Antimicrobial susceptibility pattern, and associated factors of Salmonella and Shigella infections among under five children in Arba Minch, South Ethiopia

Characteristics of Nontyphoid Salmonella Isolated from Human, Environmental, Animal, and Food Samples in Burkina Faso: A Systematic Review and Meta-Analysis

Salmonella is one of the world's leading causes of zoonotic and foodborne illnesses. Recently, antimicrobial resistance (AMR) has become one of the most critical challenges to public health and food safety. Herein, we employed a meta-analysis to determine the pooled prevalence and spatiotemporal distribution of serovars and antimicrobial resistance in NTS in Burkina Faso. To find eligible articles, a comprehensive literature search of PubMed, African Journals Online, ScienceDirect, Google Scholar, and the gray literature (university libraries) in Burkina was conducted for the period from 2008 to 2020. Studies meeting the inclusion criteria were selected and assessed for risk of bias. To assess the temporal and spatial relationships between serotypes and resistant strains from humans, animals, food, and the environment, a random-effects statistical model meta-analysis was carried out using the Comprehensive Meta-Analysis Version 3.0 program. The NTS prevalence rates were 4.6% (95% CI: 3-7) and 20.1% (95% CI: 6.6-47.4) in humans and animals, respectively, and 16.8% (95% CI: 10.5-25.8) and 15.6% (95% CI: 8.2-27.5) in food and the environment, respectively. Most NTS serovars were S. Derby, reported both in food and animals, and S. Typhimurium, reported in humans, while S. Croft II, S. Jodpur II, and S. Kentucky were the most prevalent in the environment. NTS isolates were highly resistant to erythromycin, amoxicillin, cefixime, and cephalothin, with a pooled prevalence of multidrug resistance of 29% (95% CI: 14.5-49.5). The results of this review show a high diversity of Salmonella serotypes, as well as high antibiotic resistance in Salmonella isolates from animal, human, food, and environmental samples in Burkina, calling for a consolidated "One Health" approach to better understand the drivers of pathogen emergence, spread, and antimicrobial resistance, as well as the formulation of intervention measures needed to limit the risk associated with the disease.

Prevalence of multidrug resistance Salmonella species isolated from clinical specimens at University of Gondar comprehensive specialized hospital Northwest Ethiopia: A retrospective study

BACKGROUND

Multidrug resistance Salmonellosis remains an important public health problem globally. The disease is among the leading causes of morbidity and mortality in developing countries, but there have been limited recent studies about the prevalence, antimicrobial resistance, and multidrug resistance patterns of Salmonella isolates from various clinical specimens.

OBJECTIVE

Aimed to assess the prevalence, antimicrobial resistance, and multidrug resistance patterns of Salmonella isolates from clinical specimens at the University of Gondar Comprehensive Specialised Hospital, northwestern Ethiopia.

METHOD

A retrospective hospital-based cross-sectional study was conducted to determine the prevalence, antimicrobial resistance, and multidrug resistance patterns of isolated from all clinical specimens at the University of Gondar Salmonella Comprehensive Specialised Hospital from June 1st, 2017 to June 3rd, 2022. A total of 26,154 data points were collected using a checklist of records of laboratory registration. Clinical specimens were collected, inoculated, and incubated for about a week with visual inspection for growth and gram staining. The isolates were grown on MacConkey agar and Xylose Lysine Deoxycholate agar. Pure colonies were identified with a conventional biochemical test, and those unidentified at the species level were further identified by the analytical profile index-20E. Then, antimicrobial susceptibility was determined by the Kirby-Bauer disc diffusion technique. The multidrug resistance Salmonella isolates was identified using the criteria set by Magiorakos. Finally, the data was cleaned and checked for completeness and then entered into SPSS version 26 for analysis. Then the results were displayed using tables and figures.

RESULTS

Of the total 26,154 Salmonella suspected clinical samples, 41 (0.16%) Salmonella species were isolated. Most of the Salmonella isolates, 19 (46.3%), were in the age group of less than 18 years, followed by the age group of 19-44 years, 11 (26.8%). In this study, S. enterica subsp. arizonae accounts for the highest 21 (51%), followed by S. paratyphi A 9 (22%). Of the Salmonella isolates, S. typhi were highly resistant to ampicillin (100%), followed by tetracycline and trimethoprim-sulfamethoxazole, each accounting for 83.3%. Furthermore, S. paratyphi A was resistant to ampicillin (100%), tetracycline (88.9%), and chloramphenicol (88.9%). The overall multi-drug resistance prevalence was 22 (53.7%; 95% CI: 39.7-61). Accordingly, S. paratyphi A was 100% multidrug-resistant, followed by S. typhi (66.6%).

CONCLUSION

A low prevalence of Salmonella species was observed in the past six years. Moreover, most S. typhi and S. paratyphi strains in the study area were found to be resistant to routinely recommended antibiotics like ciprofloxacin and ceftriaxone, compared to what was reported earlier. In addition, all isolates of S. paratyphi A and the majority of S. typhi were multidrug resistant. Therefore, health professionals should consider antimicrobial susceptibility tests and use antibiotics with caution for Salmonellosis management.

