Exploring the association between unintended pregnancies and unmet contraceptive needs among Ugandan women of reproductive age: an analysis of the 2016 Uganda demographic and health survey.

BACKGROUND: Unintended pregnancy and unmet contraceptive needs pose significant public health challenges, particularly in developing nations, where they contribute to maternal health risks. While previous research has explored determinants of unintended pregnancies, there remains a gap in understanding the association between unplanned pregnancies and unmet contraceptive needs among Ugandan women of reproductive age. This study aimed to assess unmet contraceptive needs and their correlation with unintended pregnancies and other factors in Uganda, utilizing a nationally representative sample. METHODS: Data was extracted from the 2016 Uganda Demographic Health Survey (UDHS), a cross-sectional survey conducted in the latter half of 2016. The study encompassed 18,506 women aged 15-49 with a history of at least one prior pregnancy. The primary outcome variable was the planning status of the most recent pregnancy, while the principal independent variable was unmet contraceptive need. Additional variables were controlled in the analysis. Data analysis was performed using STATA version 17, involving descriptive analysis, cross-tabulation, chi-square testing, and logistic regression. Statistical significance was set at p < 0.05. RESULTS: A substantial proportion of women reported unintended pregnancies (44.5%), with approximately 21.09% experiencing an unmet need for contraception. In the adjusted model, women with unmet contraceptive needs had 3.97 times higher odds of unintended pregnancy (95% CI = 3.61-4.37) compared to those with met contraceptive needs. Significant factors linked to unintended pregnancies included women's age, place of residence, household wealth status, decision-making authority regarding contraceptive use, educational attainment, husband's occupation, and educational level. CONCLUSION: This study revealed that both the rate of unintended pregnancies and unmet contraceptive needs in Uganda exceeded the global average, warranting urgent policy attention. Addressing unmet contraceptive needs emerges as a potential strategy to curtail unintended pregnancies. Further qualitative research may be necessary to elucidate the sociocultural and behavioral determinants of unwanted pregnancies, facilitating context-specific interventions.

Genomic Epidemiology of Carbapenemase-Producing and Colistin-Resistant Enterobacteriaceae among Sepsis Patients in Ethiopia: a Whole-Genome Analysis.

Sepsis due to carbapenemase-producing and colistin-resistant Enterobacteriaceae is a global health threat. A multicenter study was conducted between October 2019 and September 2020 at four hospitals located in different parts of Ethiopia. From a total of 1,416 sepsis patients, blood culture was performed. Enterobacteriaceae were confirmed using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Carbapenem and colistin susceptibility testing was performed using disk diffusion, broth microdilution, and Etest strip. Enterobacteriaceae isolates (n = 301) were subjected to whole-genome sequencing using Illumina HiSeq 2500. SPAdes version 3.9 was used for genome assembly. Carbapenem and colistin resistance genes, chromosomal point mutations, sequence types, and plasmid replicons were identified using tools at the Center for Genomic Epidemiology. Phylogeny structure was constructed using CSI Phylogeny 1.4. Visualization of trees and metadata was done using iTOL v6.5.2. Among 301 Enterobacteriaceae, 22 Klebsiella pneumoniae, 2 Klebsiella variicola, and 3 Enterobacter cloacae isolates showed reduced susceptibility to meropenem (7% of tested isolates). blaNDM-1, blaNDM-5, and blaOXA-181 were variants of carbapenemase genes detected. Co-occurrence of blaNDM-5 and blaOXA-181 was detected with 4 K. pneumoniae strains. K. pneumoniae and K. variicola showed chromosomal alterations of ompK36 and ompk37. Plasmid incompatibility (Inc) groups Col, IncC, IncHI, IncF, IncFII, IncR, and IncX3 were identified among carbapenem-resistant K. pneumoniae and E. cloacae isolates. Two mcr-9 genes were detected from Salmonella species and K. pneumoniae. The dissemination of carbapenemase-producing Enterobacteriaceae in all hospitals is worrying. Multiple carbapenemase genes were detected, with blaNDM variants the most frequent. The occurrence of colistin-resistant Enterobacteriaceae among sepsis patients is critical. Implementation of effective antimicrobial stewardship is urgently needed.

Carbapenemase-producing Aeromonas species isolated from the urban-impacted Akaki river in Ethiopia.

Carbapenemase-producing Aeromonas species are an emerging health threat. This study aimed to determine carbapenemase-mediated resistance among Aeromonas isolates from the Akaki river, Ethiopia during the dry and wet seasons in 2019-2020. Antimicrobial susceptibility to carbapenems and cephalosporins was determined and carbapenemase production was confirmed. Of 163 isolates, the majority were human pathogens Aeromonas caviae (62), Aeromonas hydrophila (33) and Aeromonas veronii (49). These isolates were resistant to carbapenem and cephalosporin antibiotics, with the highest resistance to cefotaxime 86 (59.7%), ertapenem 71 (49.3%) and imipenem 65 (45.1%). Resistance to carbapenem antibiotics varied between species, where most A. veronii 37 (75.5%) and A. hydrophila 28 (84.8%) were resistant to imipenem and all A. caviae were sensitive. A. veronii, A. caviae and A. hydrophila resistance to meropenem was 31 (63.3%), 3 (4.8%) and 19 (57.6%), respectively. Of isolates resistant to carbapenem, 82.1% A. hydrophila and 94.4% A. veronii were carbapenemase producers. Cephalosporin resistance also varied among the different species. The highest resistance to carbapenem antibiotics was in isolates collected during the wet season (p<0.05); however, it was not consistent across all classes of antibiotics tested. The rivers in megacities could be reservoirs of carbapenemase-producing Aeromonas spp.

