Antimicrobial resistance among children in sub-Saharan Africa

Vaccine value profile for Klebsiella pneumoniae

Klebsiella pneumoniae causes community- and healthcare-associated infections in children and adults. Globally in 2019, an estimated 1.27 million (95% Uncertainty Interval [UI]: 0.91-1.71) and 4.95 million (95% UI: 3.62-6.57) deaths were attributed to and associated with bacterial antimicrobial resistance (AMR), respectively. K. pneumoniae was the second leading pathogen in deaths attributed to AMR resistant bacteria. Furthermore, the rise of antimicrobial resistance in both community- and hospital-acquired infections is a concern for neonates and infants who are at high risk for invasive bacterial disease. There is a limited antibiotic pipeline for new antibiotics to treat multidrug resistant infections, and vaccines targeted against K. pneumoniae are considered to be of priority by the World Health Organization. Vaccination of pregnant women against K. pneumoniae could reduce the risk of invasive K.pneumoniae disease in their young offspring. In addition, vulnerable children, adolescents and adult populations at risk of K. pneumoniae disease with underlying diseases such as immunosuppression from underlying hematologic malignancy, chemotherapy, patients undergoing abdominal and/or urinary surgical procedures, or prolonged intensive care management are also potential target groups for a K. pneumoniae vaccine. A 'Vaccine Value Profile' (VVP) for K.pneumoniae, which contemplates vaccination of pregnant women to protect their babies from birth through to at least three months of age and other high-risk populations, provides a high-level, holistic assessment of the available information to inform the potential public health, economic and societal value of a pipeline of K. pneumoniae vaccines and other preventatives and therapeutics. This VVP was developed by a working group of subject matter experts from academia, non-profit organizations, public-private partnerships, and multi-lateral organizations, and in collaboration with stakeholders from the WHO. All contributors have extensive expertise on various elements of the K.pneumoniae VVP and collectively aimed to identify current research and knowledge gaps. The VVP was developed using only existing and publicly available information.

Tackling the threat of antimicrobial resistance in neonates and children: outcomes from the first WHO-convened Paediatric Drug Optimisation exercise for antibiotics

Children and neonates are highly vulnerable to the impact of antimicrobial resistance. Substantial barriers are faced in relation to research and development of antibacterial agents for use in neonates, children, and adolescents aged yonger than 19 years, and focusing finite resources on the most appropriate agents for development and paediatric optimisation is urgently needed. In November and December, 2022, following the successes of previous similar disease-focused exercises, WHO convened the first Paediatric Drug Optimisation (PADO) exercise for antibiotics, aiming to provide a shortlist of antibiotics to be prioritised for paediatric research and development, especially for use in regions with the highest burden of disease attributable to serious bacterial infection. A range of antibiotics with either existing license for children or in clinical development in adults but with little paediatric data were considered, and PADO priority and PADO watch lists were formulated. This Review provides the background and overview of the exercise processes and its outcomes as well as a concise review of the literature supporting decision making. Follow-up actions to implement the outcomes from the PADO for antibiotics process are also summarised. This Review highlights the major beneficial influence the collaborative PADO process can have, both for therapeutic drug class and disease-specific themes, in uniting efforts to ensure children have access to essential medicines across the world.

Phenotypic and molecular characterization of β-lactamase-producing Klebsiella species among children discharged from hospital in Western Kenya

BACKGROUND

The emergence and spread of β-lactamase-producing Klebsiella spp. has been associated with a substantial healthcare burden resulting in therapeutic failures. We sought to describe the proportion of phenotypic resistance to commonly used antibiotics, characterize β-lactamase genes among isolates with antimicrobial resistance (AMR), and assess the correlates of phenotypic AMR in Klebsiella spp. isolated from stool or rectal swab samples collected from children being discharged from hospital.

METHODS

We conducted a cross-sectional study involving 245 children aged 1-59 months who were being discharged from hospitals in western Kenya between June 2016 and November 2019. Whole stool or rectal swab samples were collected and Klebsiella spp. isolated by standard microbiological culture. β-lactamase genes were detected by PCR whilst phenotypic antimicrobial susceptibility was determined using the disc diffusion technique following standard microbiology protocols. Descriptive analyses were used to characterize phenotypic AMR and carriage of β-lactamase-producing genes. The modified Poisson regression models were used to assess correlates of phenotypic beta-lactam resistance.

RESULTS

The prevalence of β-lactamase carriage among Klebsiella spp. isolates at hospital discharge was 62.9% (154/245). Antibiotic use during hospitalization (adjusted prevalence ratio [aPR] = 4.51; 95%CI: 1.79-11.4, p < 0.001), longer duration of hospitalization (aPR = 1.42; 95%CI: 1.14-1.77, p < 0.002), and access to treated water (aPR = 1.38; 95%CI: 1.12-1.71, p < 0.003), were significant predictors of phenotypically determined β-lactamase. All the 154 β-lactamase-producing Klebsiella spp. isolates had at least one genetic marker of β-lactam/third-generation cephalosporin resistance. The most prevalent genes were blaCTX-M 142/154 (92.2%,) and blaSHV 142/154 (92.2%,) followed by blaTEM 88/154 (57.1%,) and blaOXA 48/154 (31.2%,) respectively.

CONCLUSION

Carriage of β-lactamase producing Klebsiella spp. in stool is common among children discharged from hospital in western Kenya and is associated with longer duration of hospitalization, antibiotic use, and access to treated water. The findings emphasize the need for continued monitoring of antimicrobial susceptibility patterns to inform the development and implementation of appropriate treatment guidelines. In addition, we recommend measures beyond antimicrobial stewardship and infection control within hospitals, improved sanitation, and access to safe drinking water to mitigate the spread of β-lactamase-producing Klebsiella pathogens in these and similar settings.

Antimicrobial resistance in Enterobacterales infections among children in sub-Saharan Africa: a systematic review and meta-analysis

Background

The burden of antimicrobial resistance (AMR) has been estimated to be the highest in sub-Saharan Africa (SSA). The current study estimated the proportion of drug-resistant Enterobacterales causing infections in SSA children.

Methods

We searched MEDLINE/PubMed, Embase and the Cochrane Library to identify retrospective and prospective studies published from 01/01/2005 to 01/06/2022 reporting AMR of Enterobacterales causing infections in sub-Saharan children (0-18 years old). Studies were excluded if they had unclear documentation of antimicrobial susceptibility testing methods or fewer than ten observations per bacteria. Data extraction and quality appraisal were conducted by two authors independently. The primary outcome was the proportion of Enterobacterales resistant to antibiotics commonly used in paediatrics. Proportions were combined across studies using mixed-effects logistic regression models per bacteria and per antibiotic. Between-study heterogeneity was assessed using the I2 statistic. The protocol was registered with PROSPERO (CRD42021260157).

Findings

After screening 1111 records, 122 relevant studies were included, providing data on more than 30,000 blood, urine and stool isolates. Escherichia coli and Klebsiella spp. were the predominant species, both presenting high proportions of resistance to third-generation cephalosporins, especially in blood cultures: 40.6% (95% CI: 27.7%-55%; I2: 85.7%, number of isolates (n): 1032) and 84.9% (72.8%-92.2%; I2: 94.1%, n: 2067), respectively. High proportions of resistance to other commonly used antibiotics were also observed. E. coli had high proportions of resistance, especially for ampicillin (92.5%; 95% CI: 76.4%-97.9%; I2: 89.8%, n: 888) and gentamicin (42.7%; 95% CI: 30%-56.5%; I2: 71.9%, n: 968). Gentamicin-resistant Klebsiella spp. were also frequently reported (77.6%; 95% CI: 65.5%-86.3%; I2: 91.6%, n: 1886).

Interpretation

High proportions of resistance to antibiotics commonly used for empirical treatment of infectious syndromes were found for Enterobacterales in sub-Saharan children. There is a critical need to better identify local patterns of AMR to inform and update clinical guidelines for better treatment outcomes.

Funding

No funding was received.

Evaluating blood culture collection practice in children hospitalized with acute illness at a tertiary hospital in Malawi

BACKGROUND

Blood culture collection practice in low-resource settings where routine blood culture collection is available has not been previously described.

METHODOLOGY

We conducted a secondary descriptive analysis of children aged 2-23 months enrolled in the Malawi Childhood Acute Illness and Nutrition (CHAIN) study, stratified by whether an admission blood culture had been undertaken and by nutritional status. Chi-square test was used to compare the differences between groups.

RESULTS

A total of 347 children were included, of whom 161 (46%) had a blood culture collected. Children who had a blood culture collected, compared to those who did not, were more likely to present with sepsis (43% vs. 20%, p < 0.001), gastroenteritis (43% vs. 26%, p < 0.001), fever (86% vs. 73%, p = 0.004), and with poor feeding/weight loss (30% vs. 18%, p = 0.008). In addition, hospital stay in those who had a blood culture was, on average, 2 days longer (p = 0.019). No difference in mortality was observed between those who did and did not have a blood culture obtained.

CONCLUSION

Blood culture collection was more frequent in children with sepsis and gastroenteritis, but was not associated with mortality. In low-resource settings, developing criteria for blood culture based on risk factors rather than clinician judgement may better utilize the existing resources.

Circulating markers of neutrophil activation and lung injury in pediatric pneumonia in low-resource settings

Diagnostic biomarkers for childhood pneumonia could guide management and improve antibiotic stewardship in low-resource settings where chest x-ray (CXR) is not always available. In this cross-sectional study, we measured chitinase 3-like protein 1 (CHI3L1), surfactant protein D (SP-D), lipocalin-2 (LCN2), and tissue inhibitor of metalloproteinases-1 (TIMP-1) in Ugandan children under the age of five hospitalized with acute lower respiratory tract infection. We determined the association between biomarker levels and primary end-point pneumonia, indicated by CXR consolidation. We included 89 children (median age 11 months, 39% female). Primary endpoint pneumonia was present in 22 (25%). Clinical signs were similar in children with and without CXR consolidation. Broad-spectrum antibiotics (ceftriaxone) were administered in 83 (93%). Levels of CHI3L1, SP-D, LCN2 and TIMP-1 were higher in patients with primary end-point pneumonia compared to patients with normal CXR or other infiltrates. All markers were moderately accurate predictors of primary end-point pneumonia, with area under receiver operator characteristic curves of 0.66-0.70 (p<0.05 for all markers). The probability of CXR consolidation increased monotonically with the number of markers above cut-off. Among 28 patients (31%) in whom all four markers were below the cut-off, the likelihood ratio of CXR consolidation was 0.11 (95%CI 0.015 to 0.73). CHI3L1, SP-D, LCN2 and TIMP-1 were associated with CXR consolidation in children with clinical pneumonia in a low-resource setting. Combinations of quantitative biomarkers may be useful to safely withhold antibiotics in children with a low probability of bacterial infection.

Invasive bacterial disease in young infants in rural Gambia: Population-based surveillance

Background

Invasive bacterial diseases (IBD) cause significant mortality in young infants. There are limited population-based data on IBD in young infants in Sub-Saharan Africa.

