Colonisation of hospital surfaces from low- and middle-income countries by extended spectrum ß-lactamase- and carbapenemase-producing bacteria.

Hospital surfaces can harbour bacterial pathogens, which may disseminate and cause nosocomial infections, contributing towards mortality in low- and middle-income countries (LMICs). During the BARNARDS study, hospital surfaces from neonatal wards were sampled to assess the degree of environmental surface and patient care equipment colonisation by Gram-negative bacteria (GNB) carrying antibiotic resistance genes (ARGs). Here, we perform PCR screening for extended-spectrum ß-lactamases (blaCTX-M-15) and carbapenemases (blaNDM, blaOXA-48-like and blaKPC), MALDI-TOF MS identification of GNB carrying ARGs, and further analysis by whole genome sequencing of bacterial isolates. We determine presence of consistently dominant clones and their relatedness to strains causing neonatal sepsis. Higher prevalence of carbapenemases is observed in Pakistan, Bangladesh, and Ethiopia, compared to other countries, and are mostly found in surfaces near the sink drain. Klebsiella pneumoniae, Enterobacter hormaechei, Acinetobacter baumannii, Serratia marcescens and Leclercia adecarboxylata are dominant; ST15 K. pneumoniae is identified from the same ward on multiple occasions suggesting clonal persistence within the same environment, and is found to be identical to isolates causing neonatal sepsis in Pakistan over similar time periods. Our data suggests persistence of dominant clones across multiple time points, highlighting the need for assessment of Infection Prevention and Control guidelines.

Fecal Carriage of Carbapenem Resistant Enterobacterales and Associated Factors Among Admitted Patients in Saint Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia.

Purpose: The Enterobacterales family colonizes the human gut as normal flora in all age groups, with bacterial infections being the most common cause. Resistance is currently observed in all normal flora. The aim of this study was to determine the frequency of fecal carriage of carbapenem-resistant Enterobacterales (CRE), carbapenemase-producing Enterobacterales (CPE), and associated factors in the faeces of admitted patients. Methods: A cross-sectional study was conducted in Saint Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia. A total of 384 rectal swabs were collected from various wards in admitted patients who have consented to participate. The specimens were inoculated on a MacConkey agar plate, and then they were incubated at 37 °C for 18 to 24 hours. Using the BD PhoenixTM M50 compact system identification and antimicrobial susceptibility testing were performed. Using the modified carbapenem inactivation method, it was determined whether the carbapenem-resistant bacterial isolate produced carbapenemase or not. Results: Overall prevalence of carbapenem-resistant Enterobacterales carriage and carbapenemase producing Enterobacterales in admitted patients was 17.2% (95%, Confidence Interval: 13.3-21.1%) and 7% (95%, Confidence Interval: 4.7-9.9%), respectively. The predominate carbapenem-resistant Enterobacterales in fecal carriage was K. pneumoniae, 15.4% (23/149), E. cloacae 15.4% (6/39), followed by E. coli 12.4% (37/307) of carbapenem-resistant Enterobacterales (CRE) isolate. Carbapenem-resistant Enterobacterales carriage isolates showed large level of resistance to ciprofloxacin, and sulfamethoxazole-trimethoprim. Prior intake of antibiotics (Odds Ratio 2.42, 95% CI: 11.186-4.95) was significantly associated with higher carbapenem-resistant Enterobacterales carriage. Conclusion: We observed a high prevalence of carbapenem-resistant Enterobacterales carriage and carbapenemase-producing Enterobacterales among admitted patients. There were only amikacin and colistin that could be effective for carbapenem-resistant Enterobacterales isolates. Hence, the control of carbapenem-resistant Enterobacterales carriage should be given priority by carbapenem-resistant Enterobacterales screening for fecal of admitted patients, and adhering to good infection prevention practice in hospital settings.

Characterisation of Staphylococci species from neonatal blood cultures in low- and middle-income countries.