The Magnitude of Carbapenemase and ESBL Producing Enterobacteriaceae Isolates from Patients with Urinary Tract Infections at Tikur Anbessa Specialized Teaching Hospital, Addis Ababa, Ethiopia.

BACKGROUND: The emergence of multidrug-resistant organisms, such as extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE), and carbapenemase-producing Enterobacteriaceae (CPE) is a public health concern. Therefore, this study aimed to determine the magnitude of carbapenemase and ESBL producing bacteria isolated from patients affected by Urinary Tract Infection (UTI). METHODS: A cross-sectional study was conducted from December 2018 to March 2019 at Tikur Anbessa Specialized Hospital. A total of 120 Enterobacteriaceae isolates from UTI patients were collected and identified on species level using standard microbiological methods. Antimicrobial susceptibility test was determined according to the guidelines of the Clinical and Laboratory Standards Institute. Detection of ESBL production was carried out by using ESBL ChromoSelect Agar medium and the combined disk diffusion. Production of carbapenemase was determined by using Hodge-test and modified carbapenem inactivation method as described in CLSI guidelines. RESULTS: Out of the total 120 Enterobacteriaceae isolates, 74 (61.7%) were ESBL-producers, and 8 (6.7%) were carbapenemase producers. The most common ESBL producing isolate was E.coli 38 (51.4%) and the most common carbapenemase-producing isolate was K.pneumoniae five (62.5%). Most of the ESBL and carbapenemase-producing isolates were recovered from hospitalized patients 46 (62.2%) and 7 (87.5%) respectively. The rate of ESBL and CPE production was observed high among patients taking antibiotics 64.8% (59/91) and 7.7% (7/91) respectively, but no significant association was observed p > 0.05. Furthermore, about 1.7% (2/120) isolates were found both ESBL and carbapenemase producers. Significant resistances rates were observed in ESBL and CPE isolates. CONCLUSION: Enterobacteriaceae isolates showed a significantly higher rate of ESBL production. A significant figure of carbapenemase production was observed among Enterobacteriaceae isolates causing UTI. The production of ESBL and CPE enhanced for an increased rate of MDR patterns. Efforts need to be made to introduce a system for tracking and detecting ESBL-PE and CPE-producing bacteria in hospitals, and monitoring dissemination of ESBL and CPE-producing Enterobacteriaceae is strongly recommended.

Effects of Sub-Minimum Inhibitory Concentrations of Imipenem and Colistin on Expression of Biofilm-Specific Antibiotic Resistance and Virulence Genes in Acinetobacter baumannii Sequence Type 1894.

Antibiotics at suboptimal doses promote biofilm formation and the development of antibiotic resistance. The underlying molecular mechanisms, however, were not investigated. Here, we report the effects of sub-minimum inhibitory concentrations (sub-MICs) of imipenem and colistin on genes associated with biofilm formation and biofilm-specific antibiotic resistance in a multidrug-tolerant clinical strain of Acinetobacter baumannii Sequence Type (ST) 1894. Comparative transcriptome analysis was performed in untreated biofilm and biofilm treated with sub-MIC doses of imipenem and colistin. RNA sequencing data showed that 78 and 285 genes were differentially expressed in imipenem and colistin-treated biofilm cells, respectively. Among the differentially expressed genes (DEGs), 48 and 197 genes were upregulated exclusively in imipenem and colistin-treated biofilm cells, respectively. The upregulated genes included those encoding matrix synthesis (pgaB), multidrug efflux pump (novel00738), fimbrial proteins, and homoserine lactone synthase (AbaI). Upregulation of biofilm-associated genes might enhance biofilm formation when treated with sub-MICs of antibiotics. The downregulated genes include those encoding DNA gyrase (novel00171), 30S ribosomal protein S20 (novel00584), and ribosome releasing factor (RRF) were downregulated when the biofilm cells were treated with imipenem and colistin. Downregulation of these genes affects protein synthesis, which in turn slows down cell metabolism and makes biofilm cells more tolerant to antibiotics. In this investigation, we also found that 5 of 138 small RNAs (sRNAs) were differentially expressed in biofilm regardless of antibiotic treatment or not. Of these, sRNA00203 showed the highest expression levels in biofilm. sRNAs regulate gene expression and are associated with biofilm formation, which may in turn affect the expression of biofilm-specific antibiotic resistance. In summary, when biofilm cells were exposed to sub-MIC doses of colistin and imipenem, coordinated gene responses result in increased biofilm production, multidrug efflux pump expression, and the slowdown of metabolism, which leads to drug tolerance in biofilm. Targeting antibiotic-induced or repressed biofilm-specific genes represents a new strategy for the development of innovative and effective treatments for biofilm-associated infections caused by A. baumannii.

Features of Streptococcus agalactiae strains recovered from pregnant women and newborns attending different hospitals in Ethiopia.

BACKGROUND: Streptococcus agalactiae (Group B Streptococcus, GBS) serotypes, sequence types, and antimicrobial resistance profile vary across different geographic locations affecting disease patterns in newborns. These differences are important considerations for vaccine development efforts and data from large countries in Africa is limited. The aim of this study was to determine serotypes and genotypes of GBS isolates from pregnant women and their newborns in Ethiopia. METHODS: A hospital based cross-sectional study was conducted at three hospitals in Ethiopia from June 2014 to September 2015. Out of 225 GBS isolates, 121 GBS were recovered, confirmed and characterized at CDC's Streptococcus Laboratory using conventional microbiology methods and whole genome sequencing. RESULTS: Of the 121 isolates, 87 were from rectovaginal samples of pregnant women, 32 from different body parts of their newborns and 2 from blood of newborns with suspected sepsis. There were 25 mother-infant pairs and 24 pairs had concordant strains. The most prevalent serotypes among mothers and/or their babies were II, Ia and V (41.5, 20.6, 19.5 and 40.6%, 25 and 15.6%, respectively). Multilocus sequence typing (MLST) on 83 isolates showed ST10 (24; 28.9%) and ST2 (12; 14.5%) as most predominant sequence types. All GBS strains were susceptible to penicillin, cefotaxime and vancomycin, which correlated to the presence of wildtype PBP2x types and the lack of known vancomycin-resistance genes. Tetracycline resistance was high (73; 88%, associated primarily with tetM, but also tetO and tetL). Five isolates (6%) were resistant to erythromycin and clindamycin and 3 isolates were fluoroquinolone-resistant, containing associated mutations in gyrA and parC genes. All isolates were positive for one of four homologous Alpha/Rib family determinants and 1-2 of the three main pilus types. CONCLUSIONS: Predominant serotypes were II, Ia, and V. A limited number of clonal types were identified with two STs accounting for about half of the isolates. All strains collected in this study were susceptible to beta-lactam antibiotics and vancomycin. Typical of most GBS, these isolates were positive for single alpha-like family protein, serine-rich repeat gene, as well as 1-2 pilus determinants.

Bacterial urinary tract infection among adult renal transplant recipients at St. Paul's hospital millennium medical college, Addis Ababa, Ethiopia.

BACKGROUND: Despite significant advances in surgical techniques, immunosuppression protocols, follow up periods and antimicrobial stewardship in modern medicine; post-renal transplantation urinary tract infection remained a major public health problem globally. This multiple serious squeals includes asymptomatic bacteriuria, cystitis and pyelonephritis. Among these, the bacterial origin of infection complications accounts for the most significant clinical, socio-economic impacts in many countries of the world. Therefore, the aim of the study was to investigate the prevalence of bacterial isolates that cause urinary tract infections, assess antibiotic susceptibility pattern among symptomatic and asymptomatic renal transplant recipients attending at St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia. METHODS: A hospital-based cross-sectional study was conducted from December 2017 to August 2018 among 74 renal transplant recipients St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia. A first morning voided clean-catch mid-stream urine specimens were collected and 0.001 ml inoculated onto blood and MacConkey agar plates following the standard bacteriological protocols. It was incubated aerobically at 35-37 °C for 24-48 h. Cultural characteristics and series of biochemical tests were used for the identification of isolates to species level based on the standard bacteriological protocols. RESULTS: A hospital-based cross-sectional study has shown that significant bacteriuria was found in 11/74 (14.9, 95% CI =8.2-24.7) patients. The prevalence among females 6/32 (18.75%) was higher among males 5/42 (11.9%) without significant association (COR = 2.09, 95% CI = 1.04-8.45, P = 0.253). Urinary tract infection was higher in the age group of 35-49 years old (19.3%). Age was statistically significant and stronger independent associated risk factor with crude odds ratio = 3.67, 95% CI = 2.89-20.07 and P = 0.003, respectively. The most prevalent bacteria isolates were Escherichia coli 2(18.2%), Staphylococcus aureus 2(18.2%), Acinetobacter spp. 2(18.2%), Enterococcus spp. 2(18.2%), Coagulase-negative Staphylococci 2(18.2%) followed by Porteus mirabilis 1(9.1%). The majority (80%) of Gram-negative bacteria were resistant to ciprofloxacin, chloramphenicol, and trimethoprim/sulfamethoxazole. Simultaneously, the multidrug-resistant bacterial isolates accounts for 82% among tested kidney allograft recipients. CONCLUSIONS: In conclusion, the overall prevalence of urinary tract infection in the study participants was relatively low with a prevalence of 14.9%. Majority of the study participants were asymptomatic and a higher percentage of females were involved. The multidrug-resistant bacterial isolates in the present study account for 82%.

Household-stored drinking water quality among households of under-five children with and without acute diarrhea in towns of Wegera District, in North Gondar, Northwest Ethiopia.

Contamination of drinking water in household water storage containers and inadequate water supplies are common public burdens in low- and middle-income countries, including towns in Wegera District, Ethiopia. Our study aimed to assess the quality of drinking water and identify factors associated with diarrhea in households with under-five (U5) children with and without diarrhea in Ambagiorgis and Gedebge towns in Wegera District. Stored drinking water samples from households with U5 children with and without diarrhea had fecal coliform (FC) counts of 59 (86.8%) and 55 (82.1%) (p > 0.05) and fecal streptococci (FS) counts of 29 (42.7%) and 24 (35.8%) (p > 0.05), respectively. The very high sanitary risk scores were 32 (47.1%) and 21 (31.3%) for FC (p > 0.05); 25 (36.8%) and 3 (4.5%) for FS (p < 0.001), respectively. Contamination of the stored drinking water samples with FS was significantly higher in households with diarrhetic U5 children in the low- and medium-risk ranges (p < 0.05). Water turbidity of 47 (69.1%) and 23 (34.3%) in households with U5 children with and without diarrhea, respectively, was above the permissible level (p < 0.001). The residual free chlorine (RFC) in all the household-stored drinking water samples was below the World Health Organization (WHO) permissible level and temperatures of all the household-stored drinking water samples were permissible. Promotion and advocacy of good stored drinking water handling practices are essential for decreasing the high risk of microbial contamination in both study areas. We recommend education interventions targeting personal hygiene and drinking water handling at the household level.

Fecal prevalence, serotype distribution and antimicrobial resistance of Salmonellae in dairy cattle in central Ethiopia.

BACKGROUND: Salmonellae are major worldwide zoonotic pathogens infecting a wide range of vertebrate species including humans. Consumption of contaminated dairy products and contact with dairy cattle represent a common source of non-typhoidal Salmonella infection in humans. Despite a large number of small-scale dairy farms in Addis Ababa and its surrounding districts, little is known about the status of Salmonella in these farms. RESULTS: Salmonella was recovered from the feces of at least one animal in 7.6% (10/132) of the dairy farms. Out of 1203 fecal samples examined, 30 were positive for Salmonella resulting in a weighted animal level prevalence of 2.3%. Detection of diarrhea in an animal and in a farm was significantly associated with animal level (p = 0.012) and herd level (p < 0.001) prevalence of Salmonella. Animal level prevalence of Salmonella was significantly associated with age (p = 0.023) and study location; it was highest among those under 6 months of age and in farms from Adaa district and Addis Ababa (p < 0.001). Nine different serotypes were identified using standard serological agglutination tests. The most frequently recovered serotypes were Salmonella Typhimurium (23.3%), S. Saintpaul (20%), S. Kentucky (16.7%) and S. Virchow (16.7%). All isolates were resistant or intermediately resistant to at least one of the 18 drugs tested. Twenty-six (86.7%), 19 (63.3 %), 18 (60%), 16 (53.3%) of the isolates were resistant to streptomycin, nitrofurantoin, sulfisoxazole and tetracycline , respectively. Resistance to 2 drugs was detected in 27 (90%) of the isolates. Resistance to 3 or more drugs was detected in 21 (70%) of the isolates, while resistance to 7 or more drugs was detected in 11 (36.7%) of the isolates. The rate of occurrence of multi-drug resistance (MDR) in Salmonella strains isolated from dairy farms in Addis Ababa was significantly higher than those isolated from farms outside of Addis Ababa (p = 0.009). MDR was more common in S. Kentucky, S. Virchow and S. Saintpaul. CONCLUSION: Isolation of Salmonella serotypes commonly known for causing human salmonellosis that are associated with an MDR phenotype in dairy farms in close proximity with human population is a major public health concern. These findings imply the need for a strict pathogen reduction strategy.

Throat culture positivity rate and antibiotic susceptibility pattern of beta-hemolytic streptococci in children on secondary prophylaxis for rheumatic heart disease.

BACKGROUND: Among children diagnosed to have chronic rheumatic valvular heart disease (RHD) in Ethiopia, many have been observed to develop recurrence of rheumatic fever (RF) despite secondary prophylaxis. This study determined the throat culture positivity rate and drug susceptibility pattern of beta hemolytic streptococci (BHS) isolated from children attending a specialized cardiac clinic in Ethiopia. METHODS: Throat swabs were collected from 233 children receiving benzathine penicillin injection as secondary prophylaxis for RHD and cultured. The bacterial isolates were characterized using Matrix Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) mass spectrometry. Drug susceptibility was tested with the Kirby Bauer disc diffusion method. Anti-streptolysin O (ASO) titers were determined using ASO latex reagents. RESULTS: The throat culture positivity rate for BHS was 24 % (56/233). Among the BHS bacterial strains isolated, four were characterized as S. pyogenes and another four as S. dysgalactiae subsp. equisimilis (Lancefield group A, C and G). All BHS were susceptible to penicillin except one isolate of S. agalactiae. Among 233 children enrolled, 46(19.7 %) showed increased ASO titer. Children who received antibiotic prophylaxis within 2-weeks of last injection had significantly lower BHS throat culture positivity rate than those injected every 4-weeks (p = 0.02). Children who missed at least one prophylaxis within the last 6 months had a higher BHS culture positivity rate than those who did not miss any (p = 0.0003). CONCLUSIONS: The presence of groups A, C and G streptococci in the throat of children under secondary prophylaxis for RHD and increased ASO titer suggests failure of the regimen. This calls for further investigation into the causes of inadequate prophylaxis (including bioavailability of drugs used, optimal duration and patient compliance) and intervention.

Non-typhoidal Salmonella serotypes, antimicrobial resistance and co-infection with parasites among patients with diarrhea and other gastrointestinal complaints in Addis Ababa, Ethiopia.

BACKGROUND: Non-typhoidal Salmonella (NTS) is an important public health problem worldwide. Consumption of animal-derived food products and direct and/or indirect contact with animals are the major routes of acquiring infection with NTS. Published information, particularly on the serotype distribution of NTS among human patients with gastroenteritis and associated risk factors, is scarce in Ethiopia. This study investigated the prevalence, risk factors, serotype distribution and antimicrobial susceptibility of Salmonella species among diarrheic out-patients attending health centers in Addis Ababa and patients with various gastrointestinal complaints at Tikur Anbessa Specialized Hospital (TASH). METHODS: Stool samples were cultured for Salmonella species according to the WHO Global Foodborne Infections Network laboratory protocol. Salmonella serotyping was conducted using slide agglutination and microplate agglutination techniques. Antibiotic susceptibility testing was performed using the disk diffusion method according to Clinical and Laboratory Standards Institute guidelines. RESULTS: A total of 59 (6.2 %) stool samples, out of 957 were culture positive for Salmonella species. Fifty-five (7.2 %) of 765 diarrheic patients from health centers and 4 (2.1 %) of 192 patients from TASH were culture positive for Salmonella species. Multivariable logistic regression analysis after adjusting for all other variables revealed statistically significant association of Salmonella infection with consumption of raw vegetables (OR = 1.91, 95 % CI = 1.29-2.83, χ(2) = 4.74, p = 0.025) and symptom of watery diarrhea (OR = 3.3, 95 % CI = 1.23-8.88, χ(2) = 10.54, p = 0.005). Eleven serotypes were detected, and the most prominent were S. Typhimurium (37.3 %), S. Virchow (34 %), and S. Kottbus (10.2 %). Other serotypes were S. Miami, S. Kentucky, S. Newport, S. Enteritidis, S. Braenderup, S. Saintpaul, S. Concord and S. V:ROUGH-O. Resistance to three or more antimicrobials was detected in 27 (40.3 %) of the isolates. Resistance to five or more antimicrobials was detected in 17 (25.4 %). Resistance to individual antimicrobials was found at varying proportions: streptomycin (50; 74.6 %), nitrofurantoin (27; 40.3 %), sulfisoxazole (26; 38.8 %), kanamycin (23; 34.3 %), cephalothin (12; 17.9 %), and ampicillin (11; 16.4 %) respectively. Two S. Kentucky, one S. Typhimurium and one S. Concord isolates were multi-drug resistant to more than 10 antimicrobials. CONCLUSIONS: The study demonstrated significant association of Salmonella infection with consumption of raw vegetables. There was no significant association of Salmonella infection with co-occurring parasites. The study also showed the dominance of S. Typhimurium and S. Virchow in primary health care units. Overall, prevalence of MDR was low compared to previous studies. Although their proportion was low, S. Kentucky and S. Concord demonstrated wider spectrum of MDR. Continuous monitoring of circulating serotypes, antimicrobial resistance profile and characterization on molecular resistance determinants is essential for proper treatment of patients and for identifying potential environmental origins of antimicrobial resistance.

Association of multicellular behaviour and drug resistance in Salmonella enterica serovars isolated from animals and humans in Ethiopia.

AIMS: To determine the association between multicellular behaviour, integron status and antibiotic resistance among 87 Ethiopian Salmonella enterica isolates of animal and human origin. METHODS AND RESULTS: Isolates were characterized for their biofilm forming ability, antimicrobial susceptibility and the presence and characteristics of a class 1 integron and Salmonella genomic island 1 (SGI1). The majority of isolates grown at environmental temperatures (20°C) exhibited robust biofilm formation (72·4%) and displayed RDAR colony morphology on Congo red agar plates. The presence of a class 1 integron correlated with the extent of drug resistance and ability to exhibit multicellular behaviour. CONCLUSIONS: Although cellulose production and RDAR morphology correlated with increased multicellular behaviour, neither was required for biofilm formation. Contrary to previous reports, colony morphology was generally consistent within a serovar. No integrons were detected in isolates deficient for multicellular behaviour, indicating a potential role of bacterial community formation in transfer of genetic elements among environmental isolates. SIGNIFICANCE AND IMPACT OF STUDY: Infection by Salm. enterica is a major public health problem worldwide. The dominance of multidrug resistance and multicellular behaviour in Salmonella isolates of Ethiopian origin highlights a need for integrated surveillance and further detailed phenotypic and molecular studies of isolates from this region.

The pattern of bacterial isolates and drug sensitivities of infected ulcers in patients with leprosy in ALERT, Kuyera and Gambo hospitals, Ethiopia.