Prevalence, associated factors and antimicrobial susceptibility patterns of Salmonella and Shigella species among diarrheic under five children in Sultan Sheik Hassan Yabere referral Hospital, Jigjiga, Eastern Ethiopia

BACKGROUND

Diarrhea caused by Salmonella and Shigella species are the leading cause of illness especially in developing countries. These infections are considered as the main public health problems in children, including Ethiopia. This study aimed to assess the prevalence, associated factors, and antimicrobial susceptibility patterns of Salmonella and Shigella species in Sheik Hassan Yabere Referral Hospital Jigjiga, Eastern Ethiopia from August 05 to November 15, 2022.

METHOD

A cross-sectional study was conducted among 239 under-five children with diarrhea selected through a convenient sampling technique. A structured questionnaire was used to collect associated factors. A stool sample was collected and processed for the identification of Salmonella and Shigella species using MacConkey adar, Xylose Lysine Deoxycholate agar (Oxoid Ltd) and Biochemical tests. The antimicrobial susceptibility pattern of isolates was performed using the Kirby-Bauer disc diffusion technique. The data was entered into Epi-data version 4.6 and exported to the statistical package of social science version 22 for analysis. The association between outcome and independent variables was assessed using bivariate, multivariable, and chi-square and P-value < 0.05 was considered as statistical significance.

RESULT

Overall prevalence of Salmonella and Shigella species was 6.3% (95% CI, 5.7-6.9%), of which 3.8% (95 CI, 3.2-4.4%) were Salmonella species and 2.5% (95% CI, 1.95-3%) were Shigella species. Unimproved water source (AOR = 5.08, 95% CI = 1.45, 17.25), open field (AOR = 2.3, 95% CI = 1.3, 5.03), rural residence (AOR = 1.8, 95% CI = 1.4, 7.5), Hand-washing practice (p = 0.001), and raw meat consumption (p = 0.002) were associated with occurrence of Salmonella and Shigella species. Salmonella and Shigella isolates were resistant to Ampicilin (100%). However, Salmonella isolates was sensitive to Norfloxacin (100%). About 22.2% and 16.7% of Salmonella and Shigella isolates were multi-drug resistant, respectively.

CONCLUSION

Prevalence of Salmonella and Shigella species were lower than most studies done in Ethiopia. Hand-washing habit, water source type, Open field waste disposal habit, raw meat consumption and rural residence were associated with Salmonellosis and shigellosis. All isolated Salmonella were sensitive to norfloxacin. The evidence from this study underscores the need for improved water, sanitation and hygiene (WASH) system and the imperative to implement drug susceptibility tests for the treatment of Salmonella and Shigella infection.

Fluoroquinolone resistance determinants in carbapenem-resistant Escherichia coli isolated from urine clinical samples in Thailand

Background

Escherichia coli is the most common cause of urinary tract infections and has fluoroquinolone (FQ)-resistant strains, which are a worldwide concern.

Objectives

To characterize FQ-resistant determinants among 103 carbapenem-resistant E. coli (CREc) urinary isolates using WGS.

Methods

Antimicrobial susceptibility, biofilm formation, and short-read sequencing were applied to these isolates. Complete genome sequencing of five CREcs was conducted using short- and long-read platforms.

Results

ST410 (50.49%) was the predominant ST, followed by ST405 (12.62%) and ST361 (11.65%). Clermont phylogroup C (54.37%) was the most frequent. The genes NDM-5 (74.76%) and CTX-M-15 (71.84%) were the most identified. Most CREcs were resistant to ciprofloxacin (97.09%) and levofloxacin (94.17%), whereas their resistance rate to nitrofurantoin was 33.98%. Frequently, the gene aac(6')-Ib (57.28%) was found and the coexistence of aac(6')-Ib and blaCTX-M-15 was the most widely predominant. All isolates carried the gyrA mutants of S83L and D87N. In 12.62% of the isolates, the coexistence was detected of gyrA, gyrB, parC, and parE mutations. Furthermore, the five urinary CREc-complete genomes revealed that blaNDM-5 or blaNDM-3 were located on two plasmid Inc types, comprising IncFI (60%, 3/5) and IncFI/IncQ (40%, 2/5). In addition, both plasmid types carried other resistance genes, such as blaOXA-1, blaCTX-M-15, blaTEM-1B, and aac(6')-Ib. Notably, the IncFI plasmid in one isolate carried three copies of the blaNDM-5 gene.

Conclusions

This study showed FQ-resistant determinants in urinary CREc isolates that could be a warning sign to adopt efficient strategies or new control policies to prevent further spread and to help in monitoring this microorganism.

A Systematic review on Prevalence, Serotypes and Antibiotic resistance of Salmonella in Ethiopia, 2010-2022

Background

In Ethiopia, salmonellosis is one of the most common zoonotic and foodborne illnesses. Ethiopia continues to be at risk for its fast-expanding medication resistance. For the development of preventative and control methods, summarized knowledge regarding salