High prevalence of antibiotic resistance in nasopharyngeal bacterial isolates from healthy children in rural Uganda: A cross-sectional study

Nasopharyngeal carriage of Streptococcus pneumoniae serotypes among sick and healthy children in northern India: A case-control study

BACKGROUND

Streptococcus pneumoniae is leading bacterial cause of community acquired pneumonia and according to World Health Organization, responsible for 14 % death in children. There is effective vaccine available against Streptococcus pneumoniae. Hence the primary objective was to isolate Streptococcus pneumoniae from nasopharyngeal swabs in children aged 2-59 months with and without community acquired pneumonia and to assess their serotypes.

METHODS

This case-control study was conducted in tertiary teaching institutes in northern India. Hospitalized children, aged 2-59 months, with World Health Organization-defined community acquired pneumonia were included as cases. Age matched healthy controls were recruited from immunization clinic. All enrolments were done after written informed parental consent. Nasopharyngeal swabs were taken from both cases and controls, and were cultured on 5 % sheep blood agar with gentamycin plate for growth of Streptococcus pneumoniae and incubated in a jar at 370 for 18-24 hrs. Quellung reaction test was used for serotyping.

RESULTS

From March 2017 to December 2022, 2693 children (1910 cases and 783 controls), were recruited. The median age of cases was 7 months and controls 10 months. Almost all the cases had received antibiotics prior to hospitalization. Streptococcus pneumoniae positivity in nasopharyngeal swab was 8.1 % in cases, of which 56.8 % were vaccine serotypes and 23.6 % in controls, of which 37.8 % were vaccine serotypes. Adjusted odds ratio of isolating vaccine serotypes among cases as compared to controls was 1.77 (95 % CI, 1.09-2.88).

CONCLUSION

Streptococcus pneumoniae isolation from nasopharyngeal was found to be in lower proportion in cases as compared to control, though colonization with vaccine serotypes was higher in cases as compared to control. Therefore, pneumococcal vaccine coverage must be increased to prevent community acquired pneumonia.

Asymptomatic nasopharyngeal bacterial carriage, multi-drug resistance pattern and associated factors among primary school children at Debre Berhan town, North Shewa, Ethiopia

BACKGROUND

Nasopharyngeal carriage of bacteria is the main source for transmission of pathogens across individuals and horizontal spread of organisms in the community. It is an important risk factor for the acquisition of community-acquired respiratory tract infection. It is the major public health problem among children. The asymptomatic carriage of nasopharyngeal bacteria is different globally, particularly in Africa, carriage is higher in children and decreases with increasing age, 63.2% in children less than 5 years, 42.6% in children 5-15 years, and 28.0% in adults older than 15 years.

OBJECTIVE

The aims of this study was to determine asymptomatic nasopharyngeal bacterial carriage, multi-drug resistance pattern and associated factors among primary school children at Debre Berhan town, North Shewa, Ethiopia.

METHODS

Institutional based cross-sectional study was conducted at Debre Berhan town primary schools from February 1 to April 30, 2021. Primarily, the schools were stratified into two strata, public and private primary schools. From a total of sixteen government and fourteen private primary schools, five government and five private schools were selected by using a simple random sampling technique. Socio-demographic variables and potential risk factors were assessed using a structured questionnaire. A total of 384 nasopharyngeal swab samples were collected using sterile swabs aseptically; and inoculated on Blood agar, Chocolate agar, MacConkey agar, and Mannitol salt agar. The colony was characterized to isolate bacteria, and bacterial identification was performed by Gram reaction, hemolysis patterns, colonial characteristics and pigmentation, catalase test, coagulase test, mannitol fermentation test, oxidase test, fermentation of carbohydrates, H₂S production, motility, formation of indole, triple sugar iron agar (TSI), citrate utilization, lysine decarboxylase or methyl red vogues proskur utilization, urea hydrolysis and satellitism tests. Antimicrobial sensitivity tests were performed by using modified Kirby-Bauer disk diffusion method. Data were entered into statistical package Epi data 4.0.0.6 and transferred to and analyzed using SPSS software version-23. P value of < 0.05 with Odds ratio (OR) and 95% confidence interval (CIs) was considered as statistically significant.

RESULTS

The overall prevalence of nasopharyngeal carriage of bacterial isolate was 35.7% (95% CI 30.7-40.7%). The predominant isolates were Staphylococcus aureus 54.5% followed by coagulase-negative Staphylococcus 35.8%, and Streptococcus pyogens 4.5%. Most bacterial isolates were susceptible to chloramphenicol, ciprofloxacin, gentamycin, nitrofurantoin, azithromycin, ciprofloxacin; and the overall multidrug resistance pattern of isolated bacteria was 62.03% out of 137 bacterial isolates. Numbers of rooms ≤ 2 per house [AOR = 5.88, 95%CI 1.26-27.57], having history of hospitalization [AOR = 4.08, 95%CI 1.45-11.53], passive smoking [AOR = 4.87, 95%CI 1.49-15.97], family size of > 5 members [AOR = 2.17, 95%CI 1.24-3.81], and number of students in the classroom [AOR = 2.35,95%CI 1.37-4.02] were statistically significant associated risk factors for nasopharyngeal bacteria carriage.

CONCLUSION

Asymptomatic nasopharyngeal bacteria carriage in children is alarming for community-acquired infection. The overall multidrug resistance was very high. The risk of the carriage was increased with having a history of passive smoking, being in large family size and number of students per class. Longitudinal follow-up studies would be helpful for better understanding the infection risk in bacterial pathogen carriers.

Pneumococcal nasopharyngeal carriage in children under 5 years of age at an outpatient healthcare facility in Novi Sad, Serbia during the COVID-19 pandemic

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The prevalence of nasopharyngeal pneumococcal carriage in children aged 24–60 months was 31.7%.

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The prevalence was high and increased during the coronavirus disease 2019 (COVID-19) pandemic.

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This ruled out a major role of COVID-19 in suppressing carriage and, probably, transmission.

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The dominant serotypes were 15B, 6B, 19F, 11A, 6C, 6A, 3, 23F and 19A.

Objectives

To assess whether pneumococcal nasopharyngeal carriage among children aged 24–60 months reduced during the coronavirus disease 2019 (COVID-19) pandemic in Novi Sad, Serbia, and to investigate the overall prevalence of carriage, serotype distribution and dominant serotypes 2–3 years after the introduction of pneumococcal conjugate vaccine 10.

Design and methods

This prospective, observational study was conducted in February–March 2020, September–November 2020 and April–June 2021, enabling the comparison of results in the pre-pandemic/early pandemic period with two periods during the COVID-19 pandemic. Pneumococci were identified by standard microbiological methods. Serotype identification was performed using conventional multiplex polymerase chain reaction assays.

Results

Among 1623 children tested, 515 (31.7%, 95% confidence interval 29.4–34.0%) carried pneumococci. A significant increase in prevalence was found between February–March 2020 and September–November 2020 (P=0.0085), with no difference found between September–November 2020 and April–June 2021 (P=0.0524). Pneumococcal colonization was significantly higher in children who were fully vaccinated and among children who attended day care centres. The dominant serotypes were 15B, 6B, 19F, 11A, 6C, 6A, 3, 23F and 19A, representing 66.4% of all isolates.

Conclusions

This study found that pneumococcal nasopharyngeal carriage in children aged 24–60 months was high before the COVID-19 pandemic, and then increased during the pandemic. This rules out a major role of COVID-19 in the suppression of carriage and, probably, transmission.

Alarming Levels of Multidrug Resistance in Aerobic Gram-Negative Bacilli Isolated from the Nasopharynx of Healthy Under-Five Children in Accra, Ghana

Nasopharyngeal carriage of aerobic Gram-negative bacilli (GNB) may precede the development of invasive respiratory infections. We assessed the prevalence of nasopharyngeal carriage of aerobic GNB and their antimicrobial resistance patterns among healthy under-five children attending seven selected day-care centres in the Accra metropolis of the Greater Accra region of Ghana from September to December 2016. This cross-sectional study analysed a total of 410 frozen nasopharyngeal samples for GNB and antimicrobial drug resistance. The GNB prevalence was 13.9% (95% CI: 10.8-17.6%). The most common GNB were Escherichia coli (26.3%), Klebsiella pneumoniae (24.6%), and Enterobacter cloacae (17.5%). Resistance was most frequent for cefuroxime (73.7%), ampicillin (64.9%), and amoxicillin/clavulanic acid (59.6%). The organisms were least resistant to gentamicin (7.0%), amikacin (8.8%), and meropenem (8.8%). Multidrug resistance (MDR, being resistant to ≥3 classes of antibiotics) was observed in 66.7% (95% CI: 53.3-77.8%). Extended-spectrum beta-lactamase (ESBL)-producing bacteria constituted 17.5% (95% CI: 9.5-29.9%), AmpC-producing bacteria constituted 42.1% (95% CI: 29.8-55.5%), and carbapenemase-producing bacteria constituted 10.5% (95% CI: 4.7-21.8%) of isolates. The high levels of MDR are of great concern. These findings are useful in informing the choice of antibiotics in empiric treatment of GNB infections and call for improved infection control in day-care centres to prevent further transmission.