INTRODUCTION: Leprosy remains a public health problem, mainly in Africa, Asia and Latin America. Leprosy has many complications that include leprosy reactions, development of plantar and hand ulcerations, lagophthalomus and corneal anesthesia. OBJECTIVES: In Ethiopia there is scarce information on the pattern of bacterial isolates and drug sensitivities of infected ulcers in patients with leprosy. This study was undertaken to identify the bacteriology of infected ulcers and to determine their antimicrobial susceptibility pattern. STUDY DESIGN: A descriptive cross-sectional study was conducted in 245 informed and consented leprosy patients with infected ulcers visiting ALERT, Kuyera and Gambo hospitals during the period August 2006 to May 2007. MATERIAL AND METHODS: Wound aspirate specimens were collected from ulcers of each patient aseptically and inoculated into standard bacteriological media. Antimicrobial susceptibility testing was performed for all isolates according to the criteria of the National Committee for Clinical Laboratory Standards (NCCLS) by disk diffusion method. RESULTS: Of the 245 patients investigated, 64.1% were males and 35.9% females (P < 0.05). The average age of the patients was 50 years (age range 13 to 92 years). According to Ridley-Jopling classifications, patients presented with TT (3.7%), BT, (31.4%), BL (44.5%) and LL (15.9%) types of leprosy. Plantar and hand ulcers were observed in 92.2% and 7.8% of patients, respectively. According the patients, the commonest cause of their ulcers was 'spontaneous' (56.7%). There were 44% Gram-positive and 56% Gram negative bacteria (P > 0.05). Proteus spp. accounted for 29.5% of the total isolates followed by Staphylococcus spp. (28.8%), beta-hemolytic streptococci (15.1%) and different types of Gram-negative bacteria (26.2%). Multiple organisms (two or three) were isolated from 19.6% patients. Of the 212 wound samples cultured anaerobically, 5.2% were positive for anaerobic culture. In this study both Gram-positive and Gram negative bacteria showed decreased sensitivity to most antimicrobial agents tested. CONCLUSION: Proteus spp. was the most common isolate from infected ulcers. Ciprofloxacin, norfloxacin and gentamicin were the most effective drugs against the tested bacteria mainly for Gram-negative bacteria. This refers to the in vitro-sensitivity during the study period. The results of this study may help inform clinicians about the selection of an antibiotic in situations where use of an antibiotic may be indicated.

Molecular epidemiology and antimicrobial susceptibility of Pseudomonas spp. and Acinetobacter spp. from clinical samples at Jimma medical center, Ethiopia.

Introduction: Pseudomonas aeruginosa (P. aeruginosa) and Acinetobacter baumannii (A. baumannii) can cause difficult-to-treat infections. We characterized molecular epidemiology of ceftazidime-resistant P. aeruginosa and carbapenem-resistant A. baumannii at a tertiary hospital in Ethiopia. Materials and methods: Non-fermenting gram-negative bacilli (n = 80) isolated from admitted patients were subjected for species identification by MALDI-TOF. Pseudomonas species resistant to ceftazidime or meropenem, and Acinetobacter species resistant to meropenem, or imipenem were selected for whole genome sequencing. DNA extracted with EZ1 Advanced XL instrument (Qiagen, Hilden, Germany) was sequenced on Illumina (HiSeq2500) using libraries prepared by NEXTRA-kits (Illumina). Raw reads were assembled using SPAdes 3.13.0, and assembled genomes were used to query databases for resistome profile and sequence types. Result: Among Pseudomonas species isolated, 31.7% (13/41), and 7.3% (3/41) were non-susceptible to ceftazidime, and meropenem, respectively. Carbapenem-resistance was 56.4% (22/39) among Acinetobacter species. Moreover, 92% (12/13) of Pseudomonas species non-susceptible to ceftazidime and/or meropenem, and 89.4% (17/19) of Acinetobacter species encoded multiple resistance genes for at least three classes of antimicrobials. The prevalent ß - lactamase genes were bla OXA-486 (53.8%, 7/13), bla CTX-M-15 (23.0%, 3/13) among Pseudomonas, and bla GES-11 (57.8%, 11/19) among Acinetobacter. The bla OXA-51-like ß - lactamase, bla OXA-69 (63.1%, 12/19) was the most prevalent carbapenemase gene among Acinetobacter isolates. Single isolates from both P. aeruginosa, and A. baumannii were detected with the bla NDM-1. Sequence type (ST)1 A. baumannii and ST274 P. aeruginosa were the prevalent sequence types. A cgMLST analysis of the ST1 A. baumannii isolates showed that they were closely related and belonged to the international clonal complex one (ICC1). Similarly, ST274 P. aeruginosa isolates were clonally related. Conclusion: The prevalence of MDR isolates of Pseudomonas and Acinetobacter spp. was high. A. baumannii isolates were clonally spreading in the admission wards at the hospital. Emergence of bla NDM-1 in the intensive care, and surgical wards of the hospital is a severe threat that requires urgent intervention.

Molecular Epidemiology of Extended-Spectrum Beta-Lactamase and AmpC Producing Enterobacteriaceae among Sepsis Patients in Ethiopia: A Prospective Multicenter Study.

Extended-spectrum beta-lactamases (ESBLs) and AmpC producing Enterobacteriaceae are public health threats. This study aims to characterize ESBL and AmpC producing Enterobacteriaceae isolated from sepsis patients. A multicenter study was conducted at four hospitals located in central (Tikur Anbessa and Yekatit 12), southern (Hawassa) and northern (Dessie) parts of Ethiopia. Blood culture was performed among 1416 sepsis patients. Enterobacteriaceae (n = 301) were confirmed using MALDI-TOF and subjected for whole genome sequencing using the Illumina (HiSeq 2500) system. The overall genotypic frequencies of ESBL and AmpC producing Enterobacteriaceae were 75.5% and 14%, respectively. The detection of ESBL producing Enterobacteriaceae at Hawassa, Yekatit 12, Tikur Anbessa and Dessie was 95%, 90%, 82% and 55.8%, respectively. The detection frequency of blaCTX-M, blaTEM and blaSHV genes was 73%, 63% and 33%, respectively. The most frequently detected ESBL gene was blaCTX-M-15 (70.4%). The common AmpC genes were blaACT (n = 22) and blaCMY (n = 13). Of Enterobacteriaceae that harbored AmpC (n = 42), 71% were ESBL co-producers. Both blaTEM-1B (61.5%) and blaSHV-187 (27.6%) were the most frequently detected variants of blaTEM and blaSHV, respectively. The molecular epidemiology of ESBL producing Enterobacteriaceae showed high frequencies and several variants of ESBL and AmpC genes. Good antimicrobial stewardship and standard bacteriological laboratory services are necessary for the effective treatment of ESBL producing Enterobacteriaceae.

Polyclonal spread of blaCTX-M-15 through high-risk clones of Escherichia coli at a tertiary hospital in Ethiopia.

OBJECTIVES: The burden of antimicrobial resistance and spread of epidemic clones are rarely reported from low-income countries. We aimed to investigate the genome-based epidemiology of extended-spectrum ß-lactamase-producing Escherichia coli (ESBL-EC) at a tertiary hospital in Jimma, Ethiopia. METHODS: Bacteria were isolated from clinical specimens at Jimma Medical Center and subjected to species identification (MALDI-TOF), antimicrobial susceptibility testing (disk diffusion) and whole-genome sequencing (Illumina, HiSeq2500). Genomic data analysis was performed using EnteroBase and Center for Genomic Epidemiology bioinformatics pipelines. A maximum likelihood tree was generated using FastTree/2.1.8 based on single nucleotide polymorphisms (SNPs) in shared genomic regions to identify transmission clusters. RESULTS: Escherichia coli isolates (n = 261) were collected from 1087 single non-duplicate clinical specimens over a 5-month period in 2016. The prevalence of ESBL-EC was 54.8% (143/261), 96% of which were resistant to multiple antibiotic classes. The blaCTX-M-15 ESBL gene was present in 88.4.% of isolates (122/138). Genes conferring resistance to aminoglycosides and ciprofloxacin [aac(6')-Ib-cr, 62.3% (86/138)], phenicols [catB3, 56.5% (78/138)], sulfonamides [sul1, 68.1% (94/138), trimethoprim [dfrA17, 58.0% (80/138)] and macrolides [mph(A), 67.4% (93/138) were detected. The most prevalent sequence types were ST410 (23%), ST648 (17%), ST131 (10%) and ST167 (7%). Isolates of the same sequence type collected from different units of the hospital were highly similar in the SNP analysis. CONCLUSION: A high prevalence of ESBLs and dissemination of blaCTX-M-15 through multiple high-risk E. coli clones was detected. Nosocomial spread of multidrug-resistant ESBL-EC within the hospital puts vulnerable patients at risk of difficult-to-treat infections.

Rabies research in Ethiopia: A systematic review.

Rabies is an important zoonosis in Ethiopia, where lack of research is cited as a constraint to implementation of the national rabies control strategy. We conducted a systematic review of publications and theses on rabies in Ethiopia, to document research gaps and areas of knowledge saturation in relation to geographic and species focus, methods and findings. We also examined funding sources and extent of local researcher participation. After screening titles and abstracts, the full text of 119 publications was included in data extraction. More than 40% of publications involved data collection in one region (Oromia); no publications reported findings from Benishangul-Gumuz, Dire Dawa or Gambella. Dogs and wildlife (especially Canis simensis) were the focus of research in 45% and 24% publications, respectively. Descriptive epidemiology (N = 39 publications), ethno-medicine/-pharmacology (N = 17) and knowledge, attitude, and practice surveys (KAP, N = 15) were amongst the most common study designs, while studies involving economic methods (N = 3) and experimental epidemiology to test interventions (N = 3) were under-represented. Incidence surveys (N = 9) commonly used post-exposure prophylaxis administration in humans as a proxy for exposure without laboratory confirmation of the rabies status of the animal. KAP surveys tended to highlight reasonable levels of knowledge of rabies and poor practices, including overreliance on medicinal plants. International researchers were the first or last (senior) author on 42% and 58% of publications, respectively, most of which were funded by international organizations (45/72 publications reporting funding source). Based on this systematic review, we suggest more applied research is needed to address gaps in laboratory surveillance (including in humans, domestic and wild animals); identify effective ways to overcome socio-cultural and other barriers to accessing effective rabies treatments; inform best approaches to incentivizing mass dog vaccination programs; and generate local estimates of the cost-benefit and cost-effectiveness of different control strategies to improve financing and political buy-in for rabies control in Ethiopia.

Antimicrobial resistance genes in microbiota associated with sediments and water from the Akaki river in Ethiopia.