Methods

We conducted population-based surveillance for IBD among infants aged 0-90 days in a demographic surveillance area in rural Gambia between 1 March 2011 and 31 December 2017. Infants admitted to health facilities within the study area had standardised clinical evaluation plus conventional microbiological investigation. We defined IBD as isolation of pathogenic bacteria from blood, cerebrospinal fluid, lung, or pleural aspirate. We determined incidence, aetiology and case-fatality of IBD.

Results

A total of 3794 infants were admitted and 3605 (95%) had at least one sample collected for culture. We detected 254 (8.0%) episodes of IBD (bacteraemia 241; meningitis 14; pneumonia seven). The incidence of IBD in infants aged 0-90 days was 25 episodes/1000 person-years (95% confidence interval (CI) = 22-28), the incidence in neonates was 50 episodes/1000 person-years (95% CI = 43-58) and the incidence in infants aged 29-90 days was 12 episodes/1000 person-years (95% CI = 9-15). The most common pathogens causing IBD were Staphylococcus aureus (n = 102, 40%), Escherichia coli (n = 37, 15%), Streptococcus pneumoniae (n = 24, 9%) and Klebsiella pneumoniae (n = 12, 5%). Case-fatality was 29% (95% CI = 23-37) in neonates and 19% (95% CI = 11-29) in infants aged 29-90 days. A minimum of 7.3% of all young infant deaths in the population were caused by IBD.

Conclusions

IBD are common in young infants in rural Gambia and have a high case-fatality. Strategies are needed to prevent IBD in young infants. Overcoming barriers to widespread implementation of existing vaccines and developing new vaccines against the most common pathogens causing IBD should be among top priorities for reducing the high mortality rate in young infants.

The Silent Threat: Antimicrobial-Resistant Pathogens in Food-Producing Animals and Their Impact on Public Health

The emergence of antimicrobial resistance (AMR) is a global health problem without geographic boundaries. This increases the risk of complications and, thus, makes it harder to treat infections, which can result in higher healthcare costs and a greater number of deaths. Antimicrobials are often used to treat infections from pathogens in food-producing animals, making them a potential source of AMR. Overuse and misuse of these drugs in animal agriculture can lead to the development of AMR bacteria, which can then be transmitted to humans through contaminated food or direct contact. It is therefore essential to take multifaceted, comprehensive, and integrated measures, following the One Health approach. To address this issue, many countries have implemented regulations to limit antimicrobial use. To our knowledge, there are previous studies based on AMR in food-producing animals; however, this paper adds novelty related to the AMR pathogens in livestock, as we include the recent publications of this field worldwide. In this work, we aim to describe the most critical and high-risk AMR pathogens among food-producing animals, as a worldwide health problem. We also focus on the dissemination of AMR genes in livestock, as well as its consequences in animals and humans, and future strategies to tackle this threat.

Current rates of purchasing of antibiotics without a prescription across sub-Saharan Africa; rationale and potential programmes to reduce inappropriate dispensing and resistance

INTRODUCTION

Antimicrobial resistance (AMR) is a global concern. Currently, the greatest mortality due to AMR is in Africa. A key driver continues to be high levels of dispensing of antibiotics without a prescription.

AREAS COVERED

A need to document current rates of dispensing, their rationale and potential ways forward including antimicrobial stewardship programmes (ASPs). A narrative review was undertaken. The highest rates of antibiotic purchasing were in Eritrea (up to 89.2% of antibiotics dispensed), Ethiopia (up to 87.9%), Nigeria (up to 86.5%), Tanzania (up to 92.3%) and Zambia (up to 100% of pharmacies dispensing antibiotics without a prescription). However, considerable variation was seen with no dispensing in a minority of countries and situations. Key drivers of self-purchasing included high co-payment levels for physician consultations and antibiotic costs, travel costs, convenience of pharmacies, patient requests, limited knowledge of antibiotics and AMR and weak enforcement. ASPs have been introduced in some African countries along with quality targets to reduce inappropriate dispensing, centering on educating pharmacists and patients.

EXPERT OPINION

ASP activities need accelerating among community pharmacies alongside quality targets, with greater monitoring of pharmacists' activities to reduce inappropriate dispensing. Such activities, alongside educating patients and healthcare professionals, should enhance appropriate dispensing of antibiotics and reduce AMR.

High burden of ESBL and carbapenemase-producing gram-negative bacteria in bloodstream infection patients at a tertiary care hospital in Addis Ababa, Ethiopia

BACKGROUND

Bloodstream infection due to beta-lactamase and carbapenemase-producing gram-negative bacteria poses a substantial challenge to the effectiveness of antimicrobial treatments. Therefore, this study aimed to investigate the magnitude of beta-lactamase, carbapenemase-producing gram-negative bacteria, and associated risk factors of bloodstream infections in patients at a tertiary care hospital, in Addis Ababa, Ethiopia.

METHODS

An institutional-based cross-sectional study was conducted with convenience sampling techniques from September 2018 to March 2019. Blood cultures were analyzed from 1486 bloodstream infection suspected patients across all age groups. The blood sample was collected using two BacT/ALERT blood culture bottles for each patient. Gram stain, colony characteristics, and conventional biochemical tests were used to classify the gram-negative bacteria at the species level. Antimicrobial susceptibility testing was carried out to screen beta-lactam and carbapenem drug-resistant bacteria. The E-test was conducted for extended-spectrum-beta-lactamase and AmpC-beta-lactamase-producers. A modified and EDTA-modified carbapenem inactivation method was conducted for carbapenemase and metallo-beta-lactamases producers. Data collected using structured questionnaires and medical records were reviewed, encoded, and cleaned using EpiData V3.1. software. The cleaned data were exported and analyzed using SPSS version 24 software. Descriptive statistics and multivariate logistic registration models were used to describe and assess factors associated with acquiring drug-resistant bacteria infection. A p-value <0.05 was considered statistically significant.

RESULT

Among 1486 samples, 231 gram-negative bacteria were identified; of these, 195(84.4%) produce drug-hydrolyzing enzymes, and 31(13.4%) produce more than one drug-hydrolyzing enzyme. We found 54.0% and 25.7% of the gram-negative bacteria to be extended-spectrum-beta-lactamase and carbapenemase-producing, respectively. The extended-spectrum-beta-lactamase plus AmpC-beta-lactamase-producing bacteria account for 6.9%. Among the different isolates Klebsiella pneumonia 83(36.7%) was the highest drug-hydrolyzing enzyme-producing bacteria. Acinetobacter spp 25(53.2%) was the most carbapenemase producer. Extended-spectrum-beta-lactamase and carbapenemase-producing bacteria were high in this study. A significant association between age groups and extended-spectrum-beta-lactamase producer bacterial infection was seen, with a high prevalence in neonates (p = <0.001). Carbapenemase showed a significant association with patients admitted to the intensive care unit (p = 0.008), general surgery (p = 0.001), and surgical intensive care unit (p = 0.007) departments. Delivery of neonates by caesarean section, and insertion of medical instruments into the body were exposing factors for carbapenem-resistant bacterial infection. Chronic illnesses were associated with an extended-spectrum-beta-lactamase-producing bacterial infection. Klebsiella pneumonia and Acinetobacter species showed the greatest rates of extensively drug-resistant (37.3%) and pan-drug-resistance (76.5%), respectively. According to the results of this study, the pan-drug-resistance prevalence was found to be alarming.

CONCLUSION

Gram-negative bacteria were the main pathogens responsible for drug-resistant bloodstream infections. A high percentage of extended-spectrum-beta-lactamase and carbapenemase-producer bacteria were found in this study. Neonates were more susceptible to extended-spectrum-beta-lactamase and AmpC-beta-lactamase-producer bacteria. Patients in general surgery, caesarean section delivery, and intensive care unit were more susceptible to carbapenemase-producer bacteria. The suction machines, intravenous lines, and drainage tubes play an important role in the transmission of carbapenemase and metallo-beta-lactamase-producing bacteria. The hospital management and other stakeholders should work on infection prevention protocol implementation. Moreover, special attention should be given to all types of Klebsiella pneumoniae and pan-drug resistance Acinetobacter spp transmission dynamics, drug resistance genes, and virulence factors.

Impact of antibiotics on gut microbiome composition and resistome in the first years of life in low- to middle-income countries: A systematic review

BACKGROUND

Inappropriate antimicrobial usage is a key driver of antimicrobial resistance (AMR). Low- and middle-income countries (LMICs) are disproportionately burdened by AMR and young children are especially vulnerable to infections with AMR-bearing pathogens. The impact of antibiotics on the microbiome, selection, persistence, and horizontal spread of AMR genes is insufficiently characterized and understood in children in LMICs. This systematic review aims to collate and evaluate the available literature describing the impact of antibiotics on the infant gut microbiome and resistome in LMICs.

METHODS AND FINDINGS

In this systematic review, we searched the online databases MEDLINE (1946 to 28 January 2023), EMBASE (1947 to 28 January 2023), SCOPUS (1945 to 29 January 2023), WHO Global Index Medicus (searched up to 29 January 2023), and SciELO (searched up to 29 January 2023). A total of 4,369 articles were retrieved across the databases. Duplicates were removed resulting in 2,748 unique articles. Screening by title and abstract excluded 2,666 articles, 92 articles were assessed based on the full text, and 10 studies met the eligibility criteria that included human studies conducted in LMICs among children below the age of 2 that reported gut microbiome composition and/or resistome composition (AMR genes) following antibiotic usage. The included studies were all randomized control trials (RCTs) and were assessed for risk of bias using the Cochrane risk-of-bias for randomized studies tool. Overall, antibiotics reduced gut microbiome diversity and increased antibiotic-specific resistance gene abundance in antibiotic treatment groups as compared to the placebo. The most widely tested antibiotic was azithromycin that decreased the diversity of the gut microbiome and significantly increased macrolide resistance as early as 5 days posttreatment. A major limitation of this study was paucity of available studies that cover this subject area. Specifically, the range of antibiotics assessed did not include the most commonly used antibiotics in LMIC populations.

CONCLUSION

In this study, we observed that antibiotics significantly reduce the diversity and alter the composition of the infant gut microbiome in LMICs, while concomitantly selecting for resistance genes whose persistence can last for months following treatment. Considerable heterogeneity in study methodology, timing and duration of sampling, and sequencing methodology in currently available research limit insights into antibiotic impacts on the microbiome and resistome in children in LMICs. More research is urgently needed to fill this gap in order to better understand whether antibiotic-driven reductions in microbiome diversity and selection of AMR genes place LMIC children at risk for adverse health outcomes, including infections with AMR-bearing pathogens.

Prevalence and clonal diversity of carbapenem-resistant Klebsiella pneumoniae causing neonatal infections: A systematic review of 128 articles across 30 countries

BACKGROUND

Klebsiella pneumoniae is the most common pathogen causing neonatal infections, leading to high mortality worldwide. Along with increasing antimicrobial use in neonates, carbapenem-resistant K. pneumoniae (CRKP) has emerged as a severe challenge for infection control and treatment. However, no comprehensive systematic review is available to describe the global epidemiology of neonatal CRKP infections. We therefore performed a systematic review of available data worldwide and combined a genome-based analysis to address the prevalence, clonal diversity, and carbapenem resistance genes of CRKP causing neonatal infections.