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.

The microbiome of the nasopharynx

The nasopharyngeal microbiome is a dynamic microbial interface of the aerodigestive tract, and a diagnostic window in the fight against respiratory infections and antimicrobial resistance. As its constituent bacteria, viruses and mycobacteria become better understood and sampling accuracy improves, diagnostics of the nasopharynx could guide more personalized care of infections of surrounding areas including the lungs, ears and sinuses. This review will summarize the current literature from a clinical perspective and highlight its growing importance in diagnostics and infectious disease management.

Antibiotic Susceptibility of Staphylococcus aureus and Streptococcus pneumoniae Isolates from the Nasopharynx of Febrile Children under 5 Years in Nanoro, Burkina Faso

(1) Background: nasopharynx colonization by resistant Staphylococcus aureus and Streptococcus pneumoniae can lead to serious diseases. Emerging resistance to antibiotics commonly used to treat infections due to these pathogens poses a serious threat to the health system. The present study aimed to determine the antibiotic susceptibility of S. aureus and S. pneumoniae isolates from the febrile children’s nasopharynx under 5 years in Nanoro (Burkina Faso). (2) Methods: bacterial isolates were identified from nasopharyngeal swabs prospectively collected from 629 febrile children. Antibiotic susceptibility of S. aureus and S. pneumoniae isolates was assessed by Kirby–Bauer method and results were interpreted according to the Clinical and Laboratory Standard Institute guidelines. (3) Results: bacterial colonization was confirmed in 154 (24.5%) of children of whom 96.1% carried S. aureus, 3.2% had S. pneumoniae, and 0.6% carried both bacteria. S. aureus isolates showed alarming resistance to penicillin (96.0%) and S. pneumoniae was highly resistant to tetracycline (100%) and trimethoprim–sulfamethoxazole (83.3%), and moderately resistant to penicillin (50.0%). Furthermore, 4.0% of S. aureus identified were methicillin resistant. (4) Conclusion: this study showed concerning resistance rates to antibiotics to treat suspected bacterial respiratory tract infections. The work highlights the necessity to implement continuous antibiotic resistance surveillance.

Prevalence of antibiotic-resistant bacteria among patients in two tertiary hospitals in Eastern Uganda

OBJECTIVE

The aim of this study was to determine the prevalence and antibiotic resistance patterns of bacterial isolates from inpatients and outpatients in Mbale and Soroti regional referral hospitals in Eastern Uganda.

METHODS

A retrospective analysis of culture and antibiotic sensitivity test results from the microbiology laboratories of the two tertiary hospitals was conducted for a 3-year period (January 2016-December 2018).

RESULTS

Microbiology records of 3092 patients were reviewed and analysed, with 1305 (42.1%) samples yielding clinical isolates. The most prevalent isolates were Escherichia coli (n = 442; 33.9%), Staphylococcus aureus (n = 376; 28.8%), Klebsiella pneumoniae (n = 237; 18.2%), and Streptococcus pneumoniae (n = 76; 5.8%). High rates of antimicrobial resistance were detected across both Gram-negative and Gram-positive bacteria. Escherichia coli and K. pneumoniae were resistant to several agents such as amoxicillin/clavulanate (83.5%; 64.6%), cefotaxime (74.2%; 52.7%), ciprofloxacin (92.1%; 27.8%), gentamicin (51.8%; 76%), imipenem (3.2%; 10.5%), tetracycline (98%; 74.5%), and trimethoprim-sulfamethoxazole (74.1%; 74.3%), respectively. Staphylococcus aureus and S. pneumoniae exhibited the following resistance profile: cefoxitin (44.4%; 40.9%), chloramphenicol (69.1%; 27.6%) clindamycin (21.5%; 24.4%), gentamicin (83.2%; 66.9%), penicillin (46.5%; -) tetracycline (85.6%; 97.6%), trimethoprim-sulfamethoxazole (88%; 91.3%), and vancomycin (41.2%; -).

CONCLUSION

We observed high resistance rates to antibiotics among the majority of microorganisms that were isolated from the samples collected from patients in Eastern Uganda. Furthermore, measures should be undertaken locally to improve microbiology diagnostics and to prevent the spread of antibiotic-resistant strains as this impedes the optimal treatment of bacterial infections and narrows the choice of effective therapeutic options.