BACKGROUND: In low- and middle-income countries (LMIC) Staphylococcus aureus is regarded as one of the leading bacterial causes of neonatal sepsis, however there is limited knowledge on the species diversity and antimicrobial resistance caused by Gram-positive bacteria (GPB). METHODS: We characterised GPB isolates from neonatal blood cultures from LMICs in Africa (Ethiopia, Nigeria, Rwanda, and South Africa) and South-Asia (Bangladesh and Pakistan) between 2015-2017. We determined minimum inhibitory concentrations and performed whole genome sequencing (WGS) on Staphylococci isolates recovered and clinical data collected related to the onset of sepsis and the outcome of the neonate up to 60 days of age. RESULTS: From the isolates recovered from blood cultures, Staphylococci species were most frequently identified. Out of 100 S. aureus isolates sequenced, 18 different sequence types (ST) were found which unveiled two small epidemiological clusters caused by methicillin resistant S. aureus (MRSA) in Pakistan (ST8) and South Africa (ST5), both with high mortality (n = 6/17). One-third of S. aureus was MRSA, with methicillin resistance also detected in Staphylococcus epidermidis, Staphylococcus haemolyticus and Mammaliicoccus sciuri. Through additional WGS analysis we report a cluster of M. sciuri in Pakistan identified between July-November 2017. CONCLUSIONS: In total we identified 14 different GPB bacterial species, however Staphylococci was dominant. These findings highlight the need of a prospective genomic epidemiology study to comprehensively assess the true burden of GPB neonatal sepsis focusing specifically on mechanisms of resistance and virulence across species and in relation to neonatal outcome.

Contraceptive Utilization and Unmet Need for Contraception Among Women Undergoing Treatment for Tuberculosis in Addis Ababa, Ethiopia: a Cross-Sectional Study.

Introduction: Pregnancy can pose a risk to women on tuberculosis (TB) treatment with a threat to the wellbeing of the mother and fetus. Physiological and stress-related effects result when pregnancy occurs during TB illness and while on treatment. Hence, this study aimed to assess contraceptive utilization, unmet need among women on TB treatment, and integration of family planning (FP) services with TB clinics in Addis Ababa, Ethiopia. Methods: A facility-based cross-sectional study was conducted using an interviewer-administered questionnaire. A total of 316 women aged 18-49 who were on TB treatment were enrolled. Contraceptive utilization rate, unmet need, and integration of FP and TB services were determined. Logistic regression models were conducted to identify factors associated with contraceptive utilization. Results: Among women on TB treatment 49 (41.9%) were using contraceptives. Out of contraceptive users, 10 (34.5%) used contraceptives to limit and 18 (62.1%) used to space. Only parity had a significant association with contraceptive utilization. Women who had 1-3 children were less likely to use contraception than those who had ≥4 children. Among women who were married or sexually active, 12 (18.9%) had an unmet need. Of the study participants, 144 (45.6%) had been informed about FP services at the TB clinics. Conclusion: The contraceptive utilization rate in the current study (41.9%) is slightly higher than the national prevalence (36.2%) yet it is still low. Furthermore, the unmet need (18.9%) was lower than the national report for the general population (22%). Educating women about the risk of getting pregnant while visiting the health facility for TB medication will help to improve their chances of better recovery and avoid medication side effects on the fetus. TB guidelines can consider providing FP counseling when initiating treatment to provide women with the power of information to make deliberate decisions.

Neonatal sepsis and mortality in low-income and middle-income countries from a facility-based birth cohort: an international multisite prospective observational study.

