in 176 healthy children and to determine how conjugate vaccines indirectly affect colonization of nasopharyngeal microbiota. Pneumococcal isolates were analyzed by serotyping and antimicrobial resistance tests. Nasopharyngeal microbiota were detected and identified using the culture method and real-time PCR amplification primers and hydrolysis-probe detection with the 16S rRNA gene as the target. In the vaccinated group of children, colonization was in 24.2% of children, compared to 21.4% in the unvaccinated group. Serotypes 23A and 23B constituted 41.5% of the isolates. Serotypes belonging to PCV10 and PCV13 constituted 4.9% and 17.1% of the isolates, respectively. S. pneumoniae isolates were resistant to penicillin (34.1%), erythromycin (31.7%), and co-trimoxazole (26.8%). Microbial DNA qPCR array correlated to increased amounts of Streptococcus mitis and S. sanguinis in vaccinated children, with reduced amounts of C. pseudodiphtericum, S. aureus, and M. catarrhalis. Introduction of PCV for routine infant immunization was associated with significant reductions in nasopharyngeal carriage of PCV serotypes and resistant strains amongst vaccine serotypes, yet carriage of non-PCV serotypes increased modestly, particularly serotype 23B.

A Systematic Review of Pneumococcal Carriage, Disease, Antimicrobial Resistance, and Vaccination in Egyptian Children Aged 18 Years and Younger

Streptococcus pneumoniae remains an important bacterial pathogen, particularly for young children in low- and middle-income countries. A systematic review was conducted of peer-reviewed literature from PubMed published as of May 13, 2020, to identify articles relevant to invasive pneumococcal disease, pneumonia, otitis media (OM), nasopharyngeal carriage (NPC), antimicrobial resistance (AMR), and vaccination coverage in Egypt, with particular focus on children ≤ 18 years of age. A total of 16 relevant articles spanning three decades were included in this review. Among studies reviewed, S. pneumoniae was the causative agent of meningitis in 21–30% of cases among hospitalized children between 1983 and 2003. One study showed that serotypes 6A and 6B predominated among meningitis cases of pediatric patients aged < 5 years. This review also revealed that S. pneumoniae was the most commonly identified bacterial pathogen of acute mastoiditis, a severe complication of acute OM, among children aged 9 months to 11 years. NPC studies showed that approximately 30% of Egyptian children were carriers of S. pneumoniae. AMR, especially to penicillin, continues to be a growing concern in low- and middle-income countries, including among Egyptian children. Several predominant serotypes were identified to be associated with penicillin resistance, such as 6B, 1, 19A, 23F, and 6A. Currently available pneumococcal vaccines (PCVs) such as PCV10 and PCV13 may provide coverage against the most prevalent circulating serotypes among Egyptian children. Comprehensive disease surveillance and immunization programs are needed to ensure that this vulnerable population is sufficiently protected against pneumococcal disease.

Carriage of Streptococcus pneumoniae in children under five years of age prior to pneumococcal vaccine introduction in Southeast Asia: A systematic review and meta-analysis (2001-2019)

A number of pneumococcal carriage studies in children have been conducted in recent years. However, summary data of carriage prevalence and serotype distribution from South East Asia Region (SEAR) are limited. This may lead to the misconception that Streptococcus pneumoniae vaccine-types are uncommon in the region. Systematic reviews of pneumococcal carriage and the distribution of serotypes are critically important for evidence-based decision-making. We aimed to summarize published data on the serotype prevalence of S. pneumoniae carried in the nasopharynx of children under 5 years of age in SEAR. We performed a systematic review and meta-analysis for relevant studies on S. pneumoniae carriage conducted prior to PCV program implementation from online journal databases published between January 2001 to December 2019. The pooled prevalence of S. pneumoniae in healthy children under 5 years of age in SEAR was 36.0% (95% CI 34.2%-37.8%), and ranged from 68.0% (95% CI: 61.9%-74.0%) in Cambodia to 7.6% (95% CI: 5.7%-9.6%) in Malaysia. Serotypes 6A/B, 23F and 19F were the most common serotypes in children <5 years, accounting for 12.9% (95% CI: 9.4%-16.3%), 9.3% (95% CI: 5.9%-12.8%) and 10.1% (95% CI: 6.6%-13.5%) of isolates, respectively. Vaccine policy makers should take these results into account when making decisions on pneumococcal conjugate vaccine programs implementation. Given the paucity of data, collection of more extensive and updated information of S. pneumoniae serotype epidemiology in children under five years in SEAR is also very important for future studies.

Factors Associated with Streptococcus pneumoniae Nasopharyngeal Carriage and Antimicrobial Susceptibility among Children Under the Age of 5 Years in the Southwestern Colombia

Objective This work aimed to evaluate the factors associated with Streptococcus pneumoniae nasopharyngeal colonization and antimicrobial susceptibility among pediatric outpatients in southwestern Colombia, 2019.

Methods A cross-sectional study was performed using survey-based interviews and the collection of nasopharyngeal-swab specimens for microbiological characterization and antimicrobial susceptibility testing. Logistic regression analyses were performed for factors associated with nasopharyngeal carriage.

Results A total of 452 children under the age of 5 years were examined in which 41.8% carried S. pneumoniae. Higher pneumococcal carriage frequencies were observed among participants aged <2 years and in individuals belonging to indigenous communities, which were lacking established pneumococcal-conjugated vaccine-10 immunization schemes. Additionally, children attending childcare institutions were also highly colonized by pneumococci. S. pneumoniae showed 57.7% nonsusceptibility to benzyl-penicillin (meningitis-cut); 45.5% intermediate-sensitivity to benzyl-penicillin (oral-cut) and 21.7% to cefotaxime; and resistance to erythromycin (40.7%), tetracycline (36.0%), trimethoprim/sulfamethoxazole (24.9%), clindamycin (24.3%), and ceftriaxone (27.0%).

Conclusion The 41.8% of participants carrying S. pneumoniae show a scenario with the presence of multidrug and extensively drug-resistant strains, which constitutes important reservoirs of bacterial transmission by children aged <5 years in Colombia, leading to an onset of pneumococcal diseases. Hence, there is an urgent need to expand conjugate pneumococcal immunization in the community and ensure compliance with established immunization schedules.

Phenotypic and Molecular Characterization of Penicillin and Macrolide-Resistant Streptococcus pneumoniae Serotypes Among Pediatric Patients in Addis Ababa, Ethiopia

Background

In several countries, introduction of the pneumococcal conjugate vaccine (PCV) has led to a decline in antimicrobial-resistant pneumococcal disease but has also resulted in a concomitant increase in antimicrobial-resistant, non-vaccine serotypes of Streptococcus pneumoniae. We sought to determine the magnitude of penicillin and macrolide resistance among pneumococcal serotypes and the mechanisms of macrolide resistance in Ethiopia, 5 years after the introduction of PCV10 in the country.

Methods

Susceptibility to penicillin and erythromycin of 119 pneumococcal isolates collected from pediatric patients aged 0-15 years in Addis Ababa, Ethiopia, was tested using disc diffusion, and minimum inhibitory concentration (MIC) was also determined by Etest. Pneumococcal serotypes were determined by sequencing the cpsB gene and using Quellung reaction. Polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism analysis were used to detect and differentiate the macrolide resistance genes erm(B), mef(A), and mef(B).

Results

Among the 119 isolates, 2.5% (3/119) were resistant to penicillin, while 58% (69/119) were intermediate. Resistance to erythromycin was observed in 33.6% (40/119) of the isolates with the highest level of resistance among isolates from middle ear discharge, i.e., 53.3% (8/15). Half (19/40) of the erythromycin resistant isolates were serotype 19A and among serotype 19A isolates, the majority i.e., 54.3% (19/35) were resistant to erythromycin. The most common macrolide resistance determinant was mef(E) with a prevalence of 50% (20/40).

Conclusion

Five years after introduction of PCV10 in Ethiopia, we observed that the prevalence of penicillin-resistant S. pneumoniae was low. However, there was a high level of macrolide resistance which was mostly in serotype 19A, and the resistance was mainly mediated by efflux pumps. Introduction of PCV13 (which covers serotype 19A) would significantly improve coverage of the macrolide-resistant serotypes. Continued surveillance of pneumococcal serotype distribution and their antibiotic resistance pattern in Ethiopia is warranted.

Antimicrobial resistance profile and multidrug resistance patterns of Streptococcus pneumoniae isolates from patients suspected of pneumococcal infections in Ethiopia

Background

Antimicrobial-resistant strains of Streptococcus pneumoniae have become one of the greatest challenges to global public health today and inappropriate use of antibiotics and high level of antibiotic use is probably the main factor driving the emergence of resistance worldwide. The aim of this study is, therefore, to assess the antimicrobial resistance profiles and multidrug resistance patterns of S. pneumoniae isolates from patients suspected of pneumococcal infections in Ethiopia.

Methods

A hospital-based prospective study was conducted from January 2018 to December 2019 at Addis Ababa city and Amhara National Region State Referral Hospitals. Antimicrobial resistance tests were performed from isolates of S. pneumoniae that were collected from pediatric and adult patients. Samples (cerebrospinal fluid, blood, sputum, eye discharge, ear discharge, and pleural and peritoneal fluids) from all collection sites were initially cultured on 5% sheep blood agar plates and incubated overnight at 37 °C in a 5% CO₂ atmosphere. Streptococcus pneumoniae was identified and confirmed by typical colony morphology, alpha-hemolysis, Gram staining, optochin susceptibility, and bile solubility test. Drug resistance testing was performed using the E-test method according to recommendations of the Clinical and Laboratory Standards Institute.

Results

Of the 57 isolates, 17.5% were fully resistant to penicillin. The corresponding value for both cefotaxime and ceftriaxone was 1.8%. Resistance rates to erythromycin, clindamycin, tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole were 59.6%, 17.5%, 38.6%, 17.5 and 24.6%, respectively. Multidrug resistance (MDR) was seen in 33.3% isolates. The most common pattern was co-resistance to penicillin, erythromycin, clindamycin, and tetracycline.

Conclusions

Most S. pneumoniae isolates were susceptible to ceftriaxone and cefotaxime. Penicillin has been used as a drug of choice for treating S. pneumoniae infection. However, antimicrobial resistance including multidrug resistance was observed to several commonly used antibiotics including penicillin. Hence, it is important to periodically monitor the antimicrobial resistance patterns to select empirical treatments for better management of pneumococcal infection.

Pneumococcal nasopharyngeal carriage and antimicrobial susceptibility profile in children under five in southern Ethiopia

Background: Streptococcus pneumonia causes high morbidity and mortality, particularly in children under five. Nasopharyngeal (NP) carriage predisposes individuals to pneumococcal infection and horizontal spread within the community. Overuse of antibiotics has been linked to increased risk of antimicrobial resistance to S. pneumonia. We investigated NP carriage rate and resistance to commonly prescribed antibiotics in under-five children visiting a public referral center in southern Ethiopia.

Methods: In total, 413 under 5 children who visited the outpatient department for a health check-up, immunization or acute mild illnesses underwent NP sampling. Parent/caregiver surveys were administered at the clinic. Sterile plastic applicator rayon tipped swabs were used for NP sampling. Antimicrobial susceptibility testing was performed using modified the disk diffusion method.

Results: S. pneumonia NP carriage was observed in 39% [95% confidence interval (CI): 34.4–43.8]. Living with one or more sibling (AOR (adjusted odds ratio) 1.95: 95% CI: 1.01, 3.76), age group of 3-23 months (AOR 2.31: 95% CI: 1.07, 4.98), co-sleeping with family (AOR 2.09, 95% CI: 1.16, 3.79), attendance at kindergarten/day-care (AOR 1.84: 95% CI: 1.09, 3.11) and malnutrition independently increased S. pneumonia carriage at the individual level. S. pneumonia was highly resistant to Oxacillin (38.5%), Tetracycline (37.3%), and Trimethoprim-sulfamethoxazole (34.2%). Multi-drug resistance was observed in 42.2% of isolates.

Conclusions: A high streptococcal NP carriage rate was observed in under-five children. The high level of resistance to commonly used antibiotics calls for enhancing national surveillance of resistance patterns and enforce antibiotic stewardship efforts.

Magnitude of Streptococcus pneumoniae Among Under-Five Children with Symptom of Acute Respiratory Infection at Hiwot Fana Specialized University Hospital, Harar, Ethiopia: Associated Risk Factors and Antibacterial Susceptibility Patterns

PURPOSE

Streptococcus pneumoniae is the major cause of pneumoniae infection among under-five children that leads to high morbidity and mortality. Thus, the aim of this study was to determine the magnitude of Streptococcus pneumoniae in under-five children of an acute respiratory infection, assess its antimicrobial susceptibility patterns, and define the associated factors.

METHODS

An institutional-based cross-sectional study was conducted on a total of 384 under-five children of acute respiratory infection attending outpatient department of Hiwot Fana Specialized University Hospital, Harar, Ethiopia, from March 1 to 30, 2020. Socio-demographic and clinical data were collected from the study participants using a structured questionnaire. Sputum samples were collected and processed to identify Streptococcus pneumoniae pathogen using the culture and biochemical tests as per the standard procedures. The Kirby-Bauer disk diffusion method was used for antimicrobial susceptibility testing. Data were entered into Epi-data version 3.1 and analyzed by using Statistical Product and Service Solutions version 22.

RESULTS

The proportion of Streptococcus pneumoniae in under-five children with acute respiratory infection was 11.2%. About 50% of isolated Streptococcus pneumoniae was resistant to tetracycline and cotrimoxazole, whereas more than 90% of it was susceptible to Ceftriaxone and amoxicillin-clavulanate. Children who lived in rural areas were 3.6 times more likely to have S. pneumoniae compared to children who lived in urban areas (AOR: 3.6, 95% CI: 1.2-11) and children with familysmokers in a house were 3 times at risk to be infected with S. pneumoniae (AOR: 3, 95% CI: 1.8-8.0).

CONCLUSION

High antimicrobial resistance of S. pneumoniae against tetracycline and cotrimoxazole was observed and children who lived in rural areas and live with a family of cigarette smoker are factors associated with Streptococcus pneumoniae. Therefore, providing health educations to the family of children rural residents and isolating smokers from the house where children lived are recommended actions to reduce bacteria caused by Streptococcus pneumoniae.

Serotypes and Antimicrobial Susceptibility of Nasopharyngeal Isolates of Streptococcus pneumoniae from Children Less Than 5 Years Old in Egypt

Purpose

Streptococcus pneumoniae (S. pneumoniae) is the etiology of severe and life-threatening infections in children less than 5 years old. Though pneumococcal conjugate vaccines (PCVs) are effective in the prevention of pneumococcal infections, yet they are not included in the National Immunization Program in Egypt pending the identification of pathogenic serotypes. As S. pneumoniae colonization of the pharynx predisposes to pneumonia and invasive pneumococcal disease (IPD) caused by the colonizing serotypes, identification of the nasopharyngeal (NP) serotypes can be a surrogate to the invasive serotypes. In this study, we aimed to 1. Identify the serotypes and antimicrobial susceptibility testing (AST) of Streptococcus pneumoniae colonizing the nasopharynx of Egyptian children younger than 5 years in two successive winter seasons. 2. Correlate the identified serotypes with vaccine coverage of the 13-valent conjugate pneumococcal vaccines (PCV13). 3. Compare the serotypes and AST of S. pneumoniae from NP to those of IPD that were routinely identified in our clinical laboratory during the study period.

Materials and Methods

The study was conducted in two successive winter seasons (December 2015–March 2016; December 2016–March 2017). We enrolled 334 children, aged 6 months to 5 years, attending the outpatient general clinics of Cairo University Children Hospital, excluding those with fever, signs of infection, history of antibiotic intake or hospitalization in the preceding month. We tested NP swabs for S. pneumoniae by culture and real-time PCR. Serotyping was performed by sequential multiplex PCR for all positive samples. AST was done to S. pneumoniae isolates by Vitek-2™ (BioMérieux, Marcy-L’Etoile, France). We included routinely detected S. pneumoniae from sterile body sites during the study period, and identified their serotypes and AST.

Results

PCR was positive for pneumococci in 217 out of 334 pharyngeal swabs (65%), including 186 typable samples. The most common serotypes were serotypes 1, 6ABC, 19 F, 5 and 18ABC. By culture, we isolated only 110 out of 334 pharyngeal swabs (32.9%). The theoretical coverage of the PCV13 vaccine for the detected serotypes was 77.4%. The AST of NP isolates revealed low susceptibility rates to all antimicrobials except for vancomycin, linezolid, levofloxacin and clindamycin. During the study period, we identified 40 IPD; 21 identified by PCR and 19 by culture. The commonest pneumococcal serotypes were 1, 18ABC, 6ABC and 5. The PCV13 coverage was 75%. By Vitek-2, the isolates showed 100%, 100%, 94.7%, 89.5%, 84.2%, 84.2% and 78.9% susceptibility to vancomycin, linezolid, clindamycin, levofloxacin, penicillin, cefotaxim and erythromycin, respectively.

Conclusion

Based on the serotype vaccine coverage and the emerging antimicrobial resistance of S. pneumoniae, PCVs will be valuable to Egyptian children.

Carriage rate of Neisseria meningitidis, antibiotic susceptibility pattern and associated risk factors among primary school children in Gondar town, Northwest Ethiopia

BACKGROUND

Globally, in 2012, about 1.2 million estimated cases were reported with ~ 135,000 deaths annually. In Ethiopia, specifically in our study area, limited information is found on the oropharyngeal carriage, antimicrobial resistance pattern, and associated risk factors for N. meningitidis among school children. So, the aim of this study was to assess oropharyngeal carriage rate of N. meningitidis, antibiotic susceptibility pattern and associated risk factors among primary school children in Gondar town, Northwest Ethiopia.

METHODS

A cross sectional study was conducted from January to April, 2019 in Gondar town. Multi stage simple random sampling technique was used. A total of 524 oropharyngeal swabs were collected using sterile plastic cotton swabs. Modified Thayer Martin media was used for primary isolation. Antimicrobial susceptibility pattern was done based on Kirby-Bauer method on Muller-Hinton agar supplemented with 5% sheep blood. Multidrug resistance was defined as resistance of an isolate to two or more antimicrobial classes tested. Logistic regression model was used to see the association between dependent variables (Carriage rate of Neisseria meningitidis, Serogroups of Neisseria meningitidis and Antimicrobial susceptibility patterns) and independent variables (Socio-demographic data and risk factors). Variables with a P- value ≤0.2 during bivariable analysis was taken to multivariable analysis to check significant association of meningococcal carriage with risk factors. Finally, a P-value < 0.05 was considered as statistically significant. Data was summarized using numbers, percentages and tables.

RESULTS

A total of 53(10.1%) (CI: 7.6-12.8) N. meningitidis isolates were identified. Serogroup A 13 (24.5%) was the most prevalent followed by Y/W135 11(20.7%) whereas serogroup B 4(7.6%) was the least identified serotype. Meningococcal isolates were resistant to ciprofloxacin (45.3%) and trimethoprim-sulfamethoxazole (73.6%). Overall, most of meningococcal isolates showed about 32(60.4%) multidrug resistance. Meningococcal carriage rate was significantly associated with family size, tonsillectomy, passive smoking, number of students per class, sharing utensils, history of visiting healthcare institutions, and indoor kitchen.

CONCLUSION

This study highlights the need for reinforcement of case-based, laboratory confirmed surveillance of N. meningitidis carriage in Ethiopian elementary school students to enable mapping of distribution of serotypes of the causative organisms across the country and determine the current potential necessity of vaccination.

Bacterial Infections and Their Antibiotic Resistance Pattern in Ethiopia: A Systematic Review

Background

Antibiotic resistance is a global challenge in the public health sector and also a major challenge in Ethiopia. It is truly difficult to report bacterial antibiotic resistance pattern in Ethiopia due to the absence of a review which is done comprehensively. The aim of this systematic review was to provide an overview of the works of literature on the antibiotic resistance pattern of the specific bacterial isolates that can be obtained from different clinical samples in the context of Ethiopia.

Materials and Methods

A web-based search using PubMed, Google Scholar, Hinari, Sci Hub, Scopus and the Directory of Open Access Journals was conducted from April to May 2018 for published studies without restriction in the year of publication. Works of literature potentially relevant to the study were identified by Boolean search technique using various keywords: Bacterial infection, antimicrobial resistance, antibiotic resistance, drug resistance, drug susceptibility, anti-bacterial resistance, Ethiopia. Study that perform susceptibility test from animal or healthy source using <10 isolates and methods other than prospective cross-sectional were excluded.

Results

The database search delivered a total of 3459 studies. After amendment for duplicates and inclusion and exclusion criteria, 39 articles were found suitable for the systematic review. All studies were prospective cross-sectional in nature. The review encompasses 12 gram-positive and 15 gram-negative bacteria with their resistance pattern for around 12 antibiotics. It covers most of the regions which are found in Ethiopia. The resistance pattern of the isolates ranged from 0% up to 100%. The overall resistance of M. tuberculosis for antituberculosis drugs ranges from 0% up to 32.6%. The percentage of resistance increases among previously treated tuberculosis cases. Neisseria gonorrhea, S. typhimurium, S. Virchow, Group A Streptococci (GAS), and Group B Streptococci (GBS) were highly susceptible for most of the tested antibiotics. Methicillin-Resistant Staphylococcus aureus was highly resistant to most of the antibiotics with a slightly increased susceptibility to gentamycin.

Conclusions

Total bacterial isolates obtained from a different source of sample and geographic areas were 28, including M. tuberculosis. Majority of the bacterial isolates were resistant to commonly used antibiotics. A continuous monitoring and studies on the multidrug-resistant bacterial isolates are important measures.

Colonization rate of Streptococcus pneumoniae, its associated factors and antimicrobial susceptibility pattern among children attending kindergarten school in Hawassa, southern Ethiopia

OBJECTIVE

The aim of this study was to determine the colonization rate of Streptococcus pneumoniae, antimicrobial susceptibility pattern and associated risk factors among children attending kindergarten school in Hawassa, Ethiopia.

RESULTS

Out of 317 study participants, 68 (21.5%) were colonized with S. pneumoniae. Colonization rate was significantly associated with factors such as age (3 to 4 years old) (P = 0.01), having a sibling whose age was less than 5 years (P = 0.011), sharing a bed with parents (P = 0.005), cooking within bedroom (P = 0.002), and previous hospitalization (P = 0.004). Forty-four (64.6%), 33 (48.5%), and 2942.6%) of S. pneumoniae isolated were resistant to cotrimoxazole, penicillin, and tetracycline respectively.

Pneumococcal Carriage, Serotype Distribution, and Risk Factors in Children With Community-Acquired Pneumonia, 5 Years After Introduction of the 10-Valent Pneumococcal Conjugate Vaccine in Ethiopia

Background

There is a scarcity of data on pneumococcal serotypes carried by children in Ethiopia. We studied pneumococcal nasopharyngeal carriage rate, serotypes, and risk factors among children with community acquired pneumonia (CAP).

Methods

A prospective observational cohort study was performed in children with CAP, aged 0–15 years, in 2 pediatric emergency departments in Addis Ababa, Ethiopia. Nasopharyngeal swabs were cultured, and serotypes of Streptococcus pneumoniae were determined by sequencing the cpsB gene and by the Quellung reaction. Risk factors were analyzed by using binary logistic regression.

Results

Nasopharyngeal swabs were collected from 362 children with CAP. Pneumococcal carriage rate was 21.5% (78 of 362). The most common serotypes were 19A (27%), 16F (8.5%), and 6A (4.9%). In addition, 8.5% of the pneumococcal isolates were nontypeable. In bivariate analysis, children with a parent that smokes were more likely to carry pneumococci (crude odds ratio, 3.9; 95% confidence interval [CI], 1.2–12.3; P = .023) than those with parents that do not smoke. In multivariable analysis, living in a house with ≥2 rooms (adjusted odds ratio [AOR], 0.48; 95% CI, 0.28–0.82; P = .007) and vaccination with ≥2 doses of 10-valent pneumococcal conjugate vaccine (PCV10) (AOR, 0.37; 95% CI, 0.15–0.92; P = .033) were protective of pneumococcal carriage.

Conclusions

Five years after introduction of PCV10 in Ethiopia, the vaccine-related serotype 19A was predominant in the nasopharynx of children with CAP. Continued evaluation of the direct and indirect impact of PCV10 on pneumococcal serotype distribution in Ethiopia is warranted.

Serotype and molecular diversity of nasopharyngeal Streptococcus pneumoniae isolates from children before and after vaccination with the ten-valent pneumococcal conjugate vaccine (PCV10) in Ethiopia

Background

Streptococcus pneumoniae is a major human pathogen, and nasopharyngeal colonization is the first step for transmission and pathogenesis of pneumococcal diseases. Ethiopia introduced the 10-valent pneumococcal conjugate vaccine (PCV10) in October 2011. Here we studied nasopharyngeal carriage rates of pneumococci in children and analyzed the serotype and genetic diversity of pneumococcal isolates before first dose and after completion of the vaccine.

Method

A longitudinal study was conducted from February 2013 to November 2016. Totally 789 infants were enrolled at the age of 6 weeks before first dose of PCV10 vaccination, 206 were re-sampled at the age of 9 months, and 201 at 2 years of age after the final dose of PCV10 at the age of 14 weeks. One hundred sixteen children were followed during all the three sampling periods. A total of 422 nasopharyngeal isolates were serotyped using gel diffusion and the Quellung reaction, 325 were typed with pulsed field gel electrophoresis (PFGE), and 12 were selected for multi locus sequence typing (MLST).

Results

Pneumococcal carriage rates at the age of 6 weeks, 9 months and 2 years of age were 26.6% (210/789), 56.8% (117/206) and 48.3% (97/201), respectively. Out of 116 children none of them carried the same strain during the three period and the carriage rate at the age of 6 weeks, 9 months and 2 years were 32.7% (38/116), 59.% (69/116) and 49.1% (57/116) respectively. Totally 59 pneumococcal serotypes were identified among 422 isolates. Serotype 6A (5.0%) dominated followed by 34 (4.5%), 10A (4.0%), 11A (4.0%), 19F (3.8%), 15B (3.8%), 23F (3.6%), and 15A (3.6%). The proportion of non-PCV10 serotypes among the isolates recovered at 6 weeks, 9 months and 2 years was 79.4, 88.9 and 89.7% respectively. Molecular typing of 325 isolates collected at 6 weeks and 9 months of age showed a high genetic diversity.

Conclusion

This study highlights the presence of very diverse serotypes in Ethiopia where non-vaccine serotypes were predominant. Completion of the PCV10 schedule was associated with an approximately 50% reduction of vaccine-type carriage and increase of non-vaccine types. PCV13 would potentially reduce vaccine-type carriage by further 10%.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4024-1) contains supplementary material, which is available to authorized users.

Prevalence and risk factors of pneumococcal nasopharyngeal carriage in healthy children attending kindergarten, in district of Arsi Zone, South East, Ethiopia

OBJECTIVE

S. pneumoniae responsible for a range of respiratory infections from uncomplicated to severe invasive pneumococcal disease. Nasopharyngeal specimens were collected from children attending kindergarten and aged ≤ 6 years from February, 2017 to June, 2017 to assess the nasopharyngeal carriage and antimicrobial susceptibility pattern of S. pneumoniae. Parents of children interviewed using questionnaire and check list to identify associated factors. An antimicrobial susceptibility test performed using disk diffusion method.

RESULTS

Overall pneumococcal carriage were 18.4% (88/477). No significant variation in colonization based on sex and age of children. Children living with siblings (1-2) < 6 years in household (adjusted odd ratio = 16.06; 95% confidence interval 6.21-41.55) and > 5 person per household (adjusted odd ratio = 3.27; 95% confidence interval 1.50-7.14) were associated with higher S. pneumoniae carriage. Non- exclusive breast feeding (adjust odd ratio = 6.00; 95% confidence interval 3.33-10.80) and horse cart transportation (adjusted odd ratio = 2.75; 95% confidence interval 1.05-7.22) increases carriage. S. pneumoniae showed 21 (23.9%) resistance to erythromycin, 18 (20.4%) to amoxicillin, 13 (15.0%) to penicillin, and the least 1 (1.1%) to augmentin.

High rate of antibiotic resistance among pneumococci carried by healthy children in the eastern part of the Democratic Republic of the Congo

Background

Pneumococcal conjugate vaccines have been introduced in the infant immunisation programmes in many countries to reduce the rate of fatal pneumococcal infections. In the Democratic Republic of the Congo (DR Congo) a 13-valent vaccine (PCV13) was introduced in 2013. Data on the burden of circulating pneumococci among children after this introduction are lacking. In this study, we aimed to determine the risk factors related to pneumococcal carriage in healthy Congolese children after the vaccine introduction and to assess the antibiotic resistance rates and serotype distribution among the isolated pneumococci.

Methods

In 2014 and 2015, 794 healthy children aged one to 60 months attending health centres in the eastern part of DR Congo for immunisation or growth monitoring were included in the study. Data on socio-demographic and medical factors were collected by interviews with the children’s caregivers. Nasopharyngeal swabs were obtained from all the children for bacterial culture, and isolated pneumococci were further tested for antimicrobial resistance using disc diffusion tests and, when indicated, minimal inhibitory concentration (MIC) determination, and for serotype/serogroup by molecular testing.

Results

The pneumococcal detection rate was 21%, being higher among children who had not received PCV13 vaccination, lived in rural areas, had an enclosed kitchen, were malnourished or presented with fever (p value < 0.05). The predominant serotypes were 19F, 11, 6A/B/C/D and 10A. More than 50% of the pneumococcal isolates belonged to a serotype/serogroup not included in PCV13.

Eighty per cent of the isolates were not susceptible to benzylpenicillin and non-susceptibility to ampicillin and ceftriaxone was also high (42 and 37% respectively). Almost all the isolates (94%) were resistant to trimethoprim-sulphamethoxazole, while 43% of the strains were resistant to ≥3 antibiotics.

Conclusions

Our study shows alarmingly high levels of reduced susceptibility to commonly used antibiotics in pneumococci carried by healthy Congolese children. This highlights the importance of local antibiotic resistance surveillance and indicates the needs for the more appropriate use of antibiotics in the area. The results further indicate that improved living conditions are needed to reduce the pneumococcal burden, in addition to PCV13 vaccination.

Electronic supplementary material

The online version of this article (10.1186/s12887-018-1332-3) contains supplementary material, which is available to authorized users.