METHODS AND FINDINGS

We performed a systematic review of studies reporting population-based neonatal infections caused by CRKP in combination with a genome-based analysis of all publicly available CRKP genomes with neonatal origins. We searched multiple databases (PubMed, Web of Science, Embase, Ovid MEDLINE, Cochrane, bioRxiv, and medRxiv) to identify studies that have reported data of neonatal CRKP infections up to June 30, 2022. We included studies addressing the prevalence of CRKP infections and colonization in neonates but excluded studies lacking the numbers of neonates, the geographical location, or independent data on Klebsiella or CRKP isolates. We used narrative synthesis for pooling data with JMP statistical software. We identified 8,558 articles and excluding those that did not meet inclusion criteria. We included 128 studies, none of which were preprints, comprising 127,583 neonates in 30 countries including 21 low- and middle-income countries (LMICs) for analysis. We found that bloodstream infection is the most common infection type in reported data. We estimated that the pooled global prevalence of CRKP infections in hospitalized neonates was 0.3% (95% confidence interval [CI], 0.2% to 0.3%). Based on 21 studies reporting patient outcomes, we found that the pooled mortality of neonatal CRKP infections was 22.9% (95% CI, 13.0% to 32.9%). A total of 535 neonatal CRKP genomes were identified from GenBank including Sequence Read Archive, of which 204 were not linked to any publications. We incorporated the 204 genomes with a literature review for understanding the species distribution, clonal diversity, and carbapenemase types. We identified 146 sequence types (STs) for neonatal CRKP strains and found that ST17, ST11, and ST15 were the 3 most common lineages. In particular, ST17 CRKP has been seen in neonates in 8 countries across 4 continents. The vast majority (75.3%) of the 1,592 neonatal CRKP strains available for analyzing carbapenemase have genes encoding metallo-β-lactamases and NDM (New Delhi metallo-β-lactamase) appeared to be the most common carbapenemase (64.3%). The main limitation of this study is the absence or scarcity of data from North America, South America, and Oceania.

CONCLUSIONS

CRKP contributes to a considerable number of neonatal infections and leads to significant neonatal mortality. Neonatal CRKP strains are highly diverse, while ST17 is globally prevalent and merits early detection for treatment and prevention. The dominance of blaNDM carbapenemase genes imposes challenges on therapeutic options in neonates and supports the continued inhibitor-related drug discovery.

Neonatal infection in Sub-Saharan Africa: a cross-sectional pilot study on bacterial pathogens and maternal risk factors

Introduction

Although child morbidity and mortality could be reduced in Sub-Saharan Africa during the last years both remain high. Since neonatal infections play a major role, we conducted a cross-sectional pilot study in the lake region of Western Tanzania in order to analyze not only the prevalence of neonatal infection with its bacterial etiology including antimicrobial resistance pattern but also to detect potential maternal risk factors.

Methods

We screened 156 women for potential risk factors and examined their neonates for clinical signs of an infection including microbiological verification. All women were interviewed for medical history and their socio-economic background. High-vaginal swabs (HVS) of pregnant women and blood cultures of sick infants were investigated for bacterial pathogens using culture followed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) or polymerase-chain-reaction (PCR)-based assays. Antimicrobial resistances were determined using a disk diffusion test and verified by VITEK 2. Maternal malaria, blood glucose, and hemoglobin levels were determined by rapid tests and helminth infections by stool microscopy.

Results and discussion

Our results showed a prevalence of 22% for neonatal infections. In total, 57% of them had culture-positive bloodstream infections with Gram-negative bacteria being the most prevalent. All these expressed resistance against ampicillin. The prevalence of maternal infection with helminths or Plasmodium was low, indicating that anti-worming strategies and intermittent preventive treatment of malaria for pregnant women (IPTp) are effective. The study identified maternal urinary tract infection (UTI) and an elevated blood glucose level as potential maternal risk factors for early neonatal infection, an elevated blood glucose level, and maternal anemia for a late-onset infection.

Conclusion

Our study, therefore, indicates that monitoring maternal UTI in the last trimester as well as levels of maternal hemoglobin and blood glucose might be important to predict and eventually manage neonatal infections. As Gram-negative bacteria with resistance to ampicillin were most prevalent in culture-proven neonatal sepsis, WHO recommendations for calculated antibiosis in the sick young infant should be discussed.

Polymyxin combination therapy for multidrug-resistant, extensively-drug resistant, and difficult-to-treat drug-resistant gram-negative infections: is it superior to polymyxin monotherapy?

INTRODUCTION

The increasing prevalence of infections with multidrug-resistant (MDR), extensively-drug resistant (XDR) or difficult-to-treat drug resistant (DTR) Gram-negative bacilli (GNB), including Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, Enterobacter species, and Escherichia coli poses a severe challenge.

AREAS COVERED

The rapid growing of multi-resistant GNB as well as the considerable deceleration in development of new anti-infective agents have made polymyxins (e.g. polymyxin B and colistin) a mainstay in clinical practices as either monotherapy or combination therapy. However, whether the polymyxin-based combinations lead to better outcomes remains unknown. This review mainly focuses on the effect of polymyxin combination therapy versus monotherapy on treating GNB-related infections. We also provide several factors in designing studies and their impact on optimizing polymyxin combinations.

EXPERT OPINION

An abundance of recent in vitro and preclinical in vivo data suggest clinical benefit for polymyxin-drug combination therapies, especially colistin plus meropenem and colistin plus rifampicin, with synergistic killing against MDR, XDR, and DTR P. aeruginosa, K. pneumoniae and A. baumannii. The beneficial effects of polymyxin-drug combinations (e.g. colistin or polymyxin B + carbapenem against carbapenem-resistant K. pneumoniae and carbapenem-resistant A. baumannii, polymyxin B + carbapenem + rifampin against carbapenem-resistant K. pneumoniae, and colistin + ceftolozan/tazobactam + rifampin against PDR-P. aeruginosa) have often been shown in clinical setting by retrospective studies. However, high-certainty evidence from large randomized controlled trials is necessary. These clinical trials should incorporate careful attention to patient's sample size, characteristics of patient's groups, PK/PD relationships and dosing, rapid detection of resistance, MIC determinations, and therapeutic drug monitoring.

Antibiotic use and resistance in children with severe acute malnutrition and human immunodeficiency virus infection

Severe acute malnutrition (SAM) and human immunodeficiency virus (HIV) infection underlie a major proportion of the childhood disease burden in low- and middle-income countries. These diseases commonly co-occur and lead to higher risk of other endemic infectious diseases, thereby compounding the risk of mortality and morbidity. The widespread use of antibiotics as treatment and prophylaxis in childhood SAM and HIV infections, respectively, has reduced mortality and morbidity but canlead to increasing antibiotic resistance. Development of antibiotic resistance could render future infections untreatable. This review summarises the endemic co-occurrence of undernutrition, particularly SAM, and HIV in children, and current treatment practices, specifically WHO-recommended antibiotic usage. The risks and benefits of antibiotic treatment, prophylaxis and resistance are reviewed in the context of patients with SAM and HIV and associated sub-populations. Finally, the review highlights possible research areas and populations where antibiotic resistance progression can be studied to best address concerns associated with the future impact of resistance. Current antibiotic usage is lifesaving in complicated SAM and HIV-infected populations; nevertheless, increasing baseline resistance and infection remain a significant concern. In conclusion, antibiotic usage currently addresses the immediate needs of children in SAM and HIV endemic regions; however, it is prudent to evaluate the impact of antibiotic use on resistance dynamics and long-term child health.

Awareness and knowledge of antimicrobial resistance and factors associated with knowledge among adults in Dessie City, Northeast Ethiopia: Community-based cross-sectional study

BACKGROUND

Antimicrobial resistance is an important global health challenge. The current study aimed to assess the level of awareness and knowledge of antimicrobial resistance and factors associated with knowledge among adults in Dessie City, Ethiopia.

METHODS

A community-based cross-sectional study was conducted among 407 adults in Dessie City from June to July 2021. A systematic random sampling technique was used to select respondents, and Google Form was used to collect data online. The data was analyzed by SPSS Version 26. The associated factors of knowledge of antimicrobial resistance were identified by using bivariate and multivariable logistic regression. Independent variables with a P-value <0.2 were selected as candidate variables for multivariable logistic regression. Those variables with a P-value <0.05 were declared statistically significant factors.

RESULT

Out of the required sample sizes, four hundred and seven participants were enrolled, giving a response rate of 99.3%. One hundred and fifty-two (37.3%) respondents were females. Nearly one-third of the respondents (28.3%) have taken antibiotics in the last 6 months. In this study, 73.7% of study participants were aware of the existence of germs; 58.2% were aware of the existence of antibiotic resistance to bacteria; 47.7% were aware of the existence of drug resistance; 39.8% were aware of the existence of antimicrobial resistance; and 36.6% were aware of the existence of antibiotic resistance. Sixty-four (15.7%) respondents were not aware of any of the above terms. Sixty (14.7%) of the respondents were not aware of any risk factor for antimicrobial resistance. About 63 (15.5%) of the respondents did not know the consequences of antimicrobial resistance. Two hundred and thirty-eight (58.5%) respondents had good knowledge of antimicrobial resistance. In this study, being male (AOR = 1.99; 95% CI: 1.23,3.20), college and above educational level (AOR = 3.50; 95% CI: 1.08,11.39), grade 11-12 educational level (AOR = 3.73; 95% CI: 1.20,11.61), getting advice from health professionals about how to take antibiotics (AOR = 1.84; 95% CI:1.07,3.17), using health professionals as a source of information on antibiotics (AOR = 2.51; 95% CI: 1.48,4.25), and taking antibiotics without prescription (AOR = 1.86; 95% CI: 1.04,3.30) were significantly associated with good knowledge of antimicrobial resistance.

CONCLUSION

The study identified low awareness and knowledge of antimicrobial resistance among adults. Being male, higher educational level, getting advice from health professionals about how to take antibiotics, using health professionals as a source of information on antibiotics, and taking antibiotics without a prescription were significantly associated with good knowledge of antimicrobial resistance. Educational campaigns would be highly desirable for the public to improve their awareness and knowledge of antimicrobial resistance.

Multinational consensus antimicrobial stewardship recommendations for children managed in hospital settings

Children are entitled to receive antibiotic therapy that is based on evidence and best practice, but might be overlooked in hospital programmes designed to achieve antimicrobial stewardship [AMS]. This failure to include children could be because children make up small proportion of patients in most hospitals, and are cared for by specialised paediatric staff. We reviewed the evidence and consulted experts in three global regions to develop ten recommendations for good-practice in hospital AMS programmes for children. We performed a review of scientific research, published between Jan 1, 2007, and Oct 17, 2019, concerning AMS, and formed a multinational expert group comprising members from the USA, Canada, the UK, Belgium, Switzerland, Australia, and Aotearoa New Zealand to develop the recommendations. These recommendations aim to help health-care workers who care for children in these regions to deliver best-practice care. We surveyed health-care workers with expertise in antibiotic therapy for children across these regions, and found that the recommendations were considered both very important and generally feasible. These recommendations should be implemented in hospitals to improve antibiotic therapy for children and to stimulate research into future improvements in care.

Ongoing Efforts to Improve Antimicrobial Utilization in Hospitals among African Countries and Implications for the Future

There are serious concerns with rising antimicrobial resistance (AMR) across countries increasing morbidity, mortality and costs. These concerns have resulted in a plethora of initiatives globally and nationally including national action plans (NAPs) to reduce AMR. Africa is no exception, especially with the highest rates of AMR globally. Key activities in NAPs include gaining a greater understanding of current antimicrobial utilization patterns through point prevalence surveys (PPS) and subsequently instigating antimicrobial stewardship programs (ASPs). Consequently, there is a need to comprehensively document current utilization patterns among hospitals across Africa coupled with ASP studies. In total, 33 PPS studies ranging from single up to 18 hospitals were documented from a narrative review with typically over 50% of in-patients prescribed antimicrobials, up to 97.6% in Nigeria. The penicillins, ceftriaxone and metronidazole, were the most prescribed antibiotics. Appreciable extended prescribing of antibiotics up to 6 days or more post-operatively was seen across Africa to prevent surgical site infections. At least 19 ASPs have been instigated across Africa in recent years to improve future prescribing utilizing a range of prescribing indicators. The various findings resulted in a range of suggested activities that key stakeholders, including governments and healthcare professionals, should undertake in the short, medium and long term to improve future antimicrobial prescribing and reduce AMR across Africa.

Antimicrobial Resistance Profile of Bacteria Causing Pediatric Infections at the University Teaching Hospital in Rwanda

Bacterial infections pose a global threat, especially in the pediatric population. Antimicrobials that are used to treat such infections continuously show reduced efficacy, and empirical therapy is a major treatment option in Rwanda. This study aimed to determine the resistance rate of commonly used antibiotics in pediatric patients. The study was conducted from June 1, 2018 to May 30, 2019, and microbiological samples were collected from 712 children with suspected bacterial infections. Antimicrobial sensitivity testing was performed on 177 positive cultures (24%) that were considered for data analysis. The findings show that the major bacterial isolates were Klebsiella pneumoniae (n = 50, 28.2%), Escherichia coli (n = 47, 26.5%), and Staphylococcus aureus (n = 38, 21.4%). In general, the greatest antibiotic resistance rate was observed in ampicillin (n = 125, 86.2%), amoxicillin-clavulanic acid (n = 84, 82.4%), amoxicillin (n = 64, 79%), cefadroxil (n = 83, 69.2%), tetracycline (n = 72, 59.7%), ceftazidime (n = 42, 55.3%), and cefuroxime (n = 14, 53.8%). More specifically, Klebsiella pneumoniae was 100% resistant to amoxicillin-clavulanic acid, cefuroxime, trimethoprim-sulfamethoxazole, ceftazidime, erythromycin, and clindamycin. Staphylococcus aureus was 86.7% resistant to ampicillin, and Escherichia coli was 91.7% resistant to tetracycline, 90.6% resistant to ampicillin, 83.3% resistant to amoxicillin-clavulanic acid, 79.3% resistant to cefadroxil, and 78.6% resistant to ceftazidime. Moreover, Klebsiella pneumoniae from blood and urine was 96.8% and 100% sensitive, respectively, to meropenem. Staphylococcus aureus from blood was 100% sensitive to vancomycin, whereas Escherichia coli from urine was sensitive to clindamycin (100%), nitrofurantoin (80.6%), and ciprofloxacin (72.7%). In conclusion, our findings show a high resistance rate to commonly used antibiotics, which suggests precaution in empirical therapy and continued surveillance of antimicrobial resistance.

The right antibiotic for the right neonate? A prospective observational cohort study at a district hospital in Pemba, Tanzania

BACKGROUND

The highest neonatal mortality is in Sub-Saharan Africa, where neonatal sepsis accounts for approximately 50%. At Pemba Island, Tanzania, we examined the use of prophylactic antibiotics in neonates and related it to WHO guidelines and compared clinical signs of infection with the use of antibiotic treatment; furthermore, we aimed to investigate all use of antibiotic treatment in the neonatal period.

METHOD

This prospective observational cohort study was performed from 1 January 2022 to 15 April 2022 at a district hospital on Pemba Island, Tanzania. Women admitted in early established or active labour, and their neonates, were eligible for inclusion. We used questionnaires for mother and health worker and examined the neonates 2 h after birth. Follow-up was made at discharge or at 18 h of life, and days 7 and 28.

RESULTS

We included 209 women and their 214 neonates. The neonatal mortality was 5 of 214 (23 per 1000 live births). According to WHO guidelines 29 (13.6%) had ≥ 1 risk factor for infection. Of these, three (10.3%) received prophylactic antibiotic treatment; only one (3.4%) received the correct antibiotic drug recommended in guidelines. Thirty-nine (18.2%) neonates had ≥ 1 clinical indicator of infection and 19 (48.7%) of these received antibiotic treatment. A total of 30 (14.0%) neonates received antibiotics during the study period. Twenty-three (76.7%) were treated with peroral antibiotics.

CONCLUSION

Adherence to WHO guidelines for prophylactic antibiotic treatment to prevent neonatal infection was low. Further, only half of neonates with clinical signs of infection received antibiotics.

Sepsis: emerging pathogens and antimicrobial resistance in Ethiopian referral hospitals

Background

Sepsis due to multidrug resistant (MDR) bacteria is a growing public health problem mainly in low-income countries.

Methods

A multicenter study was conducted between October 2019 and September 2020 at four hospitals located in central (Tikur Anbessa and Yekatit 12), southern (Hawassa) and northern (Dessie) parts of Ethiopia. A total of 1416 patients clinically investigated for sepsis were enrolled. The number of patients from Tikur Anbessa, Yekatit 12, Dessie and Hawassa hospital was 501, 298, 301 and 316, respectively. At each study site, blood culture was performed from all patients and positive cultures were characterized by their colony characteristics, gram stain and conventional biochemical tests. Each bacterial species was confirmed using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI TOF). Antimicrobial resistance pattern of bacteria was determined by disc diffusion. Logistic regression analysis was used to assess associations of dependent and independent variables. A p-value < 0.05 was considered as statistically significant. The data was analyzed using SPSS version 25.

Results

Among 1416 blood cultures performed, 40.6% yielded growth. Among these, 27.2%, 0.3% and 13.1%, were positive for pathogenic bacteria, yeast cells and possible contaminants respectively. Klebsiella pneumoniae (26.1%), Klebsiella variicola (18.1%) and E. coli (12.4%) were the most frequent. Most K. variicola were detected at Dessie (61%) and Hawassa (36.4%). Almost all Pantoea dispersa (95.2%) were isolated at Dessie. Rare isolates (0.5% or 0.2% each) included Leclercia adecarboxylata, Raoultella ornithinolytica, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Burkholderia cepacia, Kosakonia cowanii and Lelliottia amnigena. Enterobacteriaceae most often showed resistance to ampicillin (96.2%), ceftriaxone (78.3%), cefotaxime (78%), cefuroxime (78%) and ceftazidime (76.4%). MDR frequency of Enterobacteriaceae at Hawassa, Tikur Anbessa, Yekatit 12 and Dessie hospital was 95.1%, 93.2%, 87.3% and 67.7%, respectively. Carbapenem resistance was detected in 17.1% of K. pneumoniae (n = 111), 27.7% of E. cloacae (n = 22) and 58.8% of Acinetobacter baumannii (n = 34).

Conclusion

Diverse and emerging gram-negative bacterial etiologies of sepsis were identified. High multidrug resistance frequency was detected. Both on sepsis etiology types and MDR frequencies, substantial variation between hospitals was determined. Strategies to control MDR should be adapted to specific hospitals. Standard bacteriological services capable of monitoring emerging drug-resistant sepsis etiologies are essential for effective antimicrobial stewardship.

Antibiotic use in children under 5 years of age in Northern Tanzania: a qualitative study exploring the experiences of the caring mothers

Background

Antimicrobial resistance is a serious threat to the global achievements in child health thus far. Previous studies have found high use of antibiotics in children in Northern Tanzania, but the experiences of the primary care-givers, who play a key role in accessing and administering antibiotics for the sick child, have remained largely unknown. Therefore, the aim of this study was to understand mothers’ conceptions of antibiotic use in their children, which is of importance when forming strategies to improve antibiotic use in the community.

Method

A qualitative study including eight focus group discussions with mothers of under-five children in Moshi urban and rural districts, Northern Tanzania, was performed during 2019. The discussions were recorded, transcribed verbatim, translated into English and analysed according to the phenomenographic approach.

Findings

Three conceptual themes emerged during analysis; (1) conceptions of disease and antibiotics, (2) accessing treatment and (3) administering antibiotics. Antibiotics were often perceived as a universal treatment for common symptoms or diseases in children with few side-effects. Although mothers preferred to attend a healthcare facility, unforeseen costs, long waits and lack of financial support from their husbands, posed barriers for healthcare seeking. However, pharmacies were perceived as a cheap and convenient option to access previously used or prescribed antibiotics. Some mothers sought advice from a trusted neighbour regarding when to seek healthcare, thus resembling the function of the community health worker.

Conclusions

To improve antibiotic use in children under 5 years of age in Northern Tanzania, the precarious situation that women often find themselves in as they access treatment for their sick children needs to be taken into consideration. It is necessary to improve structures, including the healthcare system, socioeconomic inequalities and promoting gender equality both in the household and in the public arena to reduce misuse of antibiotics. Meanwhile, equipping community health workers to support Tanzanian women in appropriate healthcare seeking for their children, may be a feasible target for intervention.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-022-01169-w.

Molecular characterization of multi drug resistant Escherichia coli isolates at a tertiary hospital in Abuja, Nigeria

Infections caused by multi-drug resistant Escherichia coli cause significant morbidity and mortality especially in developing countries. In this study, we describe the molecular characteristics of E. coli isolated from clinical specimens and the patients’ outcomes. Phenotypic methods were used in the identification and antimicrobial susceptibility testing of E. coli from clinical specimens from a tertiary hospital in Abuja, Nigeria. Whole genome sequencing was used to describe the antimicrobial resistance genes, serotypes, sequence types/clonal complexes, and mobile genetic elements. The mean age of the patients was 20.3 years with 70.1% females and majority of isolates 75% from urine, 21% from blood cultures, and 3% each from cerebrospinal fluid and endo-cervical swabs. Of the 107 non-duplicate E. coli isolates, 101 (94.3%) were resistant to ampicillin, 95 (88.8%) to trimethoprim/sulfamethoxazole, 86 (80.4%) to ceftriaxone, 60 (56.1%) to gentamicin, and eight (7.5%) to meropenem. There were 102 (95.3%) isolates that were multi-drug resistant (MDR). Expression of Extended Spectrum Beta Lactamase (ESBL) phenotype was detected in 54 (50%) and bla_CTX-M-15 genes detected in 75 (70.1%) isolates. The carbapenemase genes bla_NDM-1 and bla_NDM-5 were detected in six (5.6%), while the AmpC gene- bla_CMY-2, was detected in seven (6.5%) isolates. Two (1.9%) isolates simultaneously harboured the bla_OXA-1, bla_CMY-2, bla_CTX-M-15, and bla_NDM-5 genes. In total, 35 sequence types (STs) were found with the majority being ST131 (n = 23; 21.5%). The most common serotype was O25:H4 associated with all 23 strains of ST131, followed by O1:H6/ST648 (n = 6). The ST410, ST671, and ST101 strains displayed phenotypic resistance to wide array of antibiotic classes and harbored high numbers of antibiotic resistance genes via in-silico analysis. The ST410 strain in particular harbored a higher number of antibiotic resistance genes and was phenotypically resistant to a wider array of antibiotics. Four pairs of isolates were closely related with three isolates (ST131, ST38, ST652) having a pairwise SNP difference of zero. 71/72 75/76 52/14. The MDR E. coli lineages circulating in this setting pose a clinical and public health threat as they can hinder effective prevention and management of infections. The genetic diversity and MDR E. coli with the emergence of ST410 and ST101 clones is concerning because of the potential for rapid dissemination in hospitals and communities- further increasing the problems of antibiotic resistance. Continuous routine surveillance of E. coli infections for AMR in hospitals becomes imperative, aimed at development of effective antimicrobial stewardship programs, facilitating prudent use of antimicrobial agents, and limiting dissemination of resistant strains.

Tackling antimicrobial resistance across sub-Saharan Africa: current challenges and implications for the future

INTRODUCTION

Antimicrobial resistance (AMR) is a concern as this increases morbidity, mortality, and costs, with sub-Saharan Africa having the highest rates globally. Concerns with rising AMR have resulted in international, Pan-African, and country activities including the development of national action plans (NAPs). However, there is variable implementation across Africa with key challenges persisting.

AREAS COVERED

Consequently, there is an urgent need to document current NAP activities and challenges across sub-Saharan Africa to provide future guidance. This builds on a narrative review of the literature.

EXPERT OPINION

All surveyed sub-Saharan African countries have developed their NAPs; however, there is variable implementation. Countries including Botswana and Namibia are yet to officially launch their NAPs with Eswatini only recently launching its NAP. Cameroon is further ahead with its NAP than these countries; though there are concerns with implementation. South Africa appears to have made the greatest strides with implementing its NAP including regular monitoring of activities and instigation of antimicrobial stewardship programs. Key challenges remain across Africa. These include available personnel, expertise, capacity, and resources to undertake agreed NAP activities including active surveillance, lack of focal points to drive NAPs, and competing demands and priorities including among donors. These challenges are being addressed, with further co-ordinated efforts needed to reduce AMR.

Genetic Diversity and Virulence Profile of Methicillin and Inducible Clindamycin-Resistant Staphylococcus aureus Isolates in Western Algeria

Staphylococcusaureus causes a wide range of life-threatening infections. In this study, we determined its prevalence in the hospital environment and investigated nasal carriage among healthcare workers and patients admitted to a hospital in western Algeria. A total of 550 specimens were collected. An antibiogram was performed and the genes encoding resistance to methicillin, inducible clindamycin and toxins were sought among the 92 S. aureus isolates. The spread of clones with a methicillin- and/or clindamycin-resistance phenotype between these ecosystems was studied using genomic analysis. A prevalence of 27%, 30% and 13% of S. aureus (including 2.7%, 5% and 1.25% of MRSA) in patients, healthcare workers and the hospital environment were observed, respectively. The presence of the mecA, erm, pvl and tsst-1 genes was detected in 10.9%, 17.4%, 7.6% and 18.5% of samples, respectively. Sequencing allowed us to identify seven sequence types, including three MRSA-IV-ST6, two MRSA-IV-ST80-PVL+, two MRSA-IV-ST22-TSST-1, two MRSA-V-ST5, and one MRSA-IV-ST398, as well as many virulence genes. Here, we reported that both the hospital environment and nasal carriage may be reservoirs contributing to the spread of the same pathogenic clone persisting over time. The circulation of different pathogenic clones of MRSA, MSSA, and iMLSB, as well as the emergence of at-risk ST398 clones should be monitored.

Antimicrobial resistance patterns in bacteria causing febrile illness in Africa, South Asia, and Southeast Asia: a systematic review of published etiological studies from 1980-2015

OBJECTIVE

In this study, we aimed to conduct a systematic review to characterize antimicrobial resistance (AMR) patterns for bacterial causes of febrile illness in Africa and Asia.

METHODS

We included published literature from 1980-2015 based on data extracted from two recent systematic reviews of nonmalarial febrile illness from Africa, South Asia, and Southeast Asia. Selection criteria included articles with full bacterial identification and antimicrobial susceptibility testing (AST) results for key normally sterile site pathogen-drug combinations. Pooled proportions of resistant isolates were combined using random effects meta-analysis. Study data quality was graded using the Microbiology Investigation Criteria for Reporting Objectively (MICRO) framework.

RESULTS

Of 3475 unique articles included in the previous reviews, 371 included the target pathogen-drug combinations. Salmonella enterica tested against ceftriaxone and ciprofloxacin were the two highest reported combinations (30,509 and 22,056 isolates, respectively). Pooled proportions of resistant isolates were high for third-generation cephalosporins for Klebsiella pneumoniae and Escherichia coli in all regions. The MICRO grading showed an overall lack of standardization.

CONCLUSION

This review highlights a general increase in AMR reporting and in resistance over time. However, there were substantial problems with diagnostic microbiological data quality. Urgent strengthening of laboratory capacity, standardized testing, and reporting of AST results is required to improve AMR surveillance.

Antimicrobial resistance including Extended Spectrum Beta Lactamases (ESBL) among E. coli isolated from kenyan children at hospital discharge

Background

Children who have been discharged from hospital in sub-Saharan Africa remain at substantial risk of mortality in the post-discharge period. Antimicrobial resistance (AMR) may be an important factor. We sought to determine the prevalence and risk factors associated with AMR in commensal Escherichia coli(E. coli) from Kenyan children at the time of discharge.

Methodology/Principle findings

Fecal samples were collected from 406 children aged 1–59 months in western Kenya at the time of discharge from hospital and cultured for E. coli. Susceptibility to ampicillin, ceftriaxone, cefotaxime, ceftazidime, cefoxitin, imipenem, ciprofloxacin, gentamicin, combined amoxicillin/clavulanic acid, trimethoprim-sulfamethoxazole, azithromycin, and chloramphenicol was determined by disc diffusion according to guidelines from the Clinical and Laboratory Standards Institute (CLSI). Poisson regression was used to determine associations between participant characteristics and the presence of extended-spectrum beta-lactamases (ESBL) producing E. coli. Non-susceptibility to ampicillin (95%), gentamicin (44%), ceftriaxone (46%), and the presence of ESBL (44%) was high. Receipt of antibiotics during the hospitalization was associated with the presence of ESBL (aPR = 2.23; 95% CI: 1.29–3.83) as was being hospitalized within the prior year (aPR = 1.32 [1.07–1.69]). Open defecation (aPR = 2.02; 95% CI: 1.39–2.94), having a toilet shared with other households (aPR = 1.49; 95% CI: 1.17–1.89), and being female (aPR = 1.42; 95% CI: 1.15–1.76) were associated with carriage of ESBL E. coli

Conclusions/Significance

AMR is common among isolates of E. coli from children at hospital discharge in Kenya, including nearly half having detectable ESBL.

Children who have been hospitalized in sub-Saharan Africa remain at a high risk of death and morbidity for at least 6 months following discharge. These children may harbor AMR in commensal bacteria following hospitalization, which may be associated with poor outcomes. There are limited data describing AMR and risk factors that are associated with AMR carriage at hospital discharge. In this cross-sectional study of Kenyan children under 5 years of age discharged from hospitals, we found AMR to be high. Children who received antibiotics in the hospital, had limited access to improved sanitation, and who were female had the highest prevalence of ESBL-producing E. coli.

Antibiogram signatures of Vibrio species recovered from surface waters in South Western districts of Uganda: Implications for environmental pollution and infection control

Reports of vibriosis and other related gastrointestinal infections have remained a recurring concern in the diverse global continent. The safety of drinking surface water and associated environmental pollution has remained a public health concern in limited resource sittings. Seen in this light, we report the antibiogram signatures of Vibrio species recovered from surface waters in the South-Western districts of Uganda. Surface water samples were collected for four months for Vibrio species isolation in four districts (Bushenyi-B, Mitooma-M, Rubirizi-R, and Sheema-S) using bacteria culture procedures, disc diffusion and Polymerase Chain Reaction (PCR) technique. Isolates were characterised, and the antibiotic fingerprints were determined using PCR and nine selected antibiotics in routine use. A total of 392 Vibrio species were confirmed from the various districts (B: 172, M: 79. R: 60, S: 81), with 163 (94.77%) resistant to colistin (polymixin), 145 (84.3%) resistant to cefotaxime, 127 (73.84%) resistant to azithromycin, and 33 (19.19%) resistant to chloramphenicol among Bushenyi isolates. A similar high resistance to fluoroquinolones and carbapenem antibiotics were also recorded in other districts of the study area. A complete multiple antibiotic resistance phenotype ((M)ARPs) to the applied antibiotics (A-CTX-CXM-MEM-ATH-K-TM-C-PB-NI-CIP-NA) were also recorded among some isolates, which produced multiple antibiotic resistance indexes of 1, suggesting a high-risk source of contamination due to the usage of several antibiotics. The PCR reports also confirm ampC gene {20 (10.9%)}, beta-lactamase TEM gene (blaTEM2), {30 (10%)} and dihydropteroate synthase type-1 and 11 gene (sul 1 & 11) {16 (8%)}. The results present an implicated environmental pollution problem and a potential concern to public health, therefore there is the need for control of such infectious bacteria and environmental pollution monitoring. Hence, it is recommended various approaches crucial to monitoring of emerging trends in drug resistance at the local and international levels.

Study protocol for a population-based observational surveillance study of culture-confirmed neonatal bloodstream infections and meningitis in South Africa: Baby GERMS-SA

INTRODUCTION

Worldwide, neonatal mortality remains high accounting for 47% of childhood deaths in 2019 and including an estimated 500 000 deaths from neonatal infections. While 42% of global neonatal deaths occur in sub-Saharan Africa, there is limited understanding of population-level burden and aetiology of neonatal infections outside tertiary-level institutions.

METHODS AND ANALYSIS

We aim to implement the first population-level surveillance for bloodstream infections and meningitis among neonates aged <28 days in South Africa. Tier 1 will include national surveillance of culture-confirmed neonatal infections at all public-sector hospitals describing infection incidence risk, pathogen profile and antimicrobial susceptibility by institution, province and healthcare level (2014-2021). Tier 2 (nested within tier 1) will be conducted at six regional neonatal units over 12 months, will compare the clinical characteristics of neonates with early-onset and late-onset infections and identify potentially modifiable risk factors for mortality. Through tier 2, we will determine the antimicrobial susceptibility of neonatal pathogens, evaluate the appropriateness of empiric antibiotic prescribing and determine the genomic epidemiology of multidrug resistant bacterial and fungal pathogens.

ETHICS AND DISSEMINATION

Ethics clearance was obtained from the Human Research Ethics Committee of the University of the Witwatersrand (M190320). Funding for the study was obtained through a grant from the Bill and Melinda Gates Foundation (OPP1208882). Baby GERMS-SA aims to impact on national policy, resource allocation and neonatal guidelines by describing the national burden of neonatal infections in South Africa. In addition, end-users in neonatal units will benefit from a facility-level dashboard displaying key indicators of the surveillance findings.

Simultaneous pharmacokinetic/pharmacodynamic (PKPD) assessment of ampicillin and gentamicin in the treatment of neonatal sepsis

Objectives

This study aimed to simultaneously investigate the pharmacokinetics of ampicillin and gentamicin, currently the WHO standard of care for treating neonatal sepsis.

Methods

Pharmacokinetic data were collected in 59 neonates receiving ampicillin and gentamicin for suspected or proven sepsis in the NeoFosfo trial (NCT03453177). A panel of 23 clinical Escherichia coli isolates from neonates with sepsis, resistant to either ampicillin, gentamicin or both, were tested for susceptibility using chequerboards. Pharmacokinetic/pharmacodynamic (PKPD) modelling and simulations were used to compare single-agent (EUCAST MIC) and combination (chequerboard MIC) target attainment with standard dosing regimens.

Results

A model was established that simultaneously estimated parameters of a one-compartment ampicillin model and a two-compartment gentamicin model. A common clearance for both drugs was used (6.89 L/h/70 kg) relating to glomerular filtration (CL_GFR), with an additional clearance term added for ampicillin (5.3 L/h/70 kg). Covariate modelling included a priori allometric weight and post-menstrual age scaling of clearance. Further covariate relationships on renal clearance were postnatal age and serum creatinine.

Simulation-based PKPD assessments suggest good Gram-positive (MIC ≤ 0.25 mg/L) cover. However, less than one-quarter of neonates were predicted to receive efficacious coverage against Enterobacterales (MIC ≤ 2 mg/L). The benefit of the ampicillin/gentamicin combination was limited, with only 2/23 E. coli clinical strains showing FIC index < 0.5 (synergy) and most in the range 0.5–1 (suggesting additivity). Simulations showed that feasible dosing strategies would be insufficient to cover resistant strains.

Conclusions

PKPD simulations showed ampicillin and gentamicin combination therapy was insufficient to cover Enterobacterales, suggesting the need for alternative empirical treatment options for neonatal sepsis.

Antibiotics Self-Medication Practice and Associated Factors Among Residents in Dessie City, Northeast Ethiopia: Community-Based Cross-Sectional Study

BACKGROUND

Taking antibiotics without prescription would result in the emergency of antibiotics resistance. The aim of this study was to assess antibiotics self-medication practice and associated factors among residents in Dessie City, Ethiopia.

METHODS

A community-based cross-sectional was employed from June to July 2021. A total of 407 participants have been selected from each Kebele by stratified and systematic random sampling techniques. The collected data were checked, translated and exported into SPSS version 26. Results were organized using frequency and percentage tables. Bi-variate and multi-variable logistic regressions were used to test the association of independent variables with antibiotics self-medication practice.

RESULTS

Four hundred and seven participants enrolled with a response of 96.7%. One hundred and fifty-two (37.3%) were females, and 115 (28.3%) respondents have taken antibiotics in the last 6 months. The prevalence of antibiotics self-medication practice was 55.3% (95% CI: 50.6-60.2). Amoxicillin (45%), Ciprofloxacin (36%), and Amoxicillin with clavulanic acid (24%) were commonly used antibiotics. Cough (34.4), fever (30.7), cold and flu (29.0), diarrhea (21.9) and headache (18.7) were the most reported conditions that necessitate antibiotics self-medication. Educational level (8-10 grade) (AOR = 4.10, 95% CI: 1.28, 13.12), using mass media as a source of information (AOR = 2.23, 95% CI: 1.24, 4.27), relying on previous experience for source of information (AOR = 2.02, 95% CI: 1.23, 3.31), having awareness of antibiotics resistance (AOR = 2.45, 95% CI: 1.34, 4.50) and good knowledge of antimicrobial resistance (AOR = 1.81, 95% CI: 1.11, 2.97) were significantly associated with antibiotics self-medication practice.

CONCLUSION

Antibiotics self-medication practice among residents was high. Educational status, using mass media and previous experiences as sources of information on antibiotics, having awareness of antibiotics resistance, and knowledge of antimicrobial resistance were significantly associated with self medication of antibiotics. Attention should be given by the stakeholders to reduce self medication practice with antibiotics.

OUP accepted manuscript

Background

Objectives

Methods

Results

Conclusions

Antibiotic susceptibility patterns of pathogens isolated from laboratory specimens at Livingstone Central Hospital in Zambia

BACKGROUND

Multidrug resistance (MDR) is a global problem that require multifaceted effort to curb it. This study aimed to evaluate the antibiotic susceptibility patterns of routinely isolated bacteria at Livingstone Central Hospital (LCH).

METHODS

A retrospective study was performed on all isolated organisms from patient specimens that were processed from January 2019 to December 2021. Specimens were cultured on standard media and Kirby-Bauer disc diffusion method was employed for susceptibility testing following the Clinical and Laboratory Standard Institute's recommendations.

RESULTS

A total of 765 specimens were processed and only 500 (65.4%) met the inclusion criteria. Of the 500, 291(58.2%) specimens were received from female and from the age-group 17-39 years (253, 50.6%) and 40-80 years (145, 29%) in form of blood (331, 66.2%), urine (165, 33%) and sputum (4, 0.8%). Amongst the bacterial isolates, Staphylococcus aureus (142, 28.4%) was the commonest followed by Escherichia coli (91, 18.2%), and Enterobacter agglomerans (76, 15.2%), and Klebsiella pneumoniae (43, 8.6%). The resistance pattern revealed ampicillin (93%) as the least effective drug followed by oxacillin (88%), penicillin (85.6%), co-trimoxazole (81.5%), erythromycin (71.9%), nalidixic acid (68%), and ceftazidime (60%) whereas the most effective antibiotics were imipenem (14.5%), and piperacillin/tazobactam (16.7%). The screening of methicillin resistant Staphylococcus aureus (MRSA) with cefoxitin showed 23.7% (9/38) resistance.

CONCLUSION

Increased levels of MDR strains and rising numbers of MRSA strains were detected. Therefore, re-establishing of the empiric therapy is needed for proper patient management, studies to determine the levels of extended spectrum beta lactamase- and carbapenemase-producing bacteria are warranted.

Effects of antibiotic resistance, drug target attainment, bacterial pathogenicity and virulence, and antibiotic access and affordability on outcomes in neonatal sepsis: an international microbiology and drug evaluation prospective substudy (BARNARDS)

BACKGROUND

Sepsis is a major contributor to neonatal mortality, particularly in low-income and middle-income countries (LMICs). WHO advocates ampicillin-gentamicin as first-line therapy for the management of neonatal sepsis. In the BARNARDS observational cohort study of neonatal sepsis and antimicrobial resistance in LMICs, common sepsis pathogens were characterised via whole genome sequencing (WGS) and antimicrobial resistance profiles. In this substudy of BARNARDS, we aimed to assess the use and efficacy of empirical antibiotic therapies commonly used in LMICs for neonatal sepsis.

METHODS

In BARNARDS, consenting mother-neonates aged 0-60 days dyads were enrolled on delivery or neonatal presentation with suspected sepsis at 12 BARNARDS clinical sites in Bangladesh, Ethiopia, India, Pakistan, Nigeria, Rwanda, and South Africa. Stillborn babies were excluded from the study. Blood samples were collected from neonates presenting with clinical signs of sepsis, and WGS and minimum inhibitory concentrations for antibiotic treatment were determined for bacterial isolates from culture-confirmed sepsis. Neonatal outcome data were collected following enrolment until 60 days of life. Antibiotic usage and neonatal outcome data were assessed. Survival analyses were adjusted to take into account potential clinical confounding variables related to the birth and pathogen. Additionally, resistance profiles, pharmacokinetic-pharmacodynamic probability of target attainment, and frequency of resistance (ie, resistance defined by in-vitro growth of isolates when challenged by antibiotics) were assessed. Questionnaires on health structures and antibiotic costs evaluated accessibility and affordability.

FINDINGS

Between Nov 12, 2015, and Feb 1, 2018, 36 285 neonates were enrolled into the main BARNARDS study, of whom 9874 had clinically diagnosed sepsis and 5749 had available antibiotic data. The four most commonly prescribed antibiotic combinations given to 4451 neonates (77·42%) of 5749 were ampicillin-gentamicin, ceftazidime-amikacin, piperacillin-tazobactam-amikacin, and amoxicillin clavulanate-amikacin. This dataset assessed 476 prescriptions for 442 neonates treated with one of these antibiotic combinations with WGS data (all BARNARDS countries were represented in this subset except India). Multiple pathogens were isolated, totalling 457 isolates. Reported mortality was lower for neonates treated with ceftazidime-amikacin than for neonates treated with ampicillin-gentamicin (hazard ratio [adjusted for clinical variables considered potential confounders to outcomes] 0·32, 95% CI 0·14-0·72; p=0·0060). Of 390 Gram-negative isolates, 379 (97·2%) were resistant to ampicillin and 274 (70·3%) were resistant to gentamicin. Susceptibility of Gram-negative isolates to at least one antibiotic in a treatment combination was noted in 111 (28·5%) to ampicillin-gentamicin; 286 (73·3%) to amoxicillin clavulanate-amikacin; 301 (77·2%) to ceftazidime-amikacin; and 312 (80·0%) to piperacillin-tazobactam-amikacin. A probability of target attainment of 80% or more was noted in 26 neonates (33·7% [SD 0·59]) of 78 with ampicillin-gentamicin; 15 (68·0% [3·84]) of 27 with amoxicillin clavulanate-amikacin; 93 (92·7% [0·24]) of 109 with ceftazidime-amikacin; and 70 (85·3% [0·47]) of 76 with piperacillin-tazobactam-amikacin. However, antibiotic and country effects could not be distinguished. Frequency of resistance was recorded most frequently with fosfomycin (in 78 isolates [68·4%] of 114), followed by colistin (55 isolates [57·3%] of 96), and gentamicin (62 isolates [53·0%] of 117). Sites in six of the seven countries (excluding South Africa) stated that the cost of antibiotics would influence treatment of neonatal sepsis.

INTERPRETATION

Our data raise questions about the empirical use of combined ampicillin-gentamicin for neonatal sepsis in LMICs because of its high resistance and high rates of frequency of resistance and low probability of target attainment. Accessibility and affordability need to be considered when advocating antibiotic treatments with variance in economic health structures across LMICs.

FUNDING

The Bill & Melinda Gates Foundation.

Bloodstream Infections at Two Neonatal Intensive Care Units in Ghana: Multidrug Resistant Enterobacterales Undermine the Usefulness of Standard Antibiotic Regimes

BACKGROUND

Bloodstream infections (BSIs) are a major cause of morbidity and mortality in hospitalized neonates. Data on antibiotic resistance in neonatal BSIs and their impact on clinical outcomes in Africa are limited.

METHODS

We conducted a prospective cohort study at 2 tertiary level neonatal intensive care units (NICUs) in Ghana. All neonates admitted to the NICUs were included from October 2017 to September 2019. We monitored BSI rates and analyzed the effect of BSI and antibiotic resistance on mortality and duration of hospitalization.

RESULTS

Of 5433 neonates included, 3514 had at least one blood culture performed and 355 had growth of a total of 368 pathogenic microorganisms. Overall incidence of BSI was 1.0 (0.9-1.1) per 100 person days. The predominant organisms were Klebsiella pneumoniae 49.7% (183/368) and Streptococcus spp. 10.6% (39/368). In addition, 512 coagulase negative Staphylococci were isolated but considered probable contaminants. Among K. pneumoniae, resistance to gentamicin and amikacin was 91.8% and 16.4%, respectively, while carbapenem resistance was 4.4%. All-cause mortality among enrolled neonates was 19.7% (1066/5416). The mortality rate was significantly higher in neonates with BSI compared with culture-negative neonates in univariate analysis (27.9%, n = 99/355 vs. 16.5%, n = 520/3148; hazard ratio 1.4, 95% confidence interval 1.07-1.70) but not in multivariate analysis.

CONCLUSION

The diversity of etiologic agents and the high-risk of antibiotic resistance suggest that standard empirical treatment is unlikely to improve the outcome of BSIs in low and middle income. Such improvements will depend on access to reliable clinical microbiologic services.

Marked reduction in antibiotic usage following intensive malaria control in a cohort of Ugandan children

BACKGROUND

Intensive malaria control may have additional benefits beyond reducing the incidence of symptomatic malaria. We compared antibiotic treatment of children before and after the implementation of highly effective malaria control interventions in Tororo, a historically high transmission area of Uganda.

METHODS

Two successive cohorts of children, aged 0.5 to 10 years, were followed from September 2011 to October 2019 in a dedicated study clinic. Universal distribution of long-lasting insecticidal nets was conducted in 2013 and 2017. Sustained indoor residual spraying of insecticide (IRS) was initiated in December 2014. Generalized linear mixed-effects models were used to compare the incidence of antimalarial and antibiotic treatments before and after vector control measures were implemented.

RESULTS

Comparing the period prior to the implementation of IRS to the period after IRS had been sustained for 4-5 years, the adjusted incidence of malaria treatments decreased from 2.68 to 0.05 per person-year (incidence rate ratio [IRR] = 0.02, 95% CI 0.01-0.03, p < 0.001), and the adjusted incidence of antibiotic treatments decreased from 4.14 to 1.26 per person-year (IRR = 0.30, 95% CI 0.27-0.34, p < 0.001). The reduction in antibiotic usage was primarily associated with fewer episodes of symptomatic malaria and fewer episodes of fever with sub-microscopic parasitemia, both of which were frequently treated with antibiotics.

CONCLUSIONS

In a historically high transmission setting, the implementation of highly effective vector control interventions was followed by a marked reduction in antibiotic treatment of children. This added benefit of malaria control could have important implications for antibiotic prescribing practices, efforts to curtail antimicrobial resistance, and health system costs.

Multi-drug resistance and high mortality associated with community-acquired bloodstream infections in children in conflict-affected northwest Nigeria

Pediatric community-acquired bloodstream infections (CA-BSIs) in sub Saharan African humanitarian contexts are rarely documented. Effective treatment of these infections is additionally complicated by increasing rates of antimicrobial resistance. We describe the findings from epidemiological and microbiological surveillance implemented in pediatric patients with suspected CA-BSIs presenting for care at a secondary hospital in the conflict affected area of Zamfara state, Nigeria. Any child (> 2 months of age) presenting to Anka General Hospital from November 2018 to August 2020 with clinical severe sepsis at admission had clinical and epidemiological information and a blood culture collected at admission. Bacterial isolates were tested for antibiotic susceptibility. We calculated frequencies of epidemiological, microbiological and clinical parameters. We explored risk factors for death amongst severe sepsis cases using univariable and multivariable Poisson regression, adjusting for time between admission and hospital exit. We included 234 severe sepsis patients with 195 blood culture results. There were 39 positive blood cultures. Of the bacterial isolates, 14 were Gram positive and 18 were Gram negative; 5 were resistant to empiric antibiotics: methicillin-resistant Staphylococcus aureus (MRSA; n = 2) and Extended Spectrum Beta-Lactamase positive enterobacterales (n = 3). We identified no significant association between sex, age-group, ward, CA-BSI, appropriate intravenous antibiotic, malaria positivity at admission, suspected focus of sepsis, clinical severity and death in the multivariable regression. There is an urgent need for access to good clinical microbiological services, including point of care methods, and awareness and practice around rational antibiotic in healthcare staff in humanitarian settings to reduce morbidity and mortality from sepsis in children.

Carriage Prevalence of Extended-Spectrum β-Lactamase Producing Enterobacterales in Outpatients Attending Community Health Centers in Blantyre, Malawi

Antimicrobial resistance due to extended-spectrum β-lactamase (ESBL) production by Enterobacterales is a global health problem contributing to increased morbidity and mortality, particularly in resource-constrained countries. We aimed to determine the prevalence of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) in community patients in Blantyre, Malawi. Clinical samples were collected from 300 patients and screened for ESBL-E using a CHROMagar^TM ESBL medium. Confirmation of ESBL production was done by a combination disk test (CDT). The prevalence of community-acquired ESBL-E was 16.67% (50/300, 95% CI = 12.43–20.91%). The most common ESBL-E species isolated was Escherichia coli (66%). All ESBL-E isolates were resistant to Trimethoprim-Sulfamethoxazole except for 2% of E. coli. Besides this, all ESBL-E were susceptible to Imipenem and only 4% were resistant to Meropenem. No patients with a positive ESBL-E phenotype had a history of hospital admission in the last three months, and the carriage of ESBL-E was neither associated with the demographic nor the clinical characteristics of participants. Our findings reveal a low presence of ESBL-E phenotypes in community patients. The low prevalence of ESBL-E in the community settings of Blantyre can be maintained if strong infection and antimicrobial use-control strategies are implemented.

Efficacy of three lytic bacteriophages for eradicating biofilms of multidrug-resistant Proteus mirabilis

Proteus mirabilis is one of the most frequent causes of catheter-associated urinary tract infections (CAUTIs) owing to its capability to colonize and develop crystalline multidrug-resistant (MDR) biofilms. Here, we report the isolation and partial characterization of three novel bacteriophages, vB_PmiM-ES1a, vB_PmiM-ES1b, and vB_PmiM-ES1c, which were active against the planktonic form and biofilms of the MDR P. mirabilis strain ES01, isolated from CAUTIs in Egypt. The antibiotic susceptibility profile of the P. mirabilis isolates showed resistance to most of the antibiotics tested. The isolated phages were identified morphologically using TEM, and each appeared to have myovirus-like morphology. The three phages displayed strong lytic activity and a narrow host range, and they were stable at different ranges of temperatures and pH values. One-step growth kinetics showed a lysis time of 180 min with a burst size of 99.6, 95, and 86 PFU/cell for phage vB_PmiM-ES1a, vB_PmiM-ES1b, and vB_PmiM-ES1c, respectively. The three phages exhibited different digestion patterns using different restriction enzymes. The genome size was estimated to be 59.39 kb, 62.19 kb, and 52.07 kb for phage vB_PmiM-ES1a, vB_PmiM-ES1b, and vB_PmiM-ES1c, respectively. A phage cocktail including the three phages showed a potential ability to reduce and eradicate a biofilm formed by the MDR Proteus mirabilis EG-ES1. Accordingly, a phage cocktail of vB_PmiM-ES1a, vB_PmiM-ES1b, and vB_PmiM-ES1c is considered a promising candidate for use as a biocontrol agent against MDR Proteus mirabilis bacteria.

Carriage of colistin-resistant Gram-negative bacteria in children from communities in Cape Town (Tuberculosis child multidrug-resistant preventive therapy trial sub-study)

Colistin is a last-resort antibiotic against multidrug-resistant, Gram-negative bacteria. Colistin resistance has been described in the clinical settings in South Africa. However, information on carriage of these bacteria in communities is limited. This study investigated gastrointestinal carriage of colistin-resistant Escherichia coli and Klebsiella spp. and mcr genes in children from communities in Cape Town. Colistin-resistant E. coli was isolated from two participants (4%, 2/50), and mcr-1-mcr-9 genes were not detected. Gastrointestinal carriage of colistin-resistant Enterobacterales was rare; however, continuous extensive surveillance is necessary to determine the extent of carriage and its contribution to resistance observed in clinical settings.

Gram-negative neonatal sepsis in low- and lower-middle-income countries and WHO empirical antibiotic recommendations: A systematic review and meta-analysis

BACKGROUND

Neonatal sepsis is a significant global health issue associated with marked regional disparities in mortality. Antimicrobial resistance (AMR) is a growing concern in Gram-negative organisms, which increasingly predominate in neonatal sepsis, and existing WHO empirical antibiotic recommendations may no longer be appropriate. Previous systematic reviews have been limited to specific low- and middle-income countries. We therefore completed a systematic review and meta-analysis of available data from all low- and lower-middle-income countries (LLMICs) since 2010, with a focus on regional differences in Gram-negative infections and AMR.

METHODS AND FINDINGS

All studies published from 1 January 2010 to 21 April 2021 about microbiologically confirmed bloodstream infections or meningitis in neonates and AMR in LLMICs were assessed for eligibility. Small case series, studies with a small number of Gram-negative isolates (<10), and studies with a majority of isolates prior to 2010 were excluded. Main outcomes were pooled proportions of Escherichia coli, Klebsiella, Enterobacter, Pseudomonas, Acinetobacter and AMR. We included 88 studies (4 cohort studies, 3 randomised controlled studies, and 81 cross-sectional studies) comprising 10,458 Gram-negative isolates from 19 LLMICs. No studies were identified outside of Africa and Asia. The estimated pooled proportion of neonatal sepsis caused by Gram-negative organisms was 60% (95% CI 55% to 65%). Klebsiella spp. was the most common, with a pooled proportion of 38% of Gram-negative sepsis (95% CI 33% to 43%). Regional differences were observed, with higher proportions of Acinetobacter spp. in Asia and Klebsiella spp. in Africa. Resistance to aminoglycosides and third-generation cephalosporins ranged from 42% to 69% and from 59% to 84%, respectively. Study limitations include significant heterogeneity among included studies, exclusion of upper-middle-income countries, and potential sampling bias, with the majority of studies from tertiary hospital settings, which may overestimate the burden caused by Gram-negative bacteria.

CONCLUSIONS

Gram-negative bacteria are an important cause of neonatal sepsis in LLMICs and are associated with significant rates of resistance to WHO-recommended first- and second-line empirical antibiotics. AMR surveillance should underpin region-specific empirical treatment recommendations. Meanwhile, a significant global commitment to accessible and effective antimicrobials for neonates is required.

A systematic review of qualitative literature on antimicrobial stewardship in Sub-Saharan Africa

BACKGROUND

Antibiotic resistance is a major problem in every region of the globe and Sub-Saharan Africa (SSA) is no exception. Several systematic reviews have addressed the prevalence of resistant organisms but few have examined the underlying causes in this region. This systematic review of qualitative literature aims to highlight barriers and facilitators to antimicrobial stewardship in SSA.

METHODS

A literature search of Embase and MEDLINE(R) was carried out. Studies were included if they were in English, conducted in SSA, and reported qualitative data on the barriers and facilitators of antimicrobial stewardship or on attitudes towards resistance promoting behaviours. Studies were screened with a simple critical appraisal tool. Secondary constructs were extracted and coded into concepts, which were then reviewed and grouped into themes in light of the complete dataset.

RESULTS

The literature search yielded 169 results, of which 14 studies from 11 countries were included in the final analysis. No studies were excluded as a result of the critical appraisal. Eight concepts emerged from initial coding, which were consolidated into five major themes: ineffective regulation, health system factors, clinical governance, patient factors and lack of resources. The ineffective regulation theme highlighted the balance between tightening drugstore regulation, reducing over-the-counter sale of antibiotics, and maintaining access to medicines for rural communities. Meanwhile, health system factors explored the tension between antimicrobial stewardship and the need of pharmacy workers to maintain profitable businesses. Additionally, a lack of resources, actions by patients and the day-to-day challenges of providing healthcare were shown to directly impede antimicrobial stewardship and exacerbate other factors which promote resistance.

CONCLUSION

Antibiotic resistance in SSA is a multi-faceted issue and while limited resources contribute to the problem they should be viewed in the context of other factors. We identify several contextual factors that affect resistance and stewardship that should be considered by policy makers when planning interventions. This literature base is also incomplete, with only 11 nations accounted for and many studies being confined to regions within countries, so more research is needed. Specifically, further studies on implementing stewardship interventions, successful or not, would be beneficial to inform future efforts.

Antimicrobial Resistance Profiling and Molecular Epidemiological Analysis of Extended Spectrum β-Lactamases Produced by Extraintestinal Invasive Escherichia coli Isolates From Ethiopia: The Presence of International High-Risk Clones ST131 and ST410 Revealed

The treatment of invasive Escherichia coli infections is a challenge because of the emergence and rapid spread of multidrug resistant strains. Particular problems are those strains that produce extended spectrum β-lactamases (ESBL’s). Although the global characterization of these enzymes is advanced, knowledge of their molecular basis among clinical E. coli isolates in Ethiopia is extremely limited. This study intends to address this knowledge gap. The study combines antimicrobial resistance profiling and molecular epidemiology of ESBL genes among 204 E. coli clinical isolates collected from patient urine, blood, and pus at four geographically distinct health facilities in Ethiopia. All isolates exhibited multidrug resistance, with extensive resistance to ampicillin and first to fourth line generation cephalosporins and sulfamethoxazole-trimethoprim and ciprofloxacin. Extended spectrum β-lactamase genes were detected in 189 strains, and all but one were positive for CTX-Ms β-lactamases. Genes encoding for the group-1 CTX-Ms enzymes were most prolific, and CTX-M-15 was the most common ESBL identified. Group-9 CTX-Ms including CTX-M-14 and CTX-27 were detected only in 12 isolates and SHV ESBL types were identified in just 8 isolates. Bacterial typing revealed a high amount of strains associated with the B2 phylogenetic group. Crucially, the international high risk clones ST131 and ST410 were among the sequence types identified. This first time study revealed a high prevalence of CTX-M type ESBL’s circulating among E. coli clinical isolates in Ethiopia. Critically, they are associated with multidrug resistance phenotypes and high-risk clones first characterized in other parts of the world.

Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction

Despite contributing to the large disease burden in West Africa, little is known about the genomic epidemiology of Streptococcus pneumoniae which cause meningitis among children under 5 years old in the region. We analysed whole-genome sequencing data from 185 S. pneumoniae isolates recovered from suspected paediatric meningitis cases as part of the World Health Organization (WHO) invasive bacterial diseases surveillance from 2010 to 2016. The phylogeny was reconstructed, accessory genome similarity was computed and antimicrobial-resistance patterns were inferred from the genome data and compared to phenotypic resistance from disc diffusion. We studied the changes in the distribution of serotypes pre- and post-pneumococcal conjugate vaccine (PCV) introduction in the Central and Western sub-regions separately. The overall distribution of non-vaccine, PCV7 (4, 6B, 9V, 14, 18C, 19F and 23F) and additional PCV13 serotypes (1, 3, 5, 6A, 19A and 7F) did not change significantly before and after PCV introduction in the Central region (Fisher's test P value 0.27) despite an increase in the proportion of non-vaccine serotypes to 40 % (n=6) in the post-PCV introduction period compared to 21.9 % (n=14). In the Western sub-region, PCV13 serotypes were more dominant among isolates from The Gambia following the introduction of PCV7, 81 % (n=17), compared to the pre-PCV period in neighbouring Senegal, 51 % (n=27). The phylogeny illustrated the diversity of strains associated with paediatric meningitis in West Africa and highlighted the existence of phylogeographical clustering, with isolates from the same sub-region clustering and sharing similar accessory genome content. Antibiotic-resistance genotypes known to confer resistance to penicillin, chloramphenicol, co-trimoxazole and tetracycline were detected across all sub-regions. However, there was no discernible trend linking the presence of resistance genotypes with the vaccine introduction period or whether the strain was a vaccine or non-vaccine serotype. Resistance genotypes appeared to be conserved within selected sub-clades of the phylogenetic tree, suggesting clonal inheritance. Our data underscore the need for continued surveillance on the emergence of non-vaccine serotypes as well as chloramphenicol and penicillin resistance, as these antibiotics are likely still being used for empirical treatment in low-resource settings. This article contains data hosted by Microreact.

Antibiotic susceptibility profile of bacterial isolates from febrile children under 5 years of age in Nanoro, Burkina Faso

Objectives

Antibiotics efficacy is severely threatened due to emerging resistance worldwide, but there is a paucity of antibiotics efficacy data for the West African region in general. Therefore, this study aimed to determine the antibiotic susceptibility profile of bacterial isolated from febrile children under 5 years of age in Nanoro (Burkina Faso).

Methods

Blood, stool and urine samples were collected from 1099 febrile children attending peripheral health facilities and the referral hospital in Nanoro Health district. Bacterial isolates from these samples were assessed for their susceptibility against commonly used antibiotics by Kirby–Bauer method.

Results

In total, 141 bacterial isolates were recovered from 127 febrile children of which 65 from blood, 65 from stool and 11 from urine. Salmonella isolates were most frequently isolated and found to be highly resistant to ampicillin (70%; 56/80) and trimethoprim–sulphamethoxazole (65%; 52/80). Escherichia coli isolates showed a high resistance rate to trimethoprim–sulphamethoxazole (100%), ampicillin (100%), ciprofloxacin (71.4%; 10/14), amoxicillin–clavulanate (64.3%; 9/14), ceftriaxone (64.3%; 9/14) and gentamycin (50%; 7/14). Moreover, half of the E. coli isolates produced ß‐lactamase suggesting multi‐drug resistance against β‐lactam as well as non‐β‐lactam antibiotics. Multi‐drug resistance was observed in 54.6% (59/108) of the isolates, mainly Gram‐negative bacteria.

Conclusions

This study showed high resistance rates to common antibiotics used to treat bacterial infections in Nanoro. The work prompts the need to expand antibiotic resistance surveillance studies in Burkina Faso.

Tanzanian primary healthcare workers' experiences of antibiotic prescription and understanding of antibiotic resistance in common childhood infections: a qualitative phenomenographic study

Background

Antibiotic resistance is a threat to global child health. Primary healthcare workers play a key role in antibiotic stewardship in the community, but few studies in low-income countries have described their experiences of initiating antibiotic treatment in children. Thus, the present study aimed to describe primary healthcare workers’ experiences of antibiotic prescription for children under 5 years of age and their conceptions of antibiotic resistance in Northern Tanzania.

Methods

A qualitative study involving individual in-depth interviews with 20 prescribing primary healthcare workers in Moshi urban and rural districts, Northern Tanzania, was performed in 2019. Interviews were transcribed verbatim, translated from Kiswahili into English and analysed according to the phenomenographic approach.

Findings

Four conceptual themes emerged during the analysis; conceptions in relation to the prescriber, the mother and child, other healthcare actors and in relation to outcome. The healthcare workers relied mainly on clinical examination and medical history provided by the mother to determine the need for antibiotics. Confidence in giving advice concerning non-antibiotic treatment varied among the participants and expectations of antibiotic treatment were perceived to be common among the mothers. Antibiotic resistance was mainly perceived as a problem for the individual patient who was misusing the antibiotics.

Conclusions

To increase rational antibiotic prescription, an awareness needs to be raised among Tanzanian primary healthcare workers of the threat of antibiotic resistance, not only to a few individuals, but to public health. Guidelines on childhood illnesses should be updated with advice concerning symptomatic treatment when antibiotics are not necessary, to support rational prescribing practices and promote trust in the clinician and mother relationship.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-021-00952-5.

White Paper: Bridging the gap between surveillance data and antimicrobial stewardship in the outpatient sector-practical guidance from the JPIAMR ARCH and COMBACTE-MAGNET EPI-Net networks

Background

The outpatient setting is a key scenario for the implementation of antimicrobial stewardship (AMS) activities, considering that overconsumption of antibiotics occurs mainly outside hospitals. This publication is the result of a joint initiative by the JPIAMR ARCH and COMBACTE-MAGNET EPI-Net networks, which is aimed at formulating a set of target actions for linking surveillance data with AMS activities in the outpatient setting.

Methods

A scoping review of the literature was carried out in three research areas: AMS leadership and accountability; antimicrobial usage and AMS; antimicrobial resistance and AMS. Consensus on the actions was reached through a RAND-modified Delphi process involving over 40 experts in infectious diseases, clinical microbiology, AMS, veterinary medicine or public health, from 18 low-, middle- and high-income countries.

Results

Evidence was retrieved from 38 documents, and an initial 25 target actions were proposed, differentiating between essential or desirable targets according to clinical relevance, feasibility and applicability to settings and resources. In the first consultation round, preliminary agreement was reached for all targets. Further to a second review, 6 statements were re-considered and 3 were deleted, leading to a final list of 22 target actions in the form of a practical checklist.

Conclusions

This White Paper is a pragmatic and flexible tool to guide the development of calibrated surveillance-based AMS interventions specific to the outpatient setting, which is characterized by substantial inter- and intra-country variability in the organization of healthcare structures, maintaining a global perspective and taking into account the feasibility of the target actions in low-resource settings.