BACKGROUND: Neonatal sepsis is a primary cause of neonatal mortality and is an urgent global health concern, especially within low-income and middle-income countries (LMICs), where 99% of global neonatal mortality occurs. The aims of this study were to determine the incidence and associations with neonatal sepsis and all-cause mortality in facility-born neonates in LMICs. METHODS: The Burden of Antibiotic Resistance in Neonates from Developing Societies (BARNARDS) study recruited mothers and their neonates into a prospective observational cohort study across 12 clinical sites from Bangladesh, Ethiopia, India, Pakistan, Nigeria, Rwanda, and South Africa. Data for sepsis-associated factors in the four domains of health care, maternal, birth and neonatal, and living environment were collected for all mothers and neonates enrolled. Primary outcomes were clinically suspected sepsis, laboratory-confirmed sepsis, and all-cause mortality in neonates during the first 60 days of life. Incidence proportion of livebirths for clinically suspected sepsis and laboratory-confirmed sepsis and incidence rate per 1000 neonate-days for all-cause mortality were calculated. Modified Poisson regression was used to investigate factors associated with neonatal sepsis and parametric survival models for factors associated with all-cause mortality. FINDINGS: Between Nov 12, 2015 and Feb 1, 2018, 29 483 mothers and 30 557 neonates were enrolled. The incidence of clinically suspected sepsis was 166·0 (95% CI 97·69-234·24) per 1000 livebirths, laboratory-confirmed sepsis was 46·9 (19·04-74·79) per 1000 livebirths, and all-cause mortality was 0·83 (0·37-2·00) per 1000 neonate-days. Maternal hypertension, previous maternal hospitalisation within 12 months, average or higher monthly household income, ward size (>11 beds), ward type (neonatal), living in a rural environment, preterm birth, perinatal asphyxia, and multiple births were associated with an increased risk of clinically suspected sepsis, laboratory-confirmed sepsis, and all-cause mortality. The majority (881 [72·5%] of 1215) of laboratory-confirmed sepsis cases occurred within the first 3 days of life. INTERPRETATION: Findings from this study highlight the substantial proportion of neonates who develop neonatal sepsis, and the high mortality rates among neonates with sepsis in LMICs. More efficient and effective identification of neonatal sepsis is needed to target interventions to reduce its incidence and subsequent mortality in LMICs. FUNDING: Bill & Melinda Gates Foundation.

Feeding Experiences of HIV-Exposed Preterm Infants Among Mothers Living with HIV in Addis Ababa, Ethiopia: A Qualitative Study.

INTRODUCTION: Providing adequate nutrition to preterm infants who are born to HIV-positive mothers is more challenging due to the mother's underlying health and nutrition status. The understanding of these issues and active participation of the mothers have a significant role in giving continuous care for HIV-exposed preterm infant. Hence, this study aimed to explore the experience of HIV-positive mothers' feeding practice of their preterm infants, and health workers to identify barriers and facilitators of feeding HIV-exposed preterm infants. METHODS: A phenomenological qualitative study design was conducted in Addis Ababa, Ethiopia, between May 1, 2016 and March 31, 2017. Mothers who gave birth to HIV-exposed preterm infants at the study sites' follow-up clinic were traced and invited by the healthcare providers to voluntarily participate in this study. Fifteen in-depth interviews with mothers of HIV-exposed preterm infants and seven key informant interviews with health professionals and policymakers were carried out. The interviews were transcribed and translated and then manually analyzed thematically. RESULTS: The health education given during antenatal care (ANC) did not consider the feeding practice needs for HIV-exposed preterm infants. Child health status, desire to have a healthy infant, financial constraints and family support were among the influential factors in the feeding practice of HIV-exposed preterm infants mentioned by the study participants. HIV-exposed preterm infant feeding procedure neither has a guideline nor is clearly mentioned in the national HIV guidelines. CONCLUSION: The desire to have a healthy infant was a major facilitator for feeding of HIV-exposed premature infants. However, financial constraints majorly limited the option to be only exclusive breastfeeding. This became even more problematic for the mother if the premature infant became ill and could not breastfeed well.

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.

Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries.

Antimicrobial resistance in neonatal sepsis is rising, yet mechanisms of resistance that often spread between species via mobile genetic elements, ultimately limiting treatments in low- and middle-income countries (LMICs), are poorly characterized. The Burden of Antibiotic Resistance in Neonates from Developing Societies (BARNARDS) network was initiated to characterize the cause and burden of antimicrobial resistance in neonatal sepsis for seven LMICs in Africa and South Asia. A total of 36,285 neonates were enrolled in the BARNARDS study between November 2015 and December 2017, of whom 2,483 were diagnosed with culture-confirmed sepsis. Klebsiella pneumoniae (n = 258) was the main cause of neonatal sepsis, with Serratia marcescens (n = 151), Klebsiella michiganensis (n = 117), Escherichia coli (n = 75) and Enterobacter cloacae complex (n = 57) also detected. We present whole-genome sequencing, antimicrobial susceptibility and clinical data for 916 out of 1,038 neonatal sepsis isolates (97 isolates were not recovered from initial isolation at local sites). Enterobacterales (K. pneumoniae, E. coli and E. cloacae) harboured multiple cephalosporin and carbapenem resistance genes. All isolated pathogens were resistant to multiple antibiotic classes, including those used to treat neonatal sepsis. Intraspecies diversity of K. pneumoniae and E. coli indicated that multiple antibiotic-resistant lineages cause neonatal sepsis. Our results will underpin research towards better treatments for neonatal sepsis in LMICs.