Pharyngeal colonization and drug resistance profiles of Morraxella catarrrhalis, Streptococcus pneumoniae, Staphylococcus aureus, and Haemophilus influenzae among HIV infected children attending ART Clinic of Felegehiwot Referral Hospital, Ethiopia

Background

Asymptomatic pharyngeal colonization by potential bacteria is the primary reservoir for bacterial species within a population and is considered a prerequisite for development of major childhood diseases such as sinusitis, otitis media, pneumonia, bacteremia, and meningitis. However, there is dearth of data on the colonization and drug resistance pattern of the main bacterial pathogens in the pharynx of HIV infected children in Ethiopia. Therefore, this study determined the pharyngeal colonization and drug resistance profile of bacterial pathogens in HIV infected children attending ART clinic of Felegehiwot Referral Hospital (FHRH), Amhara Region, Ethiopia.

Methods

A hospital based cross-sectional study was conducted from May 2016 to June 2017 at the ART clinic of FHRH. A total of 300 HIV infected children were enrolled in the study. Data on socio-demographic characteristics of the study participants were collected with face-to-face interview and patient—card review using structured questionnaire. Bacterial species were identified using standard bacteriological techniques. Drug susceptibility testing was performed using disk diffusion technique. Chi-square test was done to determine associations among variables.

Results

The median age of the participants was 11 years. Overall, 153 (51%) of children were colonized by respiratory bacteria in their pharynx. Colonization rate was higher in children from mothers who had attained college and above levels of education than others (P = 0.04). It was also higher in children without the sign of malnutrition than others (P = 0.004). The colonization rate of S.aureus, M.catarrhalis, S.pneumoniae and H.influenzae were 88 (29%), 37 (12.3%), 31 (10.3%) and 6 (2%), respectively. S.aureus—M.catarrhalis concurrent colonization was found in 14 (4.7%) of children. Age (P = 0.03), schooling (P = 0.045) and history of running nose (P = 0.043) were significantly associated with S.aureus colonization. Living in urban setting (P = 0.042) and children from mothers with college and above levels of education (P = 0.002) were significantly associated with M.catarrhalis colonization. Majority of the isolates were resistant to penicillin (68.5%) and cotrimoxazole (52.5%).S.aureus isolates were resistant to penicillin (84.1%) and cotrimoxazole (51.1%).M.catarrhalis isolates were resistant to penicillin (94.6%), erythromycin (86.5%)and cotrimoxazole (78.4%). Overall, 99 (59.3%) of the isolates were multi-drug (MDR) resistant. The overall MDR rates among S.aureus, M.catarrhalis and S.pneumoniae isolates were 65.9%, 78.4% and 22.6%, respectively.

Conclusions

Pharyngeal colonization of respiratory bacteria in HIV infected children is a major public health problem. Single and multiple antibiotic resistant is alarmingly high among respiratory colonizers. Therefore, regular screening of HIV infected children for culture and antimicrobial susceptibility testing is recommended to prevent the development of severe opportunistic infections.

Antimicrobial resistance in Africa: a systematic review

BACKGROUND

Antimicrobial resistance (AMR) is widely acknowledged as a global problem, yet in many parts of the world its magnitude is still not well understood. This review, using a public health focused approach, aimed to understand and describe the current status of AMR in Africa in relation to common causes of infections and drugs recommended in WHO treatment guidelines.

METHODS

PubMed, EMBASE and other relevant databases were searched for recent articles (2013-2016) in accordance with the PRISMA guidelines. Article retrieval and screening were done using a structured search string and strict inclusion/exclusion criteria. Median and interquartile ranges of percent resistance were calculated for each antibiotic-bacterium combination.

RESULTS

AMR data was not available for 42.6% of the countries in the African continent. A total of 144 articles were included in the final analysis. 13 Gram negative and 5 Gram positive bacteria were tested against 37 different antibiotics. Penicillin resistance in Streptococcus pneumoniae was reported in 14/144studies (median resistance (MR): 26.7%). Further 18/53 (34.0%) of Haemophilus influenza isolates were resistant to amoxicillin. MR of Escherichia coli to amoxicillin, trimethoprim and gentamicin was 88.1%, 80.7% and 29.8% respectively. Ciprofloxacin resistance in Salmonella Typhi was rare. No documented ceftriaxone resistance in Neisseria gonorrhoeae was reported, while the MR for quinolone was 37.5%. Carbapenem resistance was common in Acinetobacter spp. and Pseudomonas aeruginosa but uncommon in Enterobacteriaceae.

CONCLUSION

Our review highlights three important findings. First, recent AMR data is not available for more than 40% of the countries. Second, the level of resistance to commonly prescribed antibiotics was significant. Third, the quality of microbiological data is of serious concern. Our findings underline that to conserve our current arsenal of antibiotics it is imperative to address the gaps in AMR diagnostic standardization and reporting and use available information to optimize treatment guidelines.

Serotypes of Streptococcus pneumoniae in Egyptian children: are they covered by pneumococcal conjugate vaccines?