Nasopharyngeal Carriage of Streptococcus pneumoniae and Associated Factors among Children in Southwest Ethiopia

Background:

In Ethiopia, Streptococcus pneumoniae is the predominant causative agent of pneumonia. About, 95% of bacterial pneumonia cases in under five years of children are caused by pneumococci.

Objective:

To assess the nasopharyngeal carriage of Streptococcus pneumoniae, its antibiotic susceptibility pattern, and associated factors among children in Southwest Ethiopia.

Methods:

A cross-sectional study was conducted from October 01, 2018, to December 30, 2018. A total of 293 children aged ≤15 years were included in the study using a systematic random sampling technique. A nasopharyngeal swab was collected using a sterile cotton swab and cultured on blood agar supplemented with 5μg/ml gentamicin. The antimicrobial susceptibility testing was performed using the Kirby-Bauer disc diffusion technique.

Results:

The ages of participants ranged from 5 months to 14 years. The carriage rate of Streptococcus pneumoniae was 74/293 (25.3%). Being within the age group <3 years, the habit of sleeping with parent(s)/guardians and numbers of rooms per household were significantly associated with pneumococcal carriage. Streptococcus pneumoniae showed the highest resistance to Tetracycline, 36 (48.65%), and Trimethoprim/sulfamethoxazole, 29 (39.2%), and was found to be susceptible to Chloramphenicol, 54 (77%), and Erythromycin, 38 (51.4%).

Conclusion:

The nasopharyngeal carriage rate of Streptococcus pneumoniae is considerably high. High antimicrobial resistance of Streptococcus pneumoniae against Tetracycline and Trimethoprim/sulfamethoxazole was observed. Living in a house with a single room, children’s habit of sleeping with parents/guardians and age are associated factors of high pneumococcal carriage. Strategies need to be designed to address the modifiable associated factors and the bacterium antibiotic resistance pattern should be monitored regularly.

Species and drug susceptibility profiles of staphylococci isolated from healthy children in Eastern Uganda

Staphylococci are a key component of the human microbiota, and they mainly colonize the skin and anterior nares. However, they can cause infection in hospitalized patients and healthy individuals in the community. Although majority of the Staphylococcus aureus strains are coagulase-positive, some do not produce coagulase, and the isolation of coagulase-positive non-S. aureus isolates in humans is increasingly being reported. Therefore, sound knowledge of the species and characteristics of staphylococci in a given setting is important, especially isolates from children and immunocompromised individuals. The spectrum of Staphylococcus species colonizing children in Uganda is poorly understood; here, we aimed to determine the species and characteristics of staphylococci isolated from children in Eastern Uganda. Seven hundred and sixty four healthy children less than 5 years residing in Iganga and Mayuge districts in Eastern Uganda were enrolled. A total of 513 staphylococci belonging to 13 species were isolated from 485 children (63.5%, 485/764), with S. aureus being the dominant species (37.6%, 193/513) followed by S. epidermidis (25.5%, 131/513), S. haemolyticus (2.3%, 12/513), S. hominis (0.8%, 4/513) and S. haemolyticus/lugdunensis (0.58%, 3/513). Twenty four (4.95%, 24/485) children were co-colonized by two or more Staphylococcus species. With the exception of penicillin, antimicrobial resistance (AMR) rates were low; all isolates were susceptible to vancomycin, teicoplanin, linezolid and daptomycin. The prevalence of methicillin resistance was 23.8% (122/513) and it was highest in S. haemolyticus (66.7%, 8/12) followed by S. aureus (28.5%, 55/193) and S. epidermidis (23.7%, 31/131). The prevalence of multidrug resistance was 20.3% (104/513), and 59% (72/122) of methicillin resistant staphylococci were multidrug resistant. Four methicillin susceptible S. aureus isolates and a methicillin resistant S. scuiri isolate were mupirocin resistant (high-level). The most frequent AMR genes were mecA, vanA, ant(4')-Ia, and aac(6')-Ie- aph(2'')-Ia, pointing to presence of AMR drivers in the community.

Nasopharyngeal carriage, spa types and antibiotic susceptibility profiles of Staphylococcus aureus from healthy children less than 5 years in Eastern Uganda

Background

Staphylococcus aureus carriage is a known risk factor for staphylococcal disease. However, the carriage rates vary by country, demographic group and profession. This study aimed to determine the S. aureus carriage rate in children in Eastern Uganda, and identify S. aureus lineages that cause infection in Uganda.

Methods

Nasopharyngeal samples from 742 healthy children less than 5 years residing in the Iganga/Mayuge Health and Demographic Surveillance Site in Eastern Uganda were processed for isolation of S. aureus. Antibiotic susceptibility testing based on minimum inhibitory concentrations (MICs) was determined by the BD Phoenix™ system. Genotyping was performed by spa and SCCmec typing.

Results

The processed samples yielded 144 S. aureus isolates (one per child) therefore, the S. aureus carriage rate in children was 19.4% (144/742). Thirty one percent (45/144) of the isolates were methicillin resistant (MRSA) yielding a carriage rate of 6.1% (45/742). All isolates were susceptible to rifampicin, vancomycin and linezolid. Moreover, all MRSA were susceptible to vancomycin, linezolid and clindamycin. Compared to methicillin susceptible S. aureus (MSSA) isolates (68.8%, 99/144), MRSA isolates were more resistant to non-beta-lactam antimicrobials –trimethoprim/sulfamethoxazole 73.3% (33/45) vs. 27.3% (27/99) [p < 0.0001]; erythromycin 75.6% (34/45) vs. 24.2% (24/99) [p < 0.0001]; chloramphenicol 60% (27/45) vs. 19.2% (19/99) [p < 0.0001]; gentamicin 55.6% (25/45) vs. 25.3% (25/99) [p = 0.0004]; and ciprofloxacin 35.6% (16/45) vs. 2% (2/99) [p < 0.0001]. Furthermore, 42 MRSA (93.3%) were multidrug resistant (MDR) and one exhibited high-level resistance to mupirocin. Overall, 61 MSSA (61.6%) were MDR, including three mupirocin and clindamycin resistant isolates. Seven spa types were detected among MRSA, of which t037 and t064 were predominant and associated with SCCmec types I and IV, respectively. Fourteen spa types were detected in MSSA which consisted mainly of t645 and t4353.

Conclusions

S. aureus carriage rate in healthy children in Eastern Uganda is high and comparable to rates for hospitalized patients in Kampala. The detection of mupirocin resistance is worrying as it could rapidly increase if mupirocin is administered in a low-income setting. S. aureus strains of spa types t064, t037 (MRSA) and t645, t4353 (MSSA) are prevalent and could be responsible for majority of staphylococcal infections in Uganda.

Unnecessary prescribing of antibiotics to healthy/asymptomatic school-age carriers of potentially pathogenic bacteria

OBJECTIVES

To re-draw attention to the unnecessary prescribing of antibiotics.

METHODS

We monitored nasopharyngeal colonization by 3 potentially pathogenic bacteria, Streptococcus pyogenes, Streptococcus pneumoniae, and Haemophilus influenzae type b in 81 children between the ages of 6 and 7 years who attended the same primary school. The children's health status was also monitored, without using antimicrobial treatment for healthy/asymptomatic carriers. Nasopharyngeal swabs were collected on 6 occasions during autumn months, from mid-September to mid-December 2016. The children who fell ill during the study were treated at the Ear, Nose and Throat Clinic, Sisters of Mercy University Hospital Center, Zagreb, Croatia.

RESULTS

Four hundred and sixty-three  nasopharyngeal swabs were collected. Each child had at least one positive swab result. Bacterial colonization with Streptococcus pyogenes had the highest colonization rate. During the study, 83% of the children were healthy/asymptomatic carriers with no clinical signs of disease,  while 17% became ill. The statistical results showed that the increase in all examined bacteria was statistically significant.

CONCLUSIONS

  Our  study results showed that positive bacterial findings in nasopharyngeal swabs from clinically healthy carriers were not an indication for antibiotic therapy.

CA-MRSA and HA-MRSA coexist in community and hospital settings in Uganda

Background

Methicillin resistant Staphylococcus aureus (MRSA) strains were once confined to hospitals however, in the last 20 years MRSA infections have emerged in the community in people with no prior exposure to hospitals. Strains causing such infections were novel and referred to as community-associated MRSA (CA-MRSA). The aim of this study was to determine the MRSA carriage rate in children in eastern Uganda, and to investigate coexistence between CA-MRSA and hospital-associated (HA-MRSA).

Methods

Between February and October 2011, nasopharyngeal samples (one per child) from 742 healthy children under 5 years in rural eastern Uganda were processed for isolation of MRSA, which was identified based on inhibition zone diameter of ≤19 mm on 30 μg cefoxitin disk. SCCmec and spa typing were performed for MRSA isolates.

Results

A total of 140 S. aureus isolates (18.9%, 140/742) were recovered from the children of which 5.7% (42/742) were MRSA. Almost all (95.2%, 40/42) MRSA isolates were multidrug resistant (MDR). The most prevalent SCCmec elements were types IV (40.5%, 17/42) and I (38.1%, 16/42). The overall frequency of SCCmec types IV and V combined, hence CA-MRSA, was 50% (21/42). Likewise, the overall frequency of SCCmec types I, II and III combined, hence HA-MRSA, was 50% (21/42). Spa types t002, t037, t064, t4353 and t12939 were detected and the most frequent were t064 (19%, 8/42) and t037 (12%, 5/42).

Conclusion

The MRSA carriage rate in children in eastern Uganda is high (5.7%) and comparable to estimates for Mulago Hospital in Kampala city. Importantly, HA-MRSA (mainly of spa type t037) and CA-MRSA (mainly of spa type t064) coexist in children in the community in eastern Uganda, and due to high proportion of MDR detected, outpatient treatment of MRSA infection in eastern Uganda might be difficult.

Electronic supplementary material

The online version of this article (10.1186/s13756-019-0551-1) contains supplementary material, which is available to authorized users.

Infection control and treatment guidelines and neonatal mortality in a rural hospital in Uganda

Background: The neonatal mortality rate in Uganda has been 24-27/1000 live births for the last 14 years. Aim: To determine the impact on neonatal mortality of the introduction of infection prevention and treatment guidelines in a resource-poor setting. Methods: A prospective study was undertaken in Kagando Hospital, a rural hospital in Western Uganda of infants live-born in hospital and those admitted from the community or other hospitals between 2013 and 2017. Guidelines were developed from a literature review and informed by local doctors and nurses and a visiting paediatrician. The guidelines highlighted that unwell infants should be admitted to the neonatal unit which was a section of the paediatric ward, emphasised hand hygiene, the separation of infants with and without sepsis and that unwell infants should be treated with evidence-based antibiotic regimens and enteral feeds withheld from unwell infants. Mortality within 28 days of birth was audited for 3 months before and after the intervention; the audit was repeated 3 and 5 years later. Results: Pre-intervention, there were 137 neonatal admissions and 79 neonatal deaths in 3 months (0.58 deaths per admission). Post-intervention there were 187 admissions and the death rate was lower (0.26 deaths per admission, p < 0.001). Three years after the intervention, there were 60 deaths among 233 admissions (0.26 deaths per admission, p < 0.001) and, at 5 years, 53 deaths among 315 admissions (0.17 deaths per admission, p < 0.001). Conclusion: These data suggest that the introduction of infection, prevention and treatment guidelines can reduce neonatal mortality in a resource-poor setting.

Exploring bacterial resistome and resistance dessemination: an approach of whole genome sequencing

For several decades antibiotics are used to combat against pathogenic bacteria, but their misuse and overuse have caused the emergence of resistant bacteria. The scarcities of effective antibiotics along with unavailability of alternative solutions have exacerbated bacterial infections and mortality rate. This review provides the concept of bacterial resistome and mechanisms of resistance. It has also described the utility of whole genome sequencing in identifying resistance and its dissemination in association with available bioinformatics tools and databases. Moreover, the whole genome sequencing methodology described in this review will help to select effective antibiotics, maintain unparalleled surveillance of resistance and provide early diagnosis during resistance outbreaks. The provided information could be used to control infection caused by resistant microorganisms.

High Frequency of Macrolide-Resistant Streptococcus pneumoniae Colonization in Respiratory Tract of Healthy Children in Ardabil, Iran

BACKGROUND

Streptococcus pneumoniae (S. pneumoniae) is one of the most common causes of human diseases in young children. Macrolides are commonly antibiotics used for empirical treatment of community-acquired respiratory infections. The purpose of this study was to determine antibiotic resistance pattern as well as the relationship between macrolide resistance and the major mechanisms of resistance in pneumococci isolated from healthy children.

MATERIALS AND METHODS

In this cross-sectional study, 43 isolates of S. pneumoniae were collected from healthy children in Ardabil. Resistance pattern against tested antibiotics was determined using the disk diffusion method. The Minimum Inhibitory Concentration (MIC) of erythromycin was determined using the E-test strips. The mefA/E and ermB gene were detected in erythromycin-resistant isolates using the specific primers and Polymerase Chain Reaction (PCR) technique.

RESULTS

According to antimicrobial susceptibility testing, 74.4 % of the isolates were resistant to erythromycin, 95.3 % to penicillin, 81.3 % to co-trimoxazole, 72 % to azithromycin, 41.8 % to tetracycline, 27.9 % to clindamycin, and 16.2 % to chloramphenicol. All isolates were susceptible to levofloxacin and vancomycin. In the case of rifampin, 95.3% of the isolates were sensitive and 4.6% semi-sensitive. The MIC of erythromycin for resistant isolates was between 1.5 and ≥ 256 μg/ml. PCR results revealed that 100% of erythromycin-resistant isolates contained mefA/E gene and 81.25 % contained both the ermB and mefA/E genes.

CONCLUSION

The prevalence of antibiotic-resistant strains of S. pneumoniae, especially resistance to macrolides, was high among healthy children in Ardabil. According to the results of this study, we suggest using levofloxacin, rifampin and vancomycin antibiotics as an appropriate prophylactic regimen in pneumococcal infections.

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.

Antibiotic-Resistant Escherichia coli and Class 1 Integrons in Humans, Domestic Animals, and Wild Primates in Rural Uganda

Antibiotic resistance is a global concern, although it has been studied most extensively in developed countries. We studied Escherichia coli and class 1 integrons in western Uganda by analyzing 1,685 isolates from people, domestic animals, and wild nonhuman primates near two national parks. Overall, 499 isolates (29.6%) were resistant to at least one of 11 antibiotics tested. The frequency of resistance reached 20.3% of isolates for trimethoprim-sulfamethoxazole but was nearly zero for the less commonly available antibiotics ciprofloxacin (0.4%), gentamicin (0.2%), and ceftiofur (0.1%). The frequency of resistance was 57.4% in isolates from people, 19.5% in isolates from domestic animals, and 16.3% in isolates from wild nonhuman primates. Isolates of livestock and primate origin displayed multidrug resistance patterns identical to those of human-origin isolates. The percentage of resistant isolates in people was higher near Kibale National Park (64.3%) than near Bwindi Impenetrable National Park (34.6%), perhaps reflecting local socioeconomic or ecological conditions. Across antibiotics, resistance correlated negatively with the local price of the antibiotic, with the most expensive antibiotics (nalidixic acid and ciprofloxacin) showing near-zero resistance. Among phenotypically resistant isolates, 33.2% harbored class 1 integrons containing 11 common resistance genes arranged into nine distinct gene cassettes, five of which were present in isolates from multiple host species. Overall, these results show that phenotypic resistance and class 1 integrons are distributed broadly among E. coli isolates from different host species in this region, where local socioeconomic and ecological conditions may facilitate widespread diffusion of bacteria or resistance-conferring genetic elements.IMPORTANCE Antibiotic resistance is a global problem. This study, conducted in rural western Uganda, describes antibiotic resistance patterns in Escherichia coli bacteria near two forested national parks. Resistance was present not only in people, but also in their livestock and in nearby wild nonhuman primates. Multidrug resistance and class 1 integrons containing genes that confer resistance were common and were similar in people and animals. The percentage of resistant isolates decreased with increasing local price of the antibiotic. Antibiotic resistance in this setting likely reflects environmental diffusion of bacteria or their genes, perhaps facilitated by local ecological and socioeconomic conditions.

Pneumococcal carriage and serotype distribution among children with and without pneumonia in Mozambique, 2014-2016

Background

Pneumococcal colonization is a precursor to pneumonia, and pneumococcal conjugate vaccines (PCV) can decrease vaccine-type (VT) colonization. Pneumococcal colonization studies are traditionally done among healthy children in the community; however, VT colonization prevalence may differ between these children and those with pneumonia. We assessed overall and VT pneumococcal colonization and factors associated with colonization among children with and without pneumonia after Mozambique introduced 10-valent PCV (PCV10) in 2013.

Methods

We used data from ongoing pneumonia surveillance in children aged <5 years and from cross-sectional nasopharyngeal colonization surveys conducted in October 2014 –April 2015 and October 2015 –May 2016. Pneumonia was defined using WHO standard criteria for radiologically confirmed pneumonia. Children with pneumonia enrolled from January 2014 –April 2016 were compared to children without pneumonia enrolled from the cross-sectional surveys. Clinical data and nasopharyngeal (NP) swabs were collected from each child. NP specimens were cultured for pneumococci, and culture-negative specimens from children with pneumonia underwent polymerase chain reaction (PCR).

Results

Of 778 and 927 children with and without pneumonia, 97.4% and 27.0% were exposed to antibiotics before swab collection, respectively. Based on culture, pneumococcal colonization was 45.1% for children with and 84.5% for children without pneumonia (P<0.001); VT pneumococcal colonization was 18.6% for children with and 23.4% for children without pneumonia (P = 0.02). The addition of PCR in children with pneumonia increased overall and VT-pneumococcal colonization to 79.2% and 31.1%, respectively. In multivariable analysis including PCR results, pneumonia was associated with VT pneumococcal colonization (adjusted OR: 1.4, 95%CI: 1.10–1.78).