Bacterial Isolates and Resistance Patterns in Preterm Infants with Sepsis in Selected Hospitals in Ethiopia: A Longitudinal Observational Study.

Background: Neonatal sepsis is the third leading cause of neonatal mortality, behind prematurity and intrapartum-related complications. The main objectives of this study are to assess the proportion of sepsis in preterm newborns and identify the etiologic agents and their antibiotic sensitivity patterns. Methods: A longitudinal observational study was done from July 2016 to May 2018. Whenever clinical diagnosis of sepsis was made, blood cultures and antibiotic susceptibility tests were done. Result: We did 690 blood cultures, 255 (36.9%) showing bacterial growth. The most commonly isolated bacteria were Klebsiella species 78 (36.6%), Coagulase negative Staphylococcus 42 (19.7%) and Staphylococcus aureus 39 (18.3%). Gram-positive bacteria showed high resistance to penicillin (98.9%) and ceftriaxone (91.3%) whereas Gram-negative bacteria were highly resistant to gentamicin (83.2%) and ceftriaxone (83.2%). Conclusion: Resistance to the more commonly used antibiotics such as ampicillin and gentamycin was very high, necessitating reconsideration of the empiric use of these antibiotics.

Diagnosis and Treatment of Human Salmonellosis in Addis Ababa City, Ethiopia.

BACKGROUND: Diagnosis using reliable tools and treatment following in vitro antimicrobial susceptibility tests are critical to proper addressing of antibiotic-resistant Salmonella infection. METHODOLOGY: A cross-sectional study was conducted to assess the practice of diagnosis and treatment of salmonellosis in Addis Ababa. Tube Widal test (for blood samples only), culture, biochemical and carbohydrate fermentation, serotyping, and antimicrobial susceptibility tests were employed for both blood and stool samples. RESULTS: Of all the diseases listed in the diagnosis, nontyphoidal (n = 72, 13.71%) and typhoidal (n = 47, 8.95%) salmonellosis were the second and third common diseases. Among the 288 blood samples, almost half were positive for O, H, or both antigens. However, only 1 (0.68%) of the positive blood samples yielded Salmonella isolate during culture. The study demonstrated low specificity (0.68%) and positive predictive value (48.78%) of Widal test. Conversely, the test showed 100% sensitivity and negative predictive values. Salmonella isolates were identified from 7 (7.07%) of 99 stool samples. Two-thirds of salmonellosis suspected patients received antibiotic treatment. However, only half of the confirmed salmonellosis patients were treated with appropriate antibiotics. All of the isolates were susceptible to ciprofloxacin and ceftriaxone but resistant to ampicillin. CONCLUSIONS: Majority of the patients who participated in this study were wrongly diagnosed using symptoms, clinical signs, and tube Widal test. Consequently, most of the patients received inappropriate treatment.

In vivo expression of human cytomegalovirus (HCMV) microRNAs during latency.

Viral encoded microRNAs play key roles in regulating gene expression and the life cycle of human herpes viruses. Latency is one of the hallmarks of the human cytomegalovirus (HCMV or HHV5) life cycle, and its control may have immense practical applications. The present study aims to identify HCMV encoded microRNAs during the latency phase of the virus. We used a highly sensitive real time PCR (RTPCR) assay that involves a pre-amplification step before RTPCR. It can detect HCMV encoded microRNAs (miRNAs) during latency in purified monocytes and PBMCs from HCMV IgG positive donors and in latently infected monocytic THP-1 cell lines. During the latency phase, only eight HCMV encoded microRNAs were detected in PBMCs, monocytes and in the THP-1 cells. Five originated from the UL region of the virus genome and three from the US region. Reactivation of the virus from latency, in monocytes obtained from the same donor, using dexamethasone restored the expression of all known HCMV encoded miRNAs including those that were absent during latency. We observed a shift in the abundance of the two arms of mir-US29 between the productive and latency stages of the viral life cycle, suggesting that the star "passenger" form of this microRNA is preferentially expressed during latency. As a whole, our study demonstrates that HCMV expresses during the latency phase, both in vivo and in vitro, only a subset of its microRNAs, which may indicate that they play an important role in maintenance and reactivation of latency.