In Egypt, pneumococcal vaccines have not yet been introduced as being compulsory. Identification of the circulating serotypes in Egypt is mandatory to determine whether or not the pneumococcal vaccines will be beneficial. The current study aims to identify the serotypes, vaccine coverage, and antimicrobial resistance of Streptococcus pneumoniae colonizing the nasopharynx of Egyptian children younger than 5 years old. The study was conducted in two successive winter seasons (December 2012-February 2013 and December 2013-February 2014). Two hundred children were enrolled, aged from 6 months to 5 years, excluding those with fever, signs of infection, history of antibiotic intake, and hospitalization in the preceding month. Nasopharyngeal (NP) secretions were collected, subjected to culture, and underwent antibiotic susceptibility testing if positive for pneumococci. Real-time polymerase chain reaction (PCR) and serotyping by sequential multiplex PCR for positive cases were included as well. Streptococcus pneumoniae was isolated from 62 subjects. All isolates were sensitive to vancomycin and levofloxacin, but the majority showed resistance to multiple antibiotics. PCR was positive for pneumococci in 113 subjects (56.5%). The most commonly detected serotypes (st) were 6A6B6C (n = 21, 20.8%), 19F (n = 19, 18.8%), 1 (n = 11, 10.9%), 34 (n = 8, 7.9%), and 19A (n = 6, 5.9%). The theoretical coverage of the PCV13 vaccine for the detected serotypes was 72.4%, while that of PCV10 was 65.5%. Based on these percentages, we recommend including pneumococcal conjugate vaccines in the Egyptian national vaccination program.

Nasopharyngeal Carriage and Antimicrobial Susceptibility Patterns of Streptococcus pneumoniae among Children under Five in Southwest Ethiopia

Nasopharyngeal carriage of Streptococcus pneumoniae is found to play an important role in the development and transmission of pneumococcal diseases. In this study, we assessed the nasopharyngeal carriage, antimicrobial susceptibility patterns and associated risk factors of S. pneumoniae among children under five. A total of 361 children under five attending the outpatient department of Shanan Gibe Hospital in Jimma, Southwest Ethiopia were enrolled from June to September 2014. Nasopharyngeal specimens were collected using sterile plastic applicator rayon tipped swab and inoculated on tryptone soy agar supplemented with 5% sheep blood and 5 µg/mL gentamycin. Antimicrobial susceptibility testing was performed using the modified disk diffusion method. The overall prevalence of S. pneumoniae carriage was 43.8% (158/361) among children under five. Resistance to tetracycline, cotrimoxazole, penicillin, chloramphenicol and erythromycin was observed in 53.2% (84/158), 43.7% (69/158), 36.1% (57/158), 13.3% (21/158) and 8.9% (14/158) of isolates respectively. Multidrug resistance was seen in 17.7% (28/158) of isolates. In multivariate logistic regression analysis, children living with sibling(s) < 5 years old (adjusted odds ratio (AOR) = 1.798; 95% confidence interval (CI), 1.169–2.766) and malnutrition (AOR = 2.065; 95% CI, 1.239–3.443) were significantly associated with S. pneumoniae carriage. A high nasopharyngeal carriage of S. pneumoniae was observed among children under five in Southwest Ethiopia. There should be a strategy to prevent S. pneumoniae nasopharyngeal colonization and identify the appropriate antibiotic to the individual child.

Decline in Pneumococcal Nasopharyngeal Carriage of Vaccine Serotypes After the Introduction of the 13-Valent Pneumococcal Conjugate Vaccine in Children in Atlanta, Georgia

BACKGROUND

Streptococcus pneumoniae (SP) serotype distribution among nasopharyngeal (NP) carriage isolates changed significantly after the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7). We evaluated the impact on NP carriage and invasive disease of SP after the introduction of the 13-valent PCV (PCV13) in March 2010.

METHODS

NP swabs were collected from children 6-59 months of age in an emergency department from July 2010 to June 2013. After broth enrichment, samples were cultured for SP and isolates were serotyped. Clinical and immunization records were reviewed. Findings during 6 sequential 6-month study periods were compared. Surveillance isolates of invasive disease isolates were reviewed.

RESULTS

A total of 2048 children were enrolled, and 656 (32%) were SP carriers. Mean age of carriers was 27 months, 54% were males. Carriage was higher among day-care attendees (P < 0.01) and children with respiratory tract illnesses (P < 0.5) and otitis media (P < 0.01). Commonly carried serotypes included 35B (15.2%), 15B/C (14.2%), 19A (9.6%), 11A (8%), 23B (5.6%), 6C (5.3%), 21 (5%), and 15A (5%); 13.9% were PCV13 serotypes. The proportion of children with SP carriage remained stable but the serotype distribution changed during the study period. Among carriers, PCV13 serotypes declined from 29% (36/124) to 3% (3/99; P < 0.0001), predominantly because of decline of serotype 19A from 25.8% (32/124) to 3% (3/99; P < 0.0001); non-PCV13 serotypes (excluding 6C) increased from 68.4% (78/114) to 97% (95/98; P < 0.0001); serotype 35B significantly increased from 8.9% (11/124) to 25.3% (25/99; P < 0.05). Nonsusceptibility to ceftriaxone declined from 22.6% (28/124) to 0% (0/99; P < 0.0001), with a similar decline in penicillin nonsusceptibility.

CONCLUSIONS

Introduction of PCV13 for universal infant use was associated with significant reductions in nasopharyngeal carriage of PCV13 serotypes and resistant strains. Carriage of non-PCV13 serotypes increased modestly, particularly serotype 35B. Further investigation is warranted to determine whether nonvaccine pneumococcal serotypes carried in the nasopharynx are associated with significant replacement disease.