Conclusion

Vaccine-type pneumococcal colonization remains common among children with and without pneumonia post-PCV10 introduction in Mozambique. In a population of children with high antibiotic exposure, the use of PCR for culture-negative NP swabs can improve assessment of pneumococcal colonization and circulating serotypes.

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.

Carriage prevalence and serotype distribution of Streptococcus pneumoniae prior to 10-valent pneumococcal vaccine introduction: A population-based cross-sectional study in South Western Uganda, 2014

Background

Information on Streptococcus pneumoniae nasopharyngeal (NP) carriage before the pneumococcal conjugate vaccine (PCV) introduction is essential to monitor impact. The 10-valent PCV (PCV10) was officially introduced throughout Ugandan national childhood immunization programs in 2013 and rolled-out countrywide during 2014. We aimed to measure the age-specific Streptococcus pneumoniae carriage and serotype distribution across all population age groups in the pre-PCV10 era in South Western Uganda.

Methods

We conducted a two-stage cluster, age-stratified, cross-sectional community-based study in Sheema North sub-district between January and March 2014. One NP swab was collected and analyzed for each participant in accordance with World Health Organization guidelines.

Results

NP carriage of any pneumococcal serotype was higher among children <2 years old (77%; n = 387) than among participants aged ≥15 years (8.5%; n = 325) (chi² p < 0.001).

Results

Of the 623 positive cultures, we identified 49 serotypes among 610 (97.9%) isolates; thirteen (2.1%) isolates were non-typeable. Among <2 years old, serotypes 6A, 6B, 14, 15B, 19F and 23F accounted for half of all carriers. Carriage prevalence with PCV10 serotypes was 29.4% among individuals aged <2 years (n = 387), 23.4% in children aged 2–4 years (n = 217), 11.4% in 5–14 years (n = 417), and 0.4% among individuals ≥15 years of age (n = 325). The proportion of carried pneumococci serotypes contained in PCV10 was 38.1% (n = 291), 32.8% (n = 154), 29.4% (n = 156), and 4.4% (n = 22) among carriers aged <2 years, 2–4 years, 5–14 years and ≥15 years, respectively.

Discussion

In Sheema district, the proportion of PCV10 serotypes was low (<40%), across all age groups, especially among individuals aged 15 years or older (<5%). PCV10 introduction is likely to impact transmission among children and to older individuals, but less likely to substantially modify pneumococcal NP ecology among individuals aged 15 years or older.

Pneumococcal Carriage in Children under Five Years in Uganda-Will Present Pneumococcal Conjugate Vaccines Be Appropriate?

BACKGROUND

Pneumonia is the major cause of death in children globally, with more than 900,000 deaths annually in children under five years of age. Streptococcus pneumoniae causes most deaths, most often in the form of community acquired pneumonia. Pneumococcal conjugate vaccines (PCVs) are currently being implemented in many low-income countries. PCVs decrease vaccine-type pneumococcal carriage, a prerequisite for invasive pneumococcal disease, and thereby affects pneumococcal disease and transmission. In Uganda, PCV was launched in 2014, but baseline data is lacking for pneumococcal serotypes in carriage.

OBJECTIVES

To study pneumococcal nasopharyngeal carriage and serotype distribution in children under 5 years of age prior to PCV introduction in Uganda.

METHODS

Three cross-sectional pneumococcal carriage surveys were conducted in 2008, 2009 and 2011, comprising respectively 150, 587 and 1024 randomly selected children aged less than five years from the Iganga/Mayuge Health and Demographic Surveillance Site. The caretakers were interviewed about illness history of the child and 1723 nasopharyngeal specimens were collected. From these, 927 isolates of S. pneumoniae were serotyped.

RESULTS

Overall, the carriage rate of S. pneumoniae was 56% (957/1723). Pneumococcal carriage was associated with illness on the day of the interview (OR = 1.50, p = 0.04). The most common pneumococcal serotypes were in descending order 19F (16%), 23F (9%), 6A (8%), 29 (7%) and 6B (7%). One percent of the strains were non-typeable. The potential serotype coverage rate for PCV10 was 42% and 54% for PCV13.

CONCLUSION

About half of circulating pneumococcal serotypes in carriage in the Ugandan under-five population studied was covered by available PCVs.