Antimicrobial resistance predicts death in Tanzanian children with bloodstream infections: a prospective cohort study

Non-typhoidal Salmonella contributes to gastrointestinal infections in Morogoro: Evidence from patients attending Morogoro regional referral hospital in Tanzania

INTRODUCTION

Salmonella is one of the most common causes of food-borne outbreaks and infection worldwide. Non-typhoidal Salmonella (NTS) infections are common and remain a significant public health problem among important bacterial foodborne diseases. The current study aimed to establish the Non typhoidal Salmonella infection and antimicrobial resistance status among selected patients at Morogoro Regional Referral Hospital (MRRH), Morogoro Region, Tanzania, to inform clinical care management and public health interventions.

METHODOLOGY

A cross-sectional study was conducted using medical records and samples were collected from hospitalised and outpatients between October and December 2021. A total of 153 participants were enrolled in the study and 132 consented to being sampled. The collected samples were analysed using standard microbiological techniques. The isolates were subjected to molecular genotyping, where Polymerase Chain Reaction (PCR) was performed targeting the 16S rDNA gene. PCR products were then submitted for sequencing to establish phylogenetic relatedness. Antimicrobial susceptibility testing and resistance genes screening were also conducted.

RESULTS

The phylogenetic analysis identified two Salmonella serovars; Salmonella Enteritidis and Salmonella Typhimurium. The isolates were from four adults and seven children patients. The isolates were tested against six antimicrobial agents: tetracycline, trimethoprim, gentamycin, ciprofloxacin, ampicillin and cefotaxime. Further antimicrobial assays were performed by screening 10 antimicrobial resistance genes using PCR. Overall, the highest resistance was observed in ampicillin (100%), whereas the lowest resistance was recorded for ciprofloxacin and gentamicin (9.1%). In addition, four (36.4%) of the isolates were resistant to cefotaxime and three (27.3%) to tetracycline and trimethoprim. The isolates also exhibit the presence of resistance genes for sulfamethoxazole 1&2, tetracycline (tet) A&B, Beta-lactamase CTXM, Beta-lactamase TEM, Beta-lactamase SHV, Gentamycine, Acra and acc3-1 in different occurrences. The overall prevalence of Salmonella species in Morogoro region was 8.3% (11/132) with Salmonella Enteritidis and Salmonella Typhimurium being the only serovars detected from adults and children stool samples.

CONCLUSION

Our investigation showed that both children and adults had been exposed to Salmonella spp. However, the occurrence of NTS was higher in children (5.3% (7/132) compared to adults (3.0% (4/132). To stop zoonotic infections and the development of antimicrobial resistance in the community, this calls for Infection Prevention and Control (IPC) and stewardship programmes on rational use of antimicrobials in both health facilities and at the community level.

Polymicrobial bloodstream infections a risk factor for mortality in neonates at the national hospital, Tanzania: A case-control study

BACKGROUND

Polymicrobial bloodstream infections (BSI) are difficult to treat since empiric antibiotics treatment are frequently less effective against multiple pathogens. The study aimed to compare outcomes in patients with polymicrobial and monomicrobial BSIs.

METHODS

The study was a retrospective case-control design conducted at Muhimbili National Hospital for data processed between July 2021 and June 2022. Cases were patients with polymicrobial BSI, and controls had monomicrobial BSI. Each case was matched to three controls by age, admitting ward, and duration of admission. Logistic regression was performed to determine independent risk factors for in-hospital and 30-day mortality.

RESULTS

Fifty patients with polymicrobial BSI and 150 with monomicrobial BSI were compared: the two arms had no significant differences in sex and comorbidities. The most frequent bacteria in polymicrobial BSI were Klebsiella pneumoniae 17% (17/100) and Enterobacter species 15% (15/100). In monomicrobial BSI, S. aureus 17.33% (26/150), Klebsiella pneumoniae 16.67% (25/150), and Acinetobacter species 15% (15/150) were more prevalent. Overall, isolates were frequently resistant to multiple antibiotics tested, and 52% (130/250) were multidrug resistance. The 30-day and in-hospital mortality were 33.5% (67/200) and 36% (72/200), respectively. On multivariable analysis, polymicrobial BSIs were independent risk factors for both in-hospital mortality (aOR 2.37, 95%CI 1.20-4.69, p = 0.01) and 30-day mortality (aOR 2.05, 95%CI 1.03-4.08), p = 0.04). In sub-analyses involving only neonates, polymicrobial BSI was an independent risk factor for both 30-day mortality (aOR 3.13, 95%CI 1.07-9.10, p = 0.04) and in-hospital mortality (aOR 5.08, 95%CI 1.60-16.14, p = 0.006). Overall, the median length of hospital stay post-BSIs was numerically longer in patients with polymicrobial BSIs.

CONCLUSION

Overall, polymicrobial BSI was a significant risk for mortality. Patients with polymicrobial BSI stay longer at the hospital than those with monomicrobial BSI. These findings call for clinicians to be more aggressive in managing polymicrobial BSI.

High Child Mortality and Interventions Coverage in the City of Dar es Salaam, Tanzania: Are the Poorest Paying an Urban Penalty?

The 'urban penalty' in health refers to the loss of a presumed survival advantage due to adverse consequences of urban life. This study investigated the levels and trends in neonatal, post-neonatal and under-5 mortality rate and key determinants of child survival using data from Tanzania Demographic and Health Surveys (TDHS) (2004/05, 2010 and 2015/16), AIDS Indicator Survey (AIS), Malaria Indicator survey (MIS) and health facility data in Tanzania mainland. We compared Dar es Salaam results with other urban and rural areas in Tanzania mainland, and between the poorest and richest wealth tertiles within Dar es Salaam. Under-5 mortality declined by 41% between TDHS 2004/05 and 2015/2016 from 132 to 78 deaths per 1000 live births, with a greater decline in rural areas compared to Dar es Salaam and other urban areas. Neonatal mortality rate was consistently higher in Dar es Salaam during the same period, with the widest gap (> 50%) between Dar es Salaam and rural areas in TDHS 2015/2016. Coverage of maternal, new-born and child health interventions as well as living conditions were generally better in Dar es Salaam than elsewhere. Within the city, neonatal mortality was 63 and 44 per 1000 live births in the poorest 33% and richest 33%, respectively. The poorest had higher rates of stunting, more overcrowding, inadequate sanitation and lower coverage of institutional deliveries and C-section rate, compared to richest tertile. Children in Dar es Salaam do not have improved survival chances compared to rural children, despite better living conditions and higher coverage of essential health interventions. This urban penalty is higher among children of the poorest households which could only partly be explained by the available indicators of coverage of services and living conditions. Further research is urgently needed to understand the reasons for the urban penalty, including quality of care, health behaviours and environmental conditions.

Antibiotic use at a tertiary hospital in Tanzania: findings from a point prevalence survey

BACKGROUND

In Tanzania, data on antibiotic use at the patient level is scarce, and intervention measures to optimize antibiotic use and reduce antimicrobial resistance are rarely performed.

OBJECTIVES

To describe antibiotic use at Muhimbili National Hospital.

METHODS

This was a point prevalence survey on antibiotic use conducted at Muhimbili National Hospital in August-September 2022. The World Health Organization point prevalence survey data collection tool was used to collect patients' information from the files. All patients admitted to the wards on the day of the survey were included.

RESULTS

Overall, 47% (185/397) of admitted patients were on at least one antibiotic during the survey. All antibiotics prescribed were for empirical treatment and guideline compliance was low, at 45%. Of 185 patients who received antibiotics, the most common indication was community acquired infection (55%) and 36% had no documentation of the reasons for prescribing antibiotics. Almost 75% of the antibiotics were administered parenterally, with only 2% switching to oral route. Microbiological tests were performed in only 9 (5%) patients out of 185 and results were available for only one patient. Of all participants, 52% received two or more antibiotic in combination, with the combination ceftriaxone-metronidazole being most frequently prescribed, followed by the combination of ampicillin, cloxacillin, and gentamicin. For individual antibiotics, ceftriaxone was the most frequently prescribed antibiotic accounting for 28% (79/283), followed by metronidazole (24%) and amoxicillin-clavulanic acid (11%).

CONCLUSION

The findings of a high prevalence of antibiotic use, inadequate use of bacterial culture, and frequent empiric antibiotic treatment suggests the need for strengthening diagnostic and antimicrobial stewardship programs. Furthermore, this study has identified areas for quality improvement, including education programs focusing on prescription practice.

What Influences Patients' Adherence to Healthcare Worker Prescription in Primary Healthcare Facilities in Burkina Faso? A Qualitative Account of Barriers and Facilitators

BACKGROUND

This study explores the factors influencing patients and caregivers' adherence to prescription of healthcare workers (HCWs).

METHODS

The study was conducted in Temnaore and Pella, in the Nanoro health district in Burkina Faso. HCWs and community members were purposively recruited from 4 communities seeking care at the selected primary healthcare facilities for the clinical trial to attend in-depth interviews and focus group discussions on the factors influencing adherence to prescription. The Behaviour Change Wheel incorporating the Capability, Opportunity, and Motivation Behaviour approach was used.

RESULTS

Factors influencing the ability of patients to obtain the prescribed medicine include the availability of medicines and money and the perception of consequences for not getting the medicine. Regarding compliance with the intake of medicines, communication was considered a key factor whose effectiveness depends on the performance of HCWs and on the attention of patients. It is followed by other factors such as adequate management of patients, social influences, the patient's beliefs regarding treatment, and memory.

CONCLUSIONS

This research highlights factors influencing adherence to HCWs' prescription from the perspective of the community members and HCWs and therefore provides contextual enablers and barriers, which allows for the development of an intervention to support the clinical trial.

The hard part we often forget: providing care to children and adolescents with advanced HIV disease

INTRODUCTION

Many children and adolescents living with HIV still present with severe immunosuppression with morbidity and mortality remaining high in those starting antiretroviral therapy (ART) when hospitalized.

DISCUSSION

The major causes of morbidity and mortality in children living with HIV are pneumonia, tuberculosis, bloodstream infections, diarrhoeal disease and severe acute malnutrition. In contrast to adults, cryptococcal meningitis is rare in children under 5 years of age but increases in adolescence. In 2021, the World Health Organizations (WHO) consolidated guidelines for managing HIV disease and rapid ART included recommendations for children and adolescents. In addition, a WHO technical brief released in 2020 highlighted the various interventions that are specifically related to children and adolescents with advanced HIV disease (AHD). We discuss the common clinical presentations of children and adolescents with AHD with a focus on diagnosis, prevention and treatment, highlight some of the challenges in the implementation of the existing package of care, and emphasize the importance of additional research to address the needs of children and adolescents with AHD.

CONCLUSIONS

There are limited data informing these recommendations and an urgent need for further research on how to implement optimal strategies to ensure tailored approaches to prevent and treat AHD in children and adolescents. Holistic care that goes beyond a simple choice of ART regimen should be provided to all children and adolescents with AHD.