The spread of antimicrobial-resistant pathogens is a global health concern. Most studies report high levels of antimicrobial resistance genes (ARGs) in the aquatic environment; however, levels associated with sediments are limited. This study aimed to investigate the distribution of ARGs in the sediments and water of the Akaki river in Addis Ababa, Ethiopia. The diversity and abundance of 84 ARGs and 116 clinically important bacteria were evaluated from the sediments and water collected from five sites in the Akaki river. Most of the ARGs were found in the city close to anthropogenic activities. Water samples collected in the middle catchment of the river contained 71-75% of targeted ARGs, with genes encoding aminoglycoside acetyltransferase (aac(6)-Ib-cr), aminoglycoside adenylyl transferase (aadA1), ß-lactamase (blaOXA-10), quinolone resistance S (qnrS), macrolide efflux protein A (mefA), and tetracycline resistance (tetA), were detected at all sampling sites. Much fewer ARGs were detected in all sediments, and those near the hospitals had the highest diversity and level. Despite the lower levels and diversity, there were no unique ARGs detected in the sediments that were also not detected in the waters. A wide range of clinically relevant pathogens were also detected in the Akaki river. The findings suggest that the water phase, rather than the sediments in the Akaki river, is a potential conduit for the spread of ARGs and antibiotic-resistant bacteria.

Prevalence and Molecular Characterization of Extended Spectrum ß-Lactamase and Carbapenemase-Producing Enterobacteriaceae Isolates from Bloodstream Infection Suspected Patients in Addis Ababa, Ethiopia.

Background: Production of Extended spectrum beta-lactamase (ESBL) and Carbapenemase is the most common strategy for drug resistance in clinical isolates of Enterobacteriaceae. This study was conducted to determine the magnitude of ESBL and Carbapenemase production (CPE) among clinical isolates of Enterobacteriaceae causing bloodstream infections (BSI) in Ethiopia. Methods: A cross-sectional study was performed from September 2018 to January 2019 in Ethiopia. A total of 2397 BSI suspected patients were enrolled and blood culture was performed using a BacT/Alert instrument in combination with conventional methods for identification. After antimicrobial susceptibility test, phenotypic confirmation of ESBLs was done by combined disc-diffusion. Meanwhile carbapenemase production was done by modified carbapenem inactivation method. Multiplex PCR was conducted to detect the presence of bla CTX-M,bla SHV, bla TEM, bla KPC and bla NDM genes. Results: A total of 104 (4.3%) Enterobacteriaceae were isolated from 2397 BSI suspected patients. Klebsiella pneumoniae (55/104, 52%) was the predominant isolate followed by E. coli, (19.2%, 20/104) and K.oxytoca (17.3%, 18/104). ESBL and carbapenemase production were observed from 70 (67.3%, 57.4 -76.2% at 95% CI) and 8 (7.7%, 3.4-14.6% at 95% CI) isolates respectively. The highest frequency of ESBL and carbapenemase production was observed in K. pneumoniae 78.2% (43/55) and 9.1% (5/55), respectively. All the 70 isolates confirmed as ESBL producers harbored at least one of the ESBL genes and the majority of them carried multiple beta-lactamase genes (84.3%), where bla CTX-M, type was the most predominant (67.3%). Similarly, the entire eight isolates positive for carbapenemase carried bla NDM but none of them carried bla KPC. Conclusion: In our study, the rate of ESBL production among BSI-causing Enterobacteriaceae was alarming and most of the isolates carried multiple types of ESBL genes. A significant magnitude of CPE isolates causing BSI was recorded.

High Magnitude of Fecal Carriage of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae at Debre Berhan Comprehensive Specialized Hospital, Ethiopia.

Background: Gastrointestinal colonization rate of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) is the major risk factor for infection and dissemination of resistance clones in healthcare facilities. This study aimed to investigate the magnitude of the fecal carriage of ESBL-PE and associated factors among hospitalized patients at Debre Berhan Comprehensive Specialized Hospital, North Shoa, Amhara Regional State, Ethiopia. Methods: A hospital-based cross-sectional study was conducted among 383 hospitalized patients from November 2020 to March 2021. Stool sample or rectal swab was aseptically collected and cultured on different culture media for isolation of Enterobacteriaceae. Identification was done by conventional biochemical tests. Screening of extended-spectrum beta-lactamase (ESBL) production was done by using cefotaxime and ceftazidime and confirmed by the combination disk method. Data analysis was performed by Statistical Package for Social Sciences software version 25 and a P-value ≤0.05 was considered as statistically significant. Results: From the total of 383 hospitalized patients, a total of 347 Enterobacteriaceae were isolated. The overall gastrointestinal colonization rate of ESBL-PE was 47.3% (164/347). The predominant ESBL-PE were E. coli 54.9% (90/164) and K. pneumoniae 33.5% (55/164). The overall multi-drug resistance rate (MDR) was 87.8% (305/347). The highest resistance was observed to ampicillin (98.3%), followed by gentamicin (80.7%), and tetracycline (73.3%), respectively. ESBL-PE were highly susceptible to meropenem (90.2%) and imipenem (89.0%). History of antibiotic use in the past 3 months (p<0.001), admission in the neonatal intensive care unit (p=0.023), and presence of chronic disease (p<0.001) were independently associated with fecal carriage of ESBL-PE. Conclusion: The magnitude of ESBL-PE and MDR was high in the study area. Meropenem and imipenem were active against ESBL-PE. Therefore, strict infection control measure is needed in the study area to limit the infection and dissemination of ESBL-PE.