Multidrug-resistant Acinetobacter baumannii in healthcare settings in Africa

The emergence of multidrug-resistant Acinetobacter baumannii is a major concern to healthcare providers and facilities in many parts of the world. This bacterial pathogen is commonly implicated in hospital-acquired infections, particularly in critically ill patients admitted to the intensive care unit (ICU). The extensive use of antibiotics, particularly in ICUs, and the lack of proper infection control interventions in many hospitals have led to an increased emergence of multidrug-resistant A. baumannii. Infections due to multidrug-resistant A. baumannii are associated with prolonged hospital stays and high morbidity and mortality, particularly among hospitalized ICU patients. The lack of antibiotic stewardship programmes in many healthcare facilities has exacerbated the burden of A. baumannii infections in many parts of Africa. This review discusses the prevalence and antibiotic-resistance pattern of the multidrug-resistant A. baumannii, and the possible ways to address or minimise its emergence in healthcare settings in Africa.

Clinical features and risk factors for death in acute undifferentiated fever: A prospective observational study in rural community hospitals in six states of India

BACKGROUND

Acute undifferentiated fever (AUF) ranges from self-limiting illness to life-threatening infections, such as sepsis, malaria, dengue, leptospirosis and rickettsioses. Similar clinical presentation challenges the clinical management. This study describes risk factors for death in patients hospitalized with AUF in India.

METHODS

Patients aged ≥5 y admitted with fever for 2-14 d without localizing signs were included in a prospective observational study at seven hospitals in India during 2011-2012. Predictors identified by univariate analysis were analyzed by multivariate logistic regression for survival analysis.

RESULTS

Mortality was 2.4% (37/1521) and 46.9% (15/32) died within 2 d. History of heart disease (p=0.013), steroid use (p=0.011), altered consciousness (p<0.0001), bleeding (p<0.0001), oliguria (p=0.020) and breathlessness (p=0.015) were predictors of death, as were reduced Glasgow coma score (p=0.005), low urinary output (p=0.004), abnormal breathing (p=0.006), abdominal tenderness (p=0.023), leucocytosis (p<0.0001) and thrombocytopenia (p=0.001) at admission. Etiology was identified in 48.6% (18/37) of fatal cases.

CONCLUSIONS

Bleeding, cerebral dysfunction, respiratory failure and oliguria at admission, suggestive of severe organ failure secondary to systemic infection, were predictors of death. Almost half of the patients who died, died shortly after admission, which, together with organ failure, suggests that delay in hospitalization and, consequently, delayed treatment, contribute to death from AUF.

The Prevalence of Malaria and Bacteremia Co-Infections among Febrile Patients: A Systematic Review and Meta-Analysis

Comprehensive data on the relative contribution of bacteremia to malaria outcomes in a large number of participants are lacking. Therefore, we collated data on the co-existence of malaria and bacteremia in the literature to provide evidence-based information for future studies investigating the clinical significance of this co-infection. The study protocol was registered at PROSPERO (ID: CRD42021287971). Relevant studies were identified from PubMed, Web of Science, and Scopus. The pooled prevalence of (1) co-existent malaria and bacteremia among febrile patients, (2) the pooled prevalence of bacteremia among patients with malaria, (3) the probability of co-infection, and (4) the pooled prevalence of deaths were estimated by the random-effects model. Fifty-one studies involving 1583 cases of co-infection were included in the analyses. Typhoidal Salmonella spp. and Staphylococcus aureus were the most common Gram-negative and Gram-positive bacteria, respectively. The prevalence of co-existent malaria and bacteremia among febrile patients was 1.9% (95% confidence interval (CI) = 1.5–2.2%, I² = 96.64%, 31 studies). The prevalence of bacteremia among patients with malaria was 7.6% (95% CI = 6.7–8.7%, and I² = 96.68%, 43 studies). Co-infection by malaria and bacteremia did not occur by chance (p = 0.024, odds ratio = 0.64, 95% CI = 0.43–0.94, and I² = 95.7%, 29 studies). The pooled prevalence of deaths among patients with co-infection was 15.0% (95% CI = 8.0–23.0%, I² = 75.23%, 8 studies). On the basis of this study, we conclude that although the prevalence of co-infection was low, patients with malaria appear at greater risk of bacteremia and death.

Antimicrobial Resistance and Associated Risk Factors of Gram-Negative Bacterial Bloodstream Infections in Tikur Anbessa Specialized Hospital, Addis Ababa

Background

Bloodstream infections (BSIs) are significant causes of morbidity and mortality in Ethiopia and worldwide. Alarming is the rapid global spread of antimicrobial resistance (AMR) in bacteria.

Objective

To determine the microbial profile, antimicrobial susceptibility pattern, and associated risk factors for bloodstream infections in Tikur Anbessa Specialized Hospital (TASH) Addis Ababa Ethiopia.

Methods

A cross-sectional study was conducted between September 2018 and March 2019. Blood collected twice from each septicemia suspected patient were processed following standard bacteriological procedures. AST was performed by using the disk diffusion test according to CLSI 2017 and 2018 guidelines. Data captured in Epidata were cleaned and analyzed by SPSS version 21 software.

Results

The prevalence of BSI was 28.06% and a higher proportion of pathogene detected were gram-negative bacteria (GNB) (54.5%) and gram-positive bacteria (GPB) (45.43%). The most abundant bacterial species were Klebsiella pneumoniae 17.6%, CoNS 15.2%, and Acinetobacter spp 11.0%. Culture positivity was associated with age below 6 years, neonates AOR p=<0.001, infants AOR p=<0.001, Pre-school P=0.002, ICU admission COR p=<0.001, length of admission >5 days COR P=0.016, temperature greater than 38°C, AOR p=0.013, instrument usage during medical care AOR, p=<0.001, chronic illness AOR p=0.027, and neonatal incubation AOR p=0.013. GNB average drug resistance rate was 57.9% of the commonly used antibiotics and the most efficient and inefficient drugs were amikacin (10.8%) and ampicillin (94.6%). The gram-negative isolates showed a 95.3% rate of multi-drug resistance; and MDR, XDR, and PDR were observed at 55.8%, 32.2%, and 7.3%, of isolates respectively. This finding shows children especially neonates were highly affected by drug resistant BSI.

Conclusion

Pediatric patients and ICU patients are more affected by BSI, and drug-resistant bacteria are a major problem. Therefore, appropriate intervention approaches need to be implemented.

Aetiology, antimicrobial susceptibility and outcome of children with sepsis, admitted at Muhimbili National Hospital, Dar es Salaam

Introduction

sepsis is defined as a systemic inflammatory host response syndrome (SIRS) to infection, commonly bacterial. The global prevalence of sepsis is 8.2% with a mortality rate of 25%, whilst in Tanzania the prevalence is 6.6%. Treatment of sepsis involves early initiation of antibiotics based on local sensitivity patterns. However, there is an increase in antimicrobial resistance to commonly used antibiotics. Hence to promote rational use of antibiotics, we aimed at establishing the etiology, local susceptibility patterns and outcome of children with sepsis aged 2 months to 15 years, admitted at Muhimbili National Hospital (MNH), Dar es Salaam.

Methods

a hospital based prospective cross sectional study was conducted among 245 participants who were consecutively recruited. A standardized structured questionnaire was used to collect information. Blood cultures and complete blood counts were done. Antimicrobial susceptibility was also done on positive cultures using disc diffusion method. Data were analyzed using SPSS version 20. Frequencies and proportions were used to summarize categorical data, whilst median and interquartile range was used to summarize continuous data. Student T test was used to compare means of data which were normally distributed and the differences in proportions were tested using Chi square test or Fisher's exact test. A p value of = 0.05 was considered to be statistically significant.

Results

there was predominance of male participants (67.5%) with a median age was 2 years and an interquartile range (IQR) 10 months to 4 years. Culture positive sepsis was detected among 29.8% of the participants, and the common Gram-positive bacterial isolates were S. aureus (39.7%) Coagulase Negative Staphylococcus (CoNS) (35.6%) and Gram-negative isolates were E. coli (12.3%), Klebsiella spp (6.8%) and Pseudomonas aeruginosa (5.5%). All bacteria showed a high resistance to ampicillin (80%- 100%) followed by ceftriaxone (40 - 70%). All Pseudomonas aeruginosawere 100% resistant to ampicillin, gentamycin and ceftriaxone but were sensitive to amikacin. There was less than 40% resistance to co-amoxiclav, meropenem, ciprofloxacin, amikacin, and clindamycin. The overall case mortality rate from sepsis was 9.4%. Among children discharged 59.3% had prolonged hospital stay of more than 7 days. Age group 1 to 5 years, prior use of antibiotics, tachycardia, and leukocytosis were significantly associated with high mortality.

Conclusion

bacterial sepsis is prevalent at Muhimbili National Hospital contributing to 9.4% of mortality and a prolonged hospital stay of more than 7 days among 59.3% of the participants. Gram-positive bacteria were found to be predominant cause of sepsis, whereas both Gram-positive and Gram-negative bacteria had a high resistance to first and second line antimicrobials including: ampicillin, gentamycin, and ceftriaxone.

Mortality associated with third-generation cephalosporin resistance in Enterobacteriaceae bloodstream infections at one South African hospital

OBJECTIVES

Enterobacteriaceae are common pathogens causing bloodstream infection (BSI) in sub-Saharan Africa and frequently express third-generation cephalosporin (3GC) resistance; however, the impact of 3GC resistance on clinical outcomes is rarely studied.

METHODS

We conducted a single-site prospective cohort study at Tygerberg Hospital, Cape Town, South Africa to examine the feasibility of measuring impacts of 3GC resistance in Enterobacteriaceae BSI. We included patients with 3GC-susceptible and 3GC-resistant BSIs and matched each BSI patient to two uninfected patients. We determined the concordance of initial antibiotic treatment with the corresponding isolate's susceptibility profile. We performed exploratory impact analysis using multivariable regression models.

RESULTS

Between 1 June 2017 and 31 January 2018, we matched 177 Enterobacteriaceae BSI patients to 347 uninfected patients. Among these BSIs, 35% were phenotypically 3GC resistant. Parameters describing clinical comorbidity showed strong associations with mortality. We found that 18% of 3GC-R and 3% of 3GC-S BSI patient received non-concordant initial therapy. In multivariable Cox regression, we found a mortality impact over their matched patients for both 3GC-R (cause-specific hazard ratio 23.77; 95% CI 5.12-110.3) and 3GC-S (HR 7.49; 95%CI 3.08-18.19) BSI. There was a nonsignificant ratio of these ratios (HR 3.18; 95% CI 0.54-18.70), limited by the small sample size.

CONCLUSION

This form of impact estimation was feasible in one hospital in South Africa where 3GC-R status was associated with non-concordant initial antibiotic treatment. There was a possible increase in mortality among individuals with 3GC-resistant Enterobacteriaceae, but with broad confidence intervals. These analytical approaches could be applied to larger datasets to improve precision of estimates.

Complications and mortality of non-typhoidal salmonella invasive disease: a global systematic review and meta-analysis

BACKGROUND

Non-typhoidal salmonella can cause serious, life-threatening invasive infections involving the bloodstream and other normally sterile sites. We aimed to systematically review the prevalence of complications and case-fatality ratio (CFR) of non-typhoidal salmonella invasive disease to provide contemporary global estimates and inform the development of vaccine and non-vaccine interventions.

METHODS

We did a global systematic review and meta-analysis of studies investigating the complications and mortality associated with non-typhoidal salmonella invasive disease. We searched Embase, MEDLINE, Web of Science, and PubMed for peer-reviewed, primary research articles published from database inception up to June 4, 2021, with no restrictions on language, country, date, or participant demographics. Only studies reporting the proportion of complications or deaths associated with non-typhoidal salmonella invasive disease, confirmed by culture of samples taken from a normally sterile site (eg, blood or bone marrow) were included. We excluded case reports, case series, policy reports, commentaries, editorials, and conference abstracts. Data on the prevalence of complications and CFR were abstracted. The primary outcomes were to estimate the prevalence of complications and CFR of non-typhoidal salmonella invasive disease. We calculated an overall pooled CFR estimate and pooled CFR stratified by UN region, subregion, age group, and by serovar when available with a random-effects meta-analysis. A risk-of-bias assessment was done, and heterogeneity was assessed with Cochran's Q Test, I2, and τ2. This study was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses, and is registered with PROSPERO, CRD42020202293.

FINDINGS

The systematic review returned a total of 8770 records. After duplicates were removed, 5837 titles and abstracts were screened, yielding 84 studies from 35 countries after exclusions. Of these included studies, 77 (91·7%) were hospital-based and 66 (78·6%) were located in Africa or Asia. Among 55 studies reporting non-typhoidal salmonella disease-associated complications, a total of 45 different complications were reported and 1824 complication events were identified among 6974 study participants. The most prevalent complication was septicaemia, occurring in 171 (57·2%) of 299 participants, followed by anaemia in 580 (47·3%) of 1225 participants. From 81 studies reporting the CFR of non-typhoidal salmonella invasive disease, the overall pooled CFR estimate was 14·7% (95% CI 12·2-17·3). When stratified by UN region, the pooled CFR was 17·1% (13·6-21·0) in Africa, 14·0% (9·4-19·4) in Asia, 9·9% (6·4-14·0) in Europe, and 9·6% (0·0-25·1) in the Americas. Of all 84 studies, 66 (78·6%) had an overall high risk of bias, 18 (21·4%) had a moderate risk, and none had a low risk. Substantial heterogeneity (I2>80%) was observed in most (15 [65·2%] of 23) CFR estimates.

INTERPRETATION

Complications were frequent among individuals with non-typhoidal salmonella invasive disease and approximately 15% of patients died. Clinicians, especially in African countries, should be aware of non-typhoidal salmonella invasive disease as a cause of severe febrile illness. Prompt diagnoses and management decisions, including empiric antimicrobial therapy, would improve patient outcomes. Additionally, investments in improving clinical microbiology facilities to identify non-typhoidal salmonella and research efforts towards vaccine development and non-vaccine prevention measures would prevent non-typhoidal salmonella invasive disease-associated illness and death.

FUNDING

EU Horizon 2020 research and innovation programme.

Invasive candidiasis in Africa, what is the current picture?

Invasive candidiasis is a serious, progressive, and potentially deadly infection that can affect the brain, heart, bones, eyes, and other parts of the body. It is associated with risk factors such as the use of indwelling medical devices and prolonged hospital stay, and broad-spectrum antibiotics use. It is especially seen in immunocompromised individuals such as patients with prolonged hospital stay, gastrointestinal surgery, haematological malignancies, and respiratory diseases. We have conducted a systematic search of literature using a select group of database and appropriate search words and found that in Africa, there are 18,293 documented/reported cases of invasive candidiasis in the last few decades (1976-2021) and 16,636(91%) were cases of candidaemia. South Africa had the highest number of reported cases - 15,002(82%), which may be due to underreporting of cases in other countries. HIV positive persons with invasive candidiasis in Africa accounted for 1,052(5.8%). C. albicans was the most frequently isolated species 6,328(32.6%), followed by Candida parapsilosis 5,910(30.4%), and Candida auris 1,505(7.8%). Due to the affordability and availability of blood culture, it was used for diagnosis in most of the studies examined, while a few studies combined other techniques and just 3 studies from 2 countries used serological tests. Echinocandins are recommended as first-line therapy but are only available in 12 countries and are highly priced. The use of fluconazole because of its availability and relatively inexpensive nature has led to increased resistance of Candida species to the drug.

Multidrug-Resistant Infections in the Developing World

Antimicrobials are essential in reducing morbidity and mortality from infectious diseases globally. However, due to the lack of effective surveillance measures and widespread overuse, there is an increasing threat to the effectiveness of antimicrobials. Although there is a global increase in antimicrobial resistance, low- and middle-income countries share a much higher burden. Antimicrobial stewardship efforts such as effective surveillance and reduction in overuse can help combat the increase in antimicrobial resistance.

Bacteriological Profile and Predictors of Death Among Neonates With Blood Culture-Proven Sepsis in a National Hospital in Tanzania-A Retrospective Cohort Study

BACKGROUND

Neonatal sepsis is still a major cause of death and morbidity in newborns all over the world. Despite substantial developments in diagnosis, treatments, and prevention strategies, sepsis remains a common problem in clinical practice, particularly in low-resource countries.

METHODS

A retrospective cohort study of 238 neonates with positive blood culture-proven sepsis (in Muhimbili National Hospital) was conducted from January 2019 to December 2020. The outcomes of hospitalization were survival and death.

RESULTS

In total, 45.4% mortality resulted from 238 neonates who had sepsis exclusively based on blood culture positivity. A significant association was found between very low birth weight (VLBW), hyperglycemia, mechanical ventilation, and high neonatal mortality. Among the different clinical presentations of neonatal sepsis, lethargy, vomiting, and respiratory distress were found to be frequently associated with neonatal mortality. Furthermore, sepsis with Gram-negative bacteria and early-onset sepsis were also associated with high neonatal mortality. Of the 108 neonatal deaths, the largest proportion (40%) was observed with Staphylococcus aureus, and the remaining 38% was caused by Klebsiella, 14% by Escherichia coli, 5% by Pseudomonas, 4% by Acinetobacter, and 2% by Streptococcus. No neonatal deaths from Serratia infection were observed. The overall resistance of isolated organisms to the recommended first-line antibiotics was 84% for ampicillin and 71.3% for gentamicin. The resistance pattern for the recommended second-line antibiotics was 76.2% for ceftriaxone, 35.9% for vancomycin, and 17.5% for amikacin.

CONCLUSION

VLBW, early-onset sepsis, clinical and laboratory parameters like lethargy, vomiting, and hyperglycemia, sepsis with Gram-negative bacteria, and being on mechanical ventilation are strong predictors of death in neonatal sepsis. In addition, this study discovered extraordinarily high resistance to conventional antibiotics. These findings give light on the crucial aspects to consider in preventing this disease and poor outcomes.

COVID-19 associated mucormycosis: evolving technologies for early and rapid diagnosis

The post-coronavirus disease (COVID-19) mucormycosis is a deadly addition to the pandemic spectrum. Although it’s a rare, aggressive, and opportunistic disease, the associated morbidity and mortality are significant. The complex interplay of factors aggravating CAM is uncontrolled diabetes, irrational and excessive use of antibiotics, steroids, and an impaired immune system. Recently, India has been witnessing a rapid surge in the cases of coronavirus disease-associated mucormycosis (CAM), since the second wave of COVID-19. The devastating and lethal implications of CAM had now become a matter of global attention. A delayed diagnosis is often associated with a poor prognosis. Therefore, the rapid and early diagnosis of infection would be life-saving. Prevention and effective management of mucormycosis depend upon its early and accurate diagnosis followed by a multimodal therapeutic approach. The current review summarizes an array of detection methods and highlights certain evolving technologies for early and rapid diagnosis of CAM. Furthermore, several potential management strategies have also been discussed, which would aid in tackling the neglected yet fatal crisis of mucormycosis associated with COVID-19.

Antimicrobial resistance pattern in healthcare-associated infections: investigation of in-hospital risk factors

Background and Objectives:

Antimicrobial resistance (AMR) is an increasing threat for efficient treatment of infections. Determining the epidemiology of healthcare-associated infections and causative agents in various hospital wards helps appropriate selection of antimicrobial agents.

Materials and Methods:

This retrospective study was performed by analyzing antibiograms from March 2017 to March 2018 among patients admitted to the different wards of Imam Khomeini Hospital Complex in Tehran, Iran.

Results:

Among 2440 hospital acquired infections, 59.3% were Gram-negative bacilli: E. coli (n = 469, 22.2%), K. pneumoniae (n = 457, 21.7%), Acinetobacter spp. (n = 282, 13.4%), P. aeruginosa (n = 139, 6.6%) and important Gram-positive bacteria were Enterococcus spp. (n = 216, 10.2%), S. aureus (n = 148, 7%), S. epidermidis (n = 118, 5.6). Generally, there was a high antimicrobial resistance in bacterial isolates in this study. Methicillin resistant Staphylococcus aureus (MRSA) was 56.3 % and MRSE 62.9 %. Vancomycin resistant enterococci (VRE) was 60.7%. K. pneumoniae-ESBL was 79.6% and its resistance to carbapenem was 38.4%. E. coli-ESBL was 42% and its resistance to carbapenems was 2.3%. P. aeruginosa resistance to ceftazidime was 74.4%, to fluroquinolones 63.3%, to aminoglycosides 64.8%, to piperacillin tazobactam 47.6% and to carbapenems 62.1%. Acinetobacter baumannii resistance to ceftazidime was 98.7%, to fluroquinolones 97%, to aminoglycosides 95.9%, to ampicillin sulbactam 84%, to carbapenems 96.4% and to colistin 4%.

Conclusion:

The study revealed an alarming rate of resistance to the commonly used antimicrobial agents used in treating HAIs. Also the relationship between AMR and some risk factors and thus taking steps towards controlling them have been shown.

High Prevalence of Fecal Carriage of Extended Spectrum β-Lactamase-Producing Enterobacteriaceae Among Newly HIV-Diagnosed Adults in a Community Setting in Tanzania

Colonization in HIV-infected populations with extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) is particularly worrisome in low-income settings. This study describes the prevalence of ESBL-PE carriage and associated risk factors among newly HIV-diagnosed adults in a community setting in Tanzania. A total of 595 newly diagnosed HIV adults with a median age of 35 years with interquartile range (IQR) 29–42 years and a median CD4 count of 492 cells/μL (IQR 390–666 cells/μL) were recruited. Among these, 194/595 (32.6%, 95% confidence interval [CI] 28.9–36.6) were ESBL-PE carriers. Participants with low CD4 count (<350 cells/μL) had significantly higher prevalence of ESBL-PE carriage compared with those with CD4 count ≥350 cells/μL (26/58, 44.8%, vs. 168/537, 31.3%, p = 0.04). Antibiotic use in last 4 weeks (odds ratio [OR] 1.55, 95% CI 1.08–2.22, p = 0.02) and CD4 count ≥350 cells/μL (OR 1.78, 95% CI 1.03–3.09, p = 0.04) were independent risk factors for fecal carriage of ESBL-PE. In total, 244 isolates of ESBL-PE were isolated from 194 participants. Of these, 238/244 (97.5%) harbored bla_CTX-M genes, with bla_CTX-M-15 being predominant (219/238 (92%), followed by bla_CTX-M-27 (9/238 (3.8%), bla_CTX-M-14 (8/238 (3.4%), bla_CTX-M-55 (1/238), and bla_{CTX-M 211/3} (1/238). bla_SHV-2a genes were detected in four isolates, whereas the bla_SHV-12 gene was detected in one isolate. Phenotypic carbapenemase-producing Enterobacteriaceae was detected in one HIV-positive person with CD4 count 132 cells/μL. In conclusion prevalence of ESBL-PE carriage is high among newly diagnosed HIV adults in Dar es Salaam, and is significantly associated antibiotic use and low CD4 count.

The genomic epidemiology of multi-drug resistant invasive non-typhoidal Salmonella in selected sub-Saharan African countries

Background

Invasive non-typhoidal Salmonella (iNTS) is one of the leading causes of bacteraemia in sub-Saharan Africa. We aimed to provide a better understanding of the genetic characteristics and transmission patterns associated with multi-drug resistant (MDR) iNTS serovars across the continent.

Methods

A total of 166 iNTS isolates collected from a multi-centre surveillance in 10 African countries (2010–2014) and a fever study in Ghana (2007–2009) were genome sequenced to investigate the geographical distribution, antimicrobial genetic determinants and population structure of iNTS serotypes–genotypes. Phylogenetic analyses were conducted in the context of the existing genomic frameworks for various iNTS serovars. Population-based incidence of MDR-iNTS disease was estimated in each study site.

Results

Salmonella Typhimurium sequence-type (ST) 313 and Salmonella Enteritidis ST11 were predominant, and both exhibited high frequencies of MDR; Salmonella Dublin ST10 was identified in West Africa only. Mutations in the gyrA gene (fluoroquinolone resistance) were identified in S. Enteritidis and S. Typhimurium in Ghana; an ST313 isolate carrying bla_CTX-M-15 was found in Kenya. International transmission of MDR ST313 (lineage II) and MDR ST11 (West African clade) was observed between Ghana and neighbouring West African countries. The incidence of MDR-iNTS disease exceeded 100/100 000 person-years-of-observation in children aged <5 years in several West African countries.

Conclusions

We identified the circulation of multiple MDR iNTS serovar STs in the sampled sub-Saharan African countries. Investment in the development and deployment of iNTS vaccines coupled with intensified antimicrobial resistance surveillance are essential to limit the impact of these pathogens in Africa.

Prevalence and risk factors for antimicrobial resistance among newborns with gram-negative sepsis

INTRODUCTION

Newborn sepsis accounts for more than a third of neonatal deaths globally and one in five neonatal deaths in Ethiopia. The first-line treatment recommended by WHO is the combination of gentamicin with ampicillin or benzylpenicillin. Gram-negative bacteria (GNB) are increasingly resistant to previously effective antibiotics.

OBJECTIVES

Our goal was to estimate the prevalence of antibiotic-resistant gram-negative bacteremia and identify risk factors for antibiotic resistance, among newborns with GNB sepsis.

METHODS

At a tertiary hospital in Ethiopia, we enrolled a cohort pregnant women and their newborns, between March and December 2017. Newborns who were followed up until 60 days of life for clinical signs of sepsis. Among the newborns with clinical signs of sepsis, blood samples were cultured; bacterial species were identified and tested for antibiotic susceptibility. We described the prevalence of antibiotic resistance, identified newborn, maternal, and environmental factors associated with multidrug resistance (MDR), and combined resistance to ampicillin and gentamicin (AmpGen), using multivariable regression.

RESULTS

Of the 119 newborns with gram-negative bacteremia, 80 (67%) were born preterm and 82 (70%) had early-onset sepsis. The most prevalent gram-negative species were Klebsiella pneumoniae 94 (79%) followed by Escherichia coli 10 (8%). Ampicillin resistance was found in 113 cases (95%), cefotaxime 104 (87%), gentamicin 101 (85%), AmpGen 101 (85%), piperacillin-tazobactam 47 (39%), amikacin 10 (8.4%), and Imipenem 1 (0.8%). Prevalence of MDR was 88% (n = 105). Low birthweight and late-onset sepsis (LOS) were associated with higher risks of AmpGen-resistant infections. All-cause mortality was higher among newborns treated with ineffective antibiotics.

CONCLUSION

There was significant resistance to current first-line antibiotics and cephalosporins. Additional data are needed from primary care and community settings. Amikacin and piperacillin-tazobactam had lower rates of resistance; however, context-specific assessments of their potential adverse effects, their local availability, and cost-effectiveness would be necessary before selecting a new first-line regimen to help guide clinical decision-making.

The importance of Escherichia coli clonal complex 10 and ST131 among Tanzanian patients on antimicrobial resistance surveillance programs

The objective of this study was to characterize antimicrobial resistance (AMR) of WHO priority 1 critical pathogen (extrapathogenic Escherichia coli (ExPEC), sequence types (STs), and ST131 clades from patients in Tanzania so as to guide specific antimicrobial therapies and preventive measures. A total of 143 ExPEC strains (128 from pregnant women with urinary tract infections and 15 from children with blood stream infections) were collected between March 2016 and October 2017. These were characterized into ST-fimH clones by a 7-single nucleotide polymorphism quantitative polymerase chain reaction (7-SNP qPCR) and gene sequencing, and to ST131 clades by multiplex PCR. The extended-spectrum beta-lactamases (ESBL) production was 16.1% (23/143), and was predominantly due to the blaCTX-M-15 (91.3%, n=21). ESBL production was significantly more among strains from children (53.3%) than pregnant women (11.7%) (OR (95%CI): 8.61 (2.73-27.15); p-value <0.001)). Approximately 61.5% (n=88) ExPEC were typed into their respective STs/CCs (87 by the 7-SNP qPCR and by an additional of one or two genes sequencing). The commonest STs/CCs among typeable strains were CC10 (28.4%, n=25), ST131 (18.2%, n=16), and ST38 (10.2%, n=9). The ST131 clades (C1 (4, 25.0%) and C2 (6, 37.5%)) were predominantly associated with fluoroquinolone resistance and ESBL production, respectively. Approximately 60.8% of ExPEC strains and all dominant clones were typed by the 7-SNP qPCR by additional sequencing. The multiplex clade PCR allowed linkage of the global clone ST131 with AMR phenotypes. These feasible and user-friendly molecular tools can be routinely used for surveillance programs in resource-limited settings.

Salmonella Bloodstream Infections in Hospitalized Children with Acute Febrile Illness-Uganda, 2016-2019

Invasive Salmonella infection is a common cause of acute febrile illness (AFI) among children in sub-Saharan Africa; however, diagnosing Salmonella bacteremia is challenging in settings without blood culture. The Uganda AFI surveillance system includes blood culture-based surveillance for etiologies of bloodstream infection (BSIs) in hospitalized febrile children in Uganda. We analyzed demographic, clinical, blood culture, and antimicrobial resistance data from hospitalized children at six sentinel AFI sites from July 2016 to January 2019. A total of 47,261 children were hospitalized. Median age was 2 years (interquartile range, 1-4) and 26,695 (57%) were male. Of 7,203 blood cultures, 242 (3%) yielded bacterial pathogens including Salmonella (N = 67, 28%), Staphylococcus aureus (N = 40, 17%), Escherichia spp. (N = 25, 10%), Enterococcus spp. (N = 18, 7%), and Klebsiella pneumoniae (N = 17, 7%). Children with BSIs had longer median length of hospitalization (5 days versus 4 days), and a higher case-fatality ratio (13% versus 2%) than children without BSI (all P < 0.001). Children with Salmonella BSIs did not differ significantly in length of hospitalization or mortality from children with BSI resulting from other organisms. Serotype and antimicrobial susceptibility results were available for 49 Salmonella isolates, including 35 (71%) non-typhoidal serotypes and 14 Salmonella serotype Typhi (Typhi). Among Typhi isolates, 10 (71%) were multi-drug resistant and 13 (93%) had decreased ciprofloxacin susceptibility. Salmonella strains, particularly non-typhoidal serotypes and drug-resistant Typhi, were the most common cause of BSI. These data can inform regional Salmonella surveillance in East Africa and guide empiric therapy and prevention in Uganda.

Campylobacter and Salmonella in Scavenging Indigenous Chickens in Rural Central Tanzania: Prevalence, Antimicrobial Resistance, and Genomic Features

Introduction: Salmonella and Campylobacter spp. are commonly reported bacterial foodborne pathogens causing morbidity and mortality worldwide. In rural areas, where there is a high occurrence rate of human–animal interactions and poor hygiene practices, shedding animals present a high risk to humans in acquiring animal-associated infections. Materials and methods: Seasonal prevalence of Campylobacter jejuni, Campylobacter coli, and Salmonella spp. in scavenging indigenous chicken faeces was determined by polymerase chain reaction (PCR). Antimicrobial resistance was studied in Salmonella isolates by disc diffusion method, and whole-genome sequenced isolates were used to determine Salmonella serovars, antimicrobial resistance genes, virulence genes, and plasmid profile. Results: The overall prevalence of Campylobacter in chickens was 7.2% in the dry season and 8.0% in the rainy season (p = 0.39), and that of Salmonella was 11.1% in the dry season and 16.2% in the rainy season (p = 0.29). Salmonella serovars detected were II 35:g,m,s,t:-, Ball, Typhimurium, Haardt/Blockley, Braenderup, and Enteritidis/Gallinarum. One S. II 35:g,m,s,t:- isolate was resistant to ampicillin and the rest were either intermediate resistant or pansusceptible to the tested antimicrobials. The resistance genes observed were CatA, tetJ, and fosA7, most common in Ball than in other serovars. Seven plasmids were identified, more common in serovar Ball and less common in II 35:g,m,s,t:-. Serovar II 35:g,m,s,t:- isolates were missing some of the virulence genes important for Salmonella pathogenicity found in other serovars isolated. Conclusion: PCR detection of Campylobacter spp. and Salmonella spp. in chickens necessitate the improvement of hygiene at the household level and reducing human–chicken interaction as a strategy of preventing humans from acquiring chicken-associated bacteria, which would enter the human food chain. Infrequent use of antimicrobials in this type of poultry is most likely the reason for the low rates of antimicrobial resistance observed in this study.

Use of probiotics to reduce infections and death and prevent colonization with extended-spectrum beta-lactamase (ESBL)-producing bacteria among newborn infants in Tanzania (ProRIDE Trial): study protocol for a randomized controlled clinical trial

BACKGROUND

Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) has emerged as an urgent global health threat and is by the World Health Organization ranked as priority 1 among pathogens in need of new treatment. Studies have shown high mortality in Tanzanian children with ESBL-E infections. Gut colonization of ESBL-E, which is a potential risk factor of ESBL-E infections, is reported to be very high among children in Tanzania. Probiotics may potentially reduce gut colonization of multidrug-resistant bacteria. However, there is limited data on whether probiotics may reduce ESBL-E carriage in infants. The ProRIDE Trial aims to evaluate whether the use of probiotics can reduce morbidity and mortality among infants in Haydom, Tanzania, and whether this effect is associated with a reduction in ESBL-E colonization and/or infections.

METHODS/DESIGN

This large randomized double-blinded placebo-controlled trial aims to recruit 2000 newborn infants at Haydom Lutheran Hospital and the surrounding area in the period of November 2020 to November 2021. Participants will be enrolled from days 0 to 3 after birth and randomized to receive probiotics or placebo for 4 weeks. Participants will be followed-up for 6 months, during which three visits will be made to collect clinical and demographic information, as well as rectal swabs and fecal samples which will be subjected to laboratory analysis. The primary composite outcome is the prevalence of death and/or hospitalization at 6 months of age.

DISCUSSION

As the use of probiotics may give a more favorable gut composition, and thereby improve health and reduce morbidity and mortality, the results may have implications for future therapy guidelines in Africa and internationally.

TRIAL REGISTRATION

ClinicalTrials.gov NCT04172012. Registered on November 21, 2019.

Antimicrobial Use, Residues, Resistance and Governance in the Food and Agriculture Sectors, Tanzania

All infections are potentially curable as long as the etiological agents are susceptible to antimicrobials. The increased rate at which antimicrobials are becoming ineffective is a global health risk of increasing concern that threatens withdrawal of beneficial antimicrobials for disease control. The increased demand for food of animal origin, in particular eggs, meat and milk has led to intensification and commercial production systems where excessive use and misuse of antimicrobials may prevail. Antimicrobials, handled and used by farmers and animal attendants with no formal education, may be predisposed to incorrect dosages, misuse, incorrect applications and non-adherence to withdrawal periods. This study was conducted to assess the regulatory roles and governance of antimicrobials, establish the pattern and extent of their use, evaluate the antimicrobial residues and resistance in the food animals and crop agriculture value chains, and relate these findings to existing strategies in place for combating the emergence of antimicrobial resistance in Tanzania. A multimethod approach (desk review, field study and interviews) was used. Relevant establishments were also visited. High levels of resistance to penicillin G, chloramphenicol, streptomycin and oxytetracycline have been reported, especially for Actinobacter pyogenes, Staphylococcus hyicus, Staphylococcus intermedius and Staphylococcus aureus from dairy cattle with mastitis and in humans. Similar trends were found in poultry where eggs and meat are contaminated with Escherichia coli strains resistant to amoxicillin + clavulanate, sulphamethoxazole and neomycin. An increasing trend of emerging multidrug resistant E. coli, Klebsiella pneumoniae, Staphylococcus aureus and Salmonella was also found in food animals. An increase in methicillin resistant Staphlococcus aureus (MRSA) and extended-spectrum beta-lactamase (ESBL) in the livestock sector in Tanzania have been reported. The pathogens isolated in animals were resistant to ampicillin, augmentin, gentamicin, co-trimoxazole, tetracycline, amoxicillin, streptomycin, nalidixic acid, azithromycin, chloramphenicol, tylosin, erythromycin, cefuroxime, norfloxacin and ciprofloxacin. An increased usage of antimicrobials for prophylaxis, and therapeutics against pathogens and for growth promotion in livestock, aquaculture and crop production were observed. A One Health strategic approach is advocated to combat antimicrobial resistance (AMR) in the food and agriculture sectors in Tanzania. Practical recommendations include (a) legislation review and implementation; (b) antimicrobial use (AMU), AMR and antimicrobial residue (AR) awareness and advocacy among stakeholders along the value chain; (c) strengthening of surveillance and monitoring programs for AMU, AMR and AR; (d) enhanced development and use of rapid and innovative diagnostic tests and the promotion of biosecurity principles; and (e) good husbandry practices. The utilization of this information to improve public health policies and reduce the burden of AMR will be beneficial.

Multidrug-Resistant, Including Extended-Spectrum Beta Lactamase-Producing and Quinolone-Resistant, Escherichia coli Isolated from Poultry and Domestic Pigs in Dar es Salaam, Tanzania

We determined the phenotypic profile of multidrug-resistant (MDR) Escherichia coli isolated from 698 samples (390 and 308 from poultry and domestic pigs, respectively). In total, 562 Enterobacteria were isolated. About 80.5% of the isolates were E. coli. Occurrence of E. coli was significantly higher among domestic pigs (73.1%) than in poultry (60.5%) (p = 0.000). In both poultry and domestic pigs, E. coli isolates were highly resistant to tetracycline (63.5%), nalidixic acid (53.7%), ampicillin (52.3%), and trimethoprim/sulfamethoxazole (50.9%). About 51.6%, 65.3%, and 53.7% of E. coli were MDR, extended-spectrum beta lactamase-producing enterobacteriaceae (ESBL-PE), and quinolone-resistant, respectively. A total of 68% of the extended-spectrum beta lactamase (ESBL) producers were also resistant to quinolones. For all tested antibiotics, resistance was significantly higher in ESBL-producing and quinolone-resistant isolates than the non-ESBL producers and non-quinolone-resistant E. coli. Eight isolates were resistant to eight classes of antimicrobials. We compared phenotypic with genotypic results of 20 MDR E. coli isolates, ESBL producers, and quinolone-resistant strains and found 80% harbored blaCTX-M, 15% aac(6)-lb-cr, 10% qnrB, and 5% qepA. None harbored TEM, SHV, qnrA, qnrS, qnrC, or qnrD. The observed pattern and level of resistance render this portfolio of antibiotics ineffective for their intended use.

Identification of Pathogens Potentially Associated with Non-Malarial Fever in Children: A Pilot Study in Peri-Urban Dakar, Senegal

Fever is one of the most common reasons for pediatric consultation in Africa. Malaria incidence has now dropped considerably, yet etiologies of non-malarial febrile diseases are poorly documented. This pilot study aimed to 1) identify pathogens potentially associated with non-malarial fever in children younger than 10 years in the suburbs of Dakar and 2) describe the epidemiological characteristics of these patients. During the study period, all eligible children (< 10 years of age, body temperature ≥ 38°C, negative result for the malaria rapid diagnostic test, living in Guediawaye/Pikine for the previous four calendar months, not receiving any anti-infectious treatment since the onset of fever, and with parent's consent to participate) presenting to the health post in Medina Gounass located in Guediawaye on Mondays and Fridays were included. In total, 106 children participated in the study, and PCR from nasopharyngeal swabs, hemoculture, C-reactive protein, blood cell counts, and quantitative buffy coat from blood samples and coproculture from stool samples were performed. In 70 (66%) children, at least one pathogen was isolated. Viruses were identified in 55 children, most commonly enteroviruses, rhinoviruses, and adenoviruses, and dengue virus was identified in three children. Only five children had bacterial infections, and 10 had bacterial and viral coinfections. Ninety-seven children (92%) received prescription for antibiotics. Many strains of bacteria were found to be resistant to several antibiotics. Despite limitations, this pilot study showed that pathogens potentially associated with non-malarial fever in children younger than 10 years near Dakar were predominantly viruses, most commonly upper respiratory infections, although bacteria accounted for a small proportion.

Antimicrobial Resistance in Enterobacterales and Its Contribution to Sepsis in Sub-saharan Africa

Antibiotic resistant Enterobacterales (formerly Enterobactereaceae) are a growing threat to Sub-Saharan Africa. Genes causing antibiotic resistance are easily spread between the environment and humans and infections due to drug resistant organisms contribute to sepsis mortality via delayed time to appropriate antimicrobial therapy. Additionally, second or third-line antibiotics are often not available or are prohibitively expensive in resource-constrained settings leading to limited treatment options. Lack of access to water and sanitation facilities, unregulated use of antibiotics, and malnutrition are contributors to high rates of antibiotic resistance in the region. Improvements in the monitoring of drug resistant infections and antibiotic stewardship are needed to preserve the efficacy of antibiotics for the future.

Mortality attributable to third-generation cephalosporin resistance in Gram-negative bloodstream infections in African hospitals: a multi-site retrospective study

Background

Bloodstream infections (BSI) caused by Enterobacteriaceae show increasing frequency of resistance to third-generation cephalosporin (3GC) antibiotics on the African continent but the mortality impact has not been quantified.

Methods

We used historic data from six African hospitals to assess the impact of 3GC resistance on clinical outcomes in Escherichia coli and Klebsiella pneumoniae BSI. We matched each bacteraemic patient to two uninfected patients. We compared outcomes between 3GC-susceptible and 3GC-resistant BSI and their respective uninfected controls using Cox regression models.

Results

For 1431 E. coli BSI patients, we matched 1152 (81%) 3GC-susceptible and 279 (19%) 3GC-resistant cases to 2263 and 546 uninfected inpatient controls. For 1368 K. pneumoniae BSI patients, we matched 502 (37%) 3GC-susceptible and 866 (63%) 3GC-resistant cases to 982 and 1656 uninfected inpatient controls. We found that 3GC-resistant E. coli had similar hazard ratios (HRs) for in-hospital mortality over their matched controls as compared to susceptible infections over their controls (ratio of HRs 1.03, 95% CI 0.73–1.46). Similarly, 3GC-resistance in K. pneumoniae BSI was not associated with mortality (ratio of HR 1.10, 95% CI 0.80–1.52). Estimates of mortality impact varied by site without a consistent pattern.

Conclusions

In a retrospective analysis, including the use of matched uninfected patients, there did not appear to be an impact of 3GC-resistance on mortality in E. coli or K. pneumoniae BSI in African hospitals, as compared with susceptible BSI with equivalent species. Better information on the actual use of antibiotics in treating infections in African hospitals would improve these impact estimates.

A retrospective analysis of community-onset bloodstream infections at a tertiary-care academic hospital in South Africa. Are current empiric antimicrobial practices appropriate?

Background:

Community-onset bloodstream infection (CO-BSI) is associated with substantial morbidity and mortality. Knowledge of locally prevalent pathogens and antimicrobial susceptibility patterns can promptly guide appropriate empiric therapy and improve outcomes.

Objectives:

We sought to determine the epidemiology of CO-BSI, the blood culture positivity rate and the contamination rate. We also sought to establish appropriateness of current empiric antimicrobial therapy practices.

Methods:

We retrospectively analyzed blood cultures taken from January 2015 to December 2019 at the emergency departments (EDs) of a tertiary-care academic hospital in South Africa using extracted laboratory data.

Results:

The overall positivity rate of blood cultures taken at the EDs was 15% (95% confidence interval [CI], 0.15–0.16) and the contamination rate was 7% (95% CI, 0.06–0.07). Gram-positive bacteria predominated in the pediatric cohort: neonates, 52 (54%) of 96; infants, 57 (52%) of 109; older children, 63 (61%) of 103. Methicillin-susceptible Staphylococcus aureus was the predominant pathogen among older children: 30 (35%) of 85. Escherichia coli was the most common pathogen isolated among adults and the elderly: 225 (21%) of 1,060 and 62 (29%) of 214, respectively. Among neonates, the susceptibility of E. coli and Klebsiella pneumoniae to the combination of ampicillin and gentamicin was 17 (68%) of 25. Among adults, the susceptibility of the 5 most common pathogens to amoxicillin-clavulanate was 426 (78%) of 546 and their susceptibility to ceftriaxone was 481 (85%) of 565 (P = .20). The prevalence of methicillin-resistant S. aureus, extended-spectrum β-lactamase–producing and carbapenem-resistant Enterobacterales were low among all age groups.

Conclusions:

Review of blood culture collection techniques is warranted to reduce the contamination rate. High rates of resistance to currently prescribed empiric antimicrobial agents for CO-BSI warrants a re-evaluation of local guidelines.

Evaluation of High-Throughput Next-Generation Sequencing Applied in the Pathogenic Diagnosis of Bloodstream Infections

Background: Bloodstream infection (BSI) has been one of the biggest headaches for clinicians, as it not only aggravates symptoms but also increases the length of stay, the cost of hospitalization, and the side effects caused by antibiotics. It is an urgent need for clinicians to develop timely and accurate methods to find microorganisms. Currently, the gold standard for diagnosing BSI is blood culture, but it takes three to eight days to produce results, and its positive rate is extremely low. Next-generation sequencing (NGS) has emerged as a better technology desperately needed by doctors and patients to diagnose BSI. Objectives: This study compared NGS and blood culture methods in clinical patients with BSI. Methods: In this study, blood culture and NGS were used to analyze the blood of patients with BSI in different departments of the First Affiliated Hospital of Kunming Medical University. Results: Next-generation sequencing detected 60 pathogens in 63 blood samples, while blood culture detected 15 pathogens in 336 blood samples from 63 patients who were clinically considered to be infected. Pathogens detected by NGS included bacteria, fungi, and viruses, while blood culture only found bacteria and fungi. The positive rates of blood culture diagnosis and NGS diagnosis in BSI patients were 23.8% (15/63) (CI: 13.3% - 34.3%) and 95% (60/63) (CI: 90% - 100%), respectively. Conclusions: Our results showed that NGS creates a new diagnostic platform for patients with BSI. Its wide detection range, high positive rate, and characteristics of rapid detection will benefit patients with BSI.

Bacteraemia, Malaria, and Case Fatality Among Children Hospitalized With Fever in Dar es Salaam, Tanzania

Background

Febrile illness is the commonest cause of hospitalization in children <5 years in sub-Saharan Africa, and bacterial bloodstream infections and malaria are major causes of death.

Methods

From March 2017 to July 2018, we enrolled 2,226 children aged 0–5 years hospitalized due to fever in four major public hospitals of Dar es Salaam, namely, Amana, Temeke, and Mwananyamala Regional Hospitals and Muhimbili National Hospital. We recorded social demographic and clinical data, and we performed blood-culture and HIV-antibody testing. We used qPCR to quantify Plasmodium falciparum parasitaemia and Matrix-Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) to identify bacterial isolates. Disk diffusion method was used for antimicrobial susceptibility testing.

Results

Nineteen percent of the children (426/2,226) had pathogens detected from blood. Eleven percent (236/2,226) of the children had bacteraemia/fungaemia and 10% (204/2,063) had P. falciparum malaria. Ten children had concomitant malaria and bacteraemia. Gram-negative bacteria (64%) were more frequent than Gram-positive (32%) and fungi (4%). Over 50% of Gram-negative bacteria were extended-spectrum beta-lactamase (ESBL) producers and multidrug resistant. Methicillin resistant Staphylococcus aureus (MRSA) was found in 11/42 (26.2%). The most severe form of clinical malaria was associated with high parasitaemia (>four million genomes/μL) of P. falciparum in plasma. Overall, in-hospital death was 4% (89/2,146), and it was higher in children with bacteraemia (8%, 18/227) than malaria (2%, 4/194, p = 0.007). Risk factors for death were bacteraemia (p = 0.03), unconsciousness at admission (p < 0.001), and admission at a tertiary hospital (p = 0.003).

Conclusion

Compared to previous studies in this region, our study showed a reduction in malaria prevalence, a decrease in in-hospital mortality, and an increase in antimicrobial resistance (AMR) including ESBLs and multidrug resistance. An increase of AMR highlights the importance of continued strengthening of diagnostic capability and antimicrobial stewardship programs. We also found malaria and bacteraemia contributed equally in causing febrile illness, but bacteraemia caused higher in-hospital death. The most severe form of clinical malaria was associated with P. falciparum parasitaemia.

Horizontal Plasmid Transfer among Klebsiella pneumoniae Isolates Is the Key Factor for Dissemination of Extended-Spectrum β-Lactamases among Children in Tanzania

Horizontal spread of plasmids carrying multiple resistance genes is considered an important mechanism behind the global health problem caused by multidrug-resistant bacteria. Nevertheless, knowledge about spread of plasmids in a community is limited. Our detailed molecular analyses of K. pneumoniae isolated from hospitalized and healthy children in Tanzania disclosed an epidemic spread of a resistance plasmid. In this study population, we revealed horizontal plasmid transfer among K. pneumoniae as the key factor for dissemination of ESBLs. Traditional outbreak investigation and surveillance focus on the spread of bacterial clones, and short-read sequencing can result in erroneous plasmid composition. Our approach using long-read sequencing reveals horizontal gene transfer of antimicrobial resistance, and therefore has a potential impact on outbreak investigations and approaches to limit spread of AMR.

Increased knowledge about the role of horizontal gene transfer is key to improve our understanding of the spread of antimicrobial resistance (AMR) in human populations. We therefore studied the dissemination of the bla_CTX-M-15 extended-spectrum-β-lactamase (ESBL) gene in Klebsiella pneumoniae isolates obtained from stool samples from hospitalized children and healthy controls below 2 years of age in Dar es Salaam, Tanzania, from August 2010 to July 2011. We performed Illumina whole-genome sequencing (WGS) to characterize resistance genes, multilocus sequence type (MLST), plasmid incompatibility group (Inc), and plasmid MLST of 128 isolates of K. pneumoniae with bla_CTX-M-15 recovered from both healthy and hospitalized children. We assessed the phylogenetic relationship using single nucleotide polymorphism (SNP)-based analysis and resolved the sequences of five reference plasmids by Oxford Nanopore technology to investigate plasmid dissemination. The WGS analyses revealed the presence of a bla_CTX-M-15-positive IncFII_K5/IncR plasmid with a highly conserved backbone in 70% (90/128) of the isolates. This plasmid, harboring genes encoding resistance to most β-lactams, aminoglycosides, trimethoprim-sulfamethoxazole, and chloramphenicol, was present in phylogenetically very diverse K. pneumoniae strains (48 different MLSTs) carried by both hospitalized and healthy children. Our data strongly suggest widespread horizontal transfer of this ESBL-carrying plasmid both in hospitals and in the general population.

IMPORTANCE Horizontal spread of plasmids carrying multiple resistance genes is considered an important mechanism behind the global health problem caused by multidrug-resistant bacteria. Nevertheless, knowledge about spread of plasmids in a community is limited. Our detailed molecular analyses of K. pneumoniae isolated from hospitalized and healthy children in Tanzania disclosed an epidemic spread of a resistance plasmid. In this study population, we revealed horizontal plasmid transfer among K. pneumoniae as the key factor for dissemination of ESBLs. Traditional outbreak investigation and surveillance focus on the spread of bacterial clones, and short-read sequencing can result in erroneous plasmid composition. Our approach using long-read sequencing reveals horizontal gene transfer of antimicrobial resistance, and therefore has a potential impact on outbreak investigations and approaches to limit spread of AMR.

Impact of hand hygiene intervention: a comparative study in health care facilities in Dodoma region, Tanzania using WHO methodology

Background

Compliance with guidelines on hand hygiene (HH) is pivotal to prevent and control health-care associated infections and contributes to mitigating antimicrobial resistance. A baseline assessment in Dodoma region, Tanzania in March 2018 showed inadequate HH levels across health care facilities. We evaluated the impact of training in HH as part of a water, sanitation and hygiene (WASH) interventions of “Maji kwa Afya ya Jamii” (MKAJI) project.

Methods

A comparative HH assessment was conducted in June 2019 involving health care facilities under MKAJI project (n = 87 from which 98 units were assessed) vs non-MKAJI facilities (n = 85 from which 99 units were assessed). Irrespective of MKAJI interventional status, baseline assessment in March 2018 were compared to re-assessment in June 2019 in all health care facility units (unpaired comparison: 261 vs 236 units, respectively), and in facilities assessed in both surveys (paired comparison: 191 versus 191 units, respectively). The ‘WHO HH Self-Assessment Framework Tool, 2010’ with five indicators each counting 100 points was used. The cumulative scores stratified each health facility’s unit into inadequate (0–125), basic (126–250), intermediate (251–375) or advanced (376–500) HH level (score). The HH compliance rates were also assessed and compared.

Results

The overall post-intervention median HH score [interquartile range (IQR)] was 187.5 (112.5–260). MKAJI health facilities had significantly higher median HH scores (IQR) [190 (120–262.5)] compared with non-MKAJI facilities [165 (95–230); p = 0.038]. Similarly, the HH compliance rate of ≥51% was significantly higher in MKAJI than non-MKAJI facilities [56.1% versus 30.3%; chi2 = 13.39, p < 0.001]. However, the recommended WHO compliance rate of ≥81% was only reached by 6.1 and 3.0% units of MKAJI and non-MKAJI facilities, respectively. Both paired and unpaired comparisons during baseline and re-assessment surveys showed increase in HH level from inadequate to basic level.

Conclusion

The overall HH level after the combined WASH and training intervention was at basic level. Higher median HH scores (IQR) and HH compliance rates were evident in health facilities of the MKAJI project, underscoring the impact of the intervention and the potential value of a national roll-out.

Multi-drug resistant bacteria predict mortality in bloodstream infection in a tertiary setting in Tanzania

Background

Bloodstream infections (BSI) are serious and life-threatening, associated with high mortality and morbidity. In resource-limited settings, there is a paucity of data on predictors of outcome in patients with BSI. This study aimed at examining the predictors of mortality in patients with BSI as well as bacteria causing BSI.

Methods and materials

This was a cross-sectional study conducted at Muhimbili National Hospital between April and May 2018. Blood culture results from all inpatients at the clinical microbiology laboratory were recorded and clinical information was retrieved retrospectively from the files. Bacteria from positive blood culture were identified and antimicrobial susceptibility was performed.

Results

The overall prevalence of BSI was, 46/402 (11.4% 95% CI 8.6–15), with a case fatality rate of 37%. There was a significantly high rate of BSI in patients who had died (19.5%) compared to those who survived (9.2%) p = 0.008. Gram-negative bacteria (74%) were the common cause of BSI, with a predominance of Enterobacteriaceae (22), followed by Pseudomonas aeruginosa (11). The majority of bacteria (70.5%) isolated from patients with BSI were Multi-drug resistant (MDR). Forty-six percent of Pseudomonas aeruginosa were resistant to meropenem while 68% (15/22) of Enterobacteriaceae were extended-spectrum β lactamase producers. Carbapenemase production was detected in 27% (3/11) of Pseudomonas aeruginosa and one Proteus mirabilis. Forty percent of Staphylococcus aureus were methicillin-resistant Staphylococcus aureus. Positive blood culture (aOR 2.24, 95%CI 1.12–4.47, p 0.02) and admission to the intensive care unit (aOR 3.88, 95%CI 1.60–9.41, p = 0.003) were independent factors for mortality in suspected BSI. Isolation of MDR bacteria was an independent predictor for mortality in confirmed BSI (aOR 15.62, 95%CI 1.24–161.38, p = 0.02).

Conclusion

The prevalence of BSI was 11.4%, with the majority of bacteria in BSI were MDR. Positive blood culture, admission to the ICU and MDR were predictors for mortality.

Prevalence and outcome of bloodstream infections due to third-generation cephalosporin-resistant Enterobacteriaceae in sub-Saharan Africa: a systematic review

BACKGROUND

The prevalence of bacterial bloodstream infections (BSIs) in sub-Saharan Africa (sSA) is high and antimicrobial resistance is likely to increase mortality from these infections. Third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae are of particular concern, given the widespread reliance on ceftriaxone for management of sepsis in Africa.

OBJECTIVES

Reviewing studies from sSA, we aimed to describe the prevalence of 3GC resistance in Escherichia coli, Klebsiella and Salmonella BSIs and the in-hospital mortality from 3GC-R BSIs.

METHODS

We systematically reviewed studies reporting 3GC susceptibility testing of E. coli, Klebsiella and Salmonella BSI. We searched PubMed and Scopus from January 1990 to September 2019 for primary data reporting 3GC susceptibility testing of Enterobacteriaceae associated with BSI in sSA and studies reporting mortality from 3GC-R BSI. 3GC-R was defined as phenotypic resistance to ceftriaxone, cefotaxime or ceftazidime. Outcomes were reported as median prevalence of 3GC resistance for each pathogen.

RESULTS

We identified 40 articles, including 7 reporting mortality. Median prevalence of 3GC resistance in E. coli was 18.4% (IQR 10.5 to 35.2) from 20 studies and in Klebsiella spp. was 54.4% (IQR 24.3 to 81.2) from 28 studies. Amongst non-typhoidal salmonellae, 3GC resistance was 1.9% (IQR 0 to 6.1) from 12 studies. A pooled mortality estimate was prohibited by heterogeneity.

CONCLUSIONS

Levels of 3GC resistance amongst bloodstream Enterobacteriaceae in sSA are high, yet the mortality burden is unknown. The lack of clinical outcome data from drug-resistant infections in Africa represents a major knowledge gap and future work must link laboratory surveillance to clinical data.

Antibiotic Prescription Patterns among Children Younger than 5 Years in Nouna District, Burkina Faso

Understanding antibiotic use may help predict emergence of antimicrobial resistance. We evaluated antibiotic prescription trends in rural Burkina Faso, where little is known about antibiotic consumption. Antibiotic prescription data for 20 communities were extracted through record review in six primary health-care facilities serving the communities. The number of antibiotic prescriptions per child-year was calculated using population-based census data from the communities. A total of 1,444 antibiotic prescriptions were made from March to June 2017 among 3,401 children in the communities. The frequency of antibiotic prescription was 1.70 prescriptions per child-year (95% CI: 1.61-1.79). Penicillins were the most common (1.04 prescriptions per child-year, 95% CI: 1.01-1.06), followed by sulfonamides (0.69 prescriptions per child-year, 95% CI: 0.67-0.71) and macrolides (0.38 prescriptions per child-year, 95% CI: 0.37-0.40). Continued monitoring of antibiotic consumption in diverse settings will be important to understand the potential for emergence of antibiotic resistance.

Staphylococcus aureus Bacteremia in Children of Rural Areas of The Gambia, 2008-2015

Staphylococcus aureus bacteremia is a substantial cause of childhood disease and death, but few studies have described its epidemiology in developing countries. Using a population-based surveillance system for pneumonia, sepsis, and meningitis, we estimated S. aureus bacteremia incidence and the case-fatality ratio in children <5 years of age in 2 regions in the eastern part of The Gambia during 2008–2015. Among 33,060 children with suspected pneumonia, sepsis, or meningitis, we performed blood culture for 27,851; of 1,130 patients with bacteremia, 198 (17.5%) were positive for S. aureus. S. aureus bacteremia incidence was 78 (95% CI 67–91) cases/100,000 person-years in children <5 years of age and 2,080 (95% CI 1,621–2,627) cases/100,000 person-years in neonates. Incidence did not change after introduction of the pneumococcal conjugate vaccine. The case-fatality ratio was 14.1% (95% CI 9.6%–19.8%). Interventions are needed to reduce the S. aureus bacteremia burden in The Gambia, particularly among neonates.

A Systematic Review and Meta-analysis of the Prevalence of Community-Onset Bloodstream Infections among Hospitalized Patients in Africa and Asia

Community-onset bloodstream infections (CO-BSI) are major causes of severe febrile illness and death worldwide. In light of new data and the growing problem of antimicrobial resistance (AMR) among pathogens causing BSI, we undertook a systematic review of hospital-based studies of CO-BSI among patients hospitalized with fever.

Community-onset bloodstream infections (CO-BSI) are major causes of severe febrile illness and death worldwide. In light of new data and the growing problem of antimicrobial resistance (AMR) among pathogens causing BSI, we undertook a systematic review of hospital-based studies of CO-BSI among patients hospitalized with fever. Without restriction to language or country, we searched PubMed, Web of Science, and Scopus for prospective hospital-based studies of culture-confirmed CO-BSI among febrile inpatients. We determined by study the prevalence of BSI among participants, the pathogens responsible for BSI, and the antimicrobial susceptibility patterns of pathogens causing BSI, according to place and time. Thirty-four (77.3%) of 44 eligible studies recruited 29,022 participants in Africa and Asia combined. Among participants in these two regions, the median prevalence of BSI was 12.5% (range, 2.0 to 48.4%); of 3,220 pathogens isolated, 1,119 (34.8%) were Salmonella enterica, 425 (13.2%) Streptococcus pneumoniae, and 282 (8.8%) Escherichia coli. Antimicrobial susceptibility testing was reported in 16 (36.4%) studies. When isolates collected prior to 2008 were compared to those collected in the period of 2008 through 2018, the proportions of typhoidal Salmonella and Staphylococcus aureus isolates resistant to several clinically relevant antimicrobials increased over time, while S. pneumoniae susceptibility was stable. CO-BSI remain a major cause of severe febrile illness among hospitalized patients in Africa and Asia, with S. enterica, S. pneumoniae, and E. coli predominating. There is a concerning increase in AMR among serious infections caused by community-onset pathogens. Ongoing surveillance is needed to inform empirical management and strategies to control AMR.

C - reactive protein and urinary tract infection due to Gram-negative bacteria in a pediatric population at a tertiary hospital, Mwanza, Tanzania

Introduction

Gram-negative bacteria are the major cause of urinary tract infections (UTI) in children. There is limited data on UTI systemic response as measured using C-reactive protein (CRP). Here, we report the association of CRP and UTI among children attending the Bugando Medical Centre, Mwanza, Tanzania.

Methods

A cross-sectional study was conducted between May and July 2017. Urine and blood were collected and processed within an hour of collection. Data were analyzed using STATA version 13.

Results

Of 250 enrolled children, 76(30.4%) had significant bacteriuria with 56(22.4%, 95%CI; 11.5–33.3) having gram-negative bacteria infection. There was dual growth of gram-negative bacteria in 3 patients. Escherichia coli (32.2%, 19/59) was the most frequently pathogen detected. A total of 88/250(35.2%) children had positive CRP on qualitative assay. By multinomial logistic regression, positive CRP (RRR=4.02, 95%CI: 2.1–7.7, P<0.001) and age ≤ 2years (RRR=2.4, 95%CI: 1.23–4.73, P<0.01) significantly predicted the presence of significant bacteriuria due to gram-negative enteric bacteria.

Conclusion

C-reactive protein was significantly positive among children with UTI due to gram-negative bacteria and those with fever. In children with age ≤ 2 years, positive CRP indicates UTI due to gram-negative enteric bacteria.

Using hospital-based studies of community-onset bloodstream infections to make inferences about typhoid fever incidence

Objectives

Hospital-based studies of community-onset bloodstream infections (CO-BSI) are less resource-intensive to carry out than population-based incidence studies. We examined several metrics capturing the potential role of Salmonella Typhi as a cause of CO-BSI for making inferences about incidence.

Methods

We systematically reviewed three databases for hospital-based studies of CO-BSI. We determined, by study, the prevalence and rank order of Salmonella among pathogenic bloodstream isolates, and the prevalence ratio of Salmonella Typhi to Escherichia coli (S:E ratio). We then describe these hospital-based study metrics in relation to population-based typhoid fever incidence data from a separate systematic review.

Results

Forty-four studies met the inclusion criteria, of which 23 (52.3%) isolated Salmonella Typhi at least once. Among studies isolating Salmonella Typhi, the median (interquartile range) prevalence and rank order of Salmonella Typhi compared to other pathogens isolated in BSI was 8.3% (3.2–37.9%) and 3 (1–6), respectively. The median (interquartile range) S:E ratio was 1.0 (0.4–3.0). With respect to incidence, in Pemba Island, Tanzania, prevalence, rank order, S:E ratio, and incidence was 64.8%, 1, 9.2 and 110 cases per 100 000, respectively, and in Boulkiemdé, Burkina Faso, was 13.3%, 3, 2.3 and 249 cases per 100 000.

Conclusions

We describe considerable variation in place and time for Salmonella Typhi prevalence, rank order, and S:E ratio among hospital-based studies of CO-BSI. Data from simultaneous typhoid prevalence and incidence studies are limited. We propose that hospital-based study metrics warrant evaluation for making inference about typhoid incidence and as covariates in typhoid incidence models.

Ceftriaxone use in a tertiary care hospital in Kilimanjaro, Tanzania: A need for a hospital antibiotic stewardship programme

Excessive use of antibiotics, especially watch group antibiotics such as ceftriaxone leads to emergence and spread of antimicrobial resistance (AMR). In low and middle-income countries (LMICs), antibiotics are overused but data on consumption is scarcely available. We aimed at determining the extent and predictors of ceftriaxone use in a tertiary care university teaching hospital in Kilimanjaro, Tanzania. A hospital-based cross-sectional study was conducted from August 2013 through August 2015. Patients admitted in the medical, surgical wards and their respective intensive care units, receiving antimicrobials and other medications for various ailments were enrolled. Socio-demographic and clinical data were recorded in a structured questionnaire from patients' files and logistic regression was performed to determine the predictors for ceftriaxone use. Out of the 630 patients included in this study, 322 (51.1%) patients were on ceftriaxone during their time of hospitalization. Twenty-two patients out of 320 (6.9%) had been on ceftriaxone treatment without evidence of infection. Ceftriaxone use for surgical prophylaxis was 44 (40.7%), of which 32 (72.7%) and 9 (20.5%) received ceftriaxone prophylaxis before and after surgery, respectively. Three (6.8%) received ceftriaxone prophylaxis during surgery. Predicting factors for that the health facility administered ceftriaxone were identified as history of any medication use before referral to hospital [OR = 3.4, 95% CI (1.0-11.4), p = 0.047], bacterial infection [OR = 18.0, 95% CI (1.4-225.7, p = 0.025)], surgical ward [OR = 2.9, 95% CI (0.9-9.4), p = 0.078] and medical wards [OR = 5.0, 95% CI (0.9-28.3), p = 0.070]. Overall, a high ceftriaxone use at KCMC hospital was observed. Antimicrobial stewardship programs are highly needed to monitor and regulate hospital antimicrobial consumption, which in turn could help in halting the rising crisis of antimicrobial resistance.

Biomarkers of Systemic Inflammation in Ugandan Infants and Children Hospitalized With Respiratory Syncytial Virus Infection

BACKGROUND

Optimizing outcomes in respiratory syncytial virus (RSV) pneumonia requires accurate diagnosis and determination of severity that, in resource-limited settings, is often based on clinical assessment alone. We describe host inflammatory biomarkers and clinical outcomes among children hospitalized with RSV lower respiratory tract infection (LRTI) in Uganda and controls with rhinovirus and pneumococcal pneumonia.

METHODS

58 children hospitalized with LRTI were included. We compared 37 patients with RSV, 10 control patients with rhinovirus and 11 control patients with suspected pneumococcal pneumonia.

RESULTS

Patients in the RSV group had significantly lower levels of C-reactive protein (CRP) and chitinase-3-like protein 1 (CHI3L1) than the pneumococcal pneumonia group (P < 0.05 for both). Among children with RSV, higher admission levels of CRP predicted prolonged time to resolution of tachypnea, tachycardia and fever. Higher levels of CHI3L1 were associated with higher composite clinical severity scores and predicted prolonged time to resolution of tachypnea and tachycardia, time to wean oxygen and time to sit. Higher levels of lipocalin-2 (LCN2) predicted prolonged time to resolution of tachypnea, tachycardia and time to feed. Higher admission levels of all 3 biomarkers were predictive of a higher total volume of oxygen administered during hospitalization (P < 0.05 for all comparisons). Of note, CHI3L1 and LCN2 appeared to predict clinical outcomes more accurately than CRP, the inflammatory biomarker most widely used in clinical practice.

CONCLUSIONS

Our findings suggest that CHI3L1 and LCN2 may be clinically informative biomarkers in childhood RSV LRTI in low-resource settings.

Bacteremia in Childhood Life-Threatening Infections in Urban Gambia: EUCLIDS in West Africa

Background

The limited availability of microbiology services in sub-Saharan Africa impedes accurate diagnosis of bacterial pathogens and understanding of trends in prevalence and antibiotic sensitivities. We aimed to characterize bacteremia among hospitalized children in The Gambia and to identify factors associated with bacteremia and mortality.

Methods

We prospectively studied children presenting with suspected severe infection to 2 urban hospitals in The Gambia, between January 2013 and September 2015. Demographic and anthropometric data, clinical features, management, and blood culture results were documented. Urine screens for antibiotic activity were performed in a subset of participants.

Results

Of 411 children enrolled (median age, 29 months; interquartile range, 11–82), 79.5% (325 of 409) reported prehospital antibiotic use. Antimicrobial activity by urinary screen for antibiotic activity was detected in 70.8% (n = 80 of 113). Sixty-six bacterial pathogens were identified in 65 (15.8%) participants and Staphylococcus aureus predominated. Gram-positive organisms were more commonly identified than Gram-negative (P < .01). Antibiotic resistance against first-line antimicrobials (ampicillin and gentamicin) was common among Gram-negative bacteria (39%; range, 25%–100%). Factors significantly associated with bacteremia included the following: gender, hydration status, musculoskeletal examination findings, admission to the Medical Research Council The Gambia at London School of Hygiene & Tropical Medicine hospital, and meeting sepsis criteria. Those associated with increased mortality were presence of a comorbidity, clinical pallor, tachypnea, and altered consciousness. Tachycardia was associated with reduced mortality.

Conclusions

The bacteremia rate in children with suspected childhood life-threatening infectious diseases in The Gambia is high. The pattern of pathogen prevalence and antimicrobial resistance has changed over time compared with previous studies illustrating the importance of robust bacterial surveillance programs in resource-limited settings.

Assessment of malaria real-time PCR methods and application with focus on low-level parasitaemia

In epidemiological surveys and surveillance the application of molecular tools is essential in detecting submicroscopic malaria. A genus-specific conventional cytochrome b (cytb) PCR has shown high sensitivity in field studies, detecting 70% submicroscopic malaria. The main objective of this study was to assess the conversion from conventional to real-time PCR testing both SYBR and probe protocols, and including quantitative (q) PCR. The protocols were assessed applying well-defined clinical patient material consisting of 33 positive and 80 negative samples. Sequencing of positive PCR products was performed. In addition, a sensitivity comparison of real-time PCR methods was done by including five relevant assays investigating the effect of amplification target and platform. Sensitivity was further examined using field material consisting of 111 P.falciparum positive samples from Tanzanian children (< 5 years), as well as using related patient data to assess the application of q-PCR with focus on low-level parasitaemia. Both the cytb SYBR and probe PCR protocols showed as high sensitivity and specificity as their conventional counterpart, except missing one P. malariae sample. The SYBR protocol was more sensitive and specific than using probe. Overall, choice of amplification target applied is relevant for achieving ultra-sensitivity, and using intercalating fluorescence dye rather than labelled hydrolysis probes is favourable. Application of q-PCR analysis in field projects is important for the awareness and understanding of low-level parasitaemia. For use in clinical diagnosis and epidemiological studies the highly sensitive and user-friendly cytb SYBR q-PCR method is a relevant tool. The genus-specific method has the advantage that species identification by sequencing can be performed as an alternative to species-specific PCR.

Association between antimicrobial resistance among Enterobacteriaceae and burden of environmental bacteria in hospital acquired infections: analysis of clinical studies and national reports

BACKGROUND

WHO has named three groups of gram-negative bacteria "our critical antimicrobial resistance-related problems globally". It is thus a priority to unveil any important covariation of variables behind this three-headed epidemic, which has gained alarming proportions in Low Income Countries, and spreads rapidly. Environmental bacteria including Acinetobacter spp. are common nosocomial pathogens in institutions that have high rates of antimicrobial resistance among other groups of gram-negative bacteria.

METHODS

Based on two different data sources, we calculated the correlation coefficient (Pearson's r) between pathogenic burden of Acinetobacter spp. and antimicrobial resistance among Enterobacteriaceae in European and African nosocomial cohorts.

CLINICAL REPORTS

Database search for studies on nosocomial sepsis in Europe and Africa was followed by a PRISMA-guided selection process.

NATIONAL REPORTS

Data from Point prevalence survey of healthcare-associated infections published by European Centre for Disease Prevention and Control were used to study the correlation between prevalence of Acinetobacter spp. and antimicrobial resistance among K. pneumoniae in blood culture isolates.

FINDINGS

The two approaches both revealed a strong association between prevalence of Acinetobacter spp. and rates of resistance against 3. generation cephalosporins among Enterobacteriaceae. In the study of clinical reports (13 selected studies included), r was 0.96 (0.80-0.99) when calculated by proportions on log scale. Based on national reports, r was 0.80 (0.56-0.92) for the correlation between resistance rates of K. pneumoniae and proportion of Acinetobacter spp.

INTERPRETATION

The critical antimicrobial resistance-related epidemics that concern enteric and environmental gram-negative bacteria are not independent epidemics; they have a common promoting factor, or they are mutually supportive. Further, accumulation of antimicrobial resistance in nosocomial settings depends on the therapeutic environment. Burden of Acinetobacter spp. as defined here is a candidate measure for this dependence.

High prevalence of extended-spectrum beta-lactamase-producing Gram-negative pathogens from patients attending Felege Hiwot Comprehensive Specialized Hospital, Bahir Dar, Amhara region

Background

Infections caused by extended-spectrum beta-lactamases (ESBL) producing Gram-negative bacteria has emerge as a global threat in clinical practices. The treat is more serious in developing countries due to inappropriate use, poor adherence, use of counterfeit, sub-standard antibiotics and poor infection control practices. Data on ESBL producing Gram-negative bacteria are limited in developing countries including Ethiopia. The aim of this study was therefore, to describe the burden of ESBL producing Gram negative pathogens isolated from patients attending at Felege Hiwot Comprehensive Specialized Hospital, Bahir Dar, Amhara region.

Materials and methods

A total of 532 clinical samples of blood, urine, stool, wound, abscess, ear discharge, nasal discharge, cervical discharge and body fluid specimens were aseptically collected and bacteriologically processed. Identification of the bacterial species was performed using an automated system (Vitek-2 Compact 27530, USA) and antibiotic susceptibility test was determined by disk diffusion method and selection of antibiotics were in accordance with CLSI guidelines. The MDR pattern of the Gram-negative pathogens was assessed using phenotypic methods of ESBL and carbapenemase production following standard procedure.

Result

A total of 532 samples were processed and 263 pathogens were isolated. Of these, 185 (70.3%) were Gram-negative and 78 (29.7%) Gram-positive. Of the Gram-negative bacteria the high proportion of the isolates were identified from blood 146/185 (78.9%) and 29/185 (15.7%) were from urine cultures. The most common isolate in all clinical samples was Klebsiella pneumoniae 97/185 (52.4%) followed by Escherichia coli 23/185 (12.4%), Acinetobacter baumannii 15/185 (17.6%) and Enterobacter aerogenes 12/185(6.5%). Of the total Gram negatives, the prevalence of MDR was 148/185 (80.0%). Of the MDR isolates the prevalence of ESBL producers were, 127/148 (85.8%) and 24/148 (16.2%) were carbapenemase producers.

Conclusion and recommendation

Prevalence of MDR and ESBL producing Gram-negative pathogens in this hospital is alarmingly high. Therefore, continuous monitoring of the problem with effective infection prevention and careful selection of empirical therapy are warranted in the study area.

Fecal Colonization With Multidrug-Resistant E. coli Among Healthy Infants in Rural Bangladesh

Third generation cephalosporins (3GC) are one of the main choices for treatment of infections caused by multidrug-resistant (MDR) Gram-negative bacteria. Due to their overuse, an increasing trend of resistance to 3GC has been observed in developing countries. Here, we describe fecal colonization of 3GC-resistant (3GCr) Escherichia coli in healthy infants (1–12 months old) living in rural areas of Bangladesh. We found that stool samples of 82% of infants (n = 100) were positive for 3GCr E. coli with a mean ± standard deviation of 6.21 ± 1.32 log₁₀ CFU/g wet weight of stool. 3GCr E. coli encompasses an average one third (33%) of the total E. coli of stool. Almost 77% (n = 63) of these 3GCr E. coli were MDR (or resistant to ≥3 classes of antibiotics). Around 90% (n = 74) of 3GCr E. coli were extended spectrum beta-lactamase (ESBL)-producing in which bla_{CTX–M–group–1} was the predominant (96%, n = 71) ESBL-gene followed by bla_TEM (41%, n = 30) and bla_OXA–1 (11%, n = 8). A significant proportion (26.5%, n = 22) of 3GCr E. coli was pathogenic, comprising two types, enteroaggregative (EAEC, n = 19) and enteropathogenic (EPEC, n = 3). Colonization of 3GCr E. coli in infant guts was not associated with demographic characteristics such as age, sex, mode of delivery, maternal and infant antibiotic use, disease morbidity, and feeding practices. The high rate of colonization of 3GCr E. coli in infants’ guts is a serious public health concern which needs immediate attention and warrants further studies to explore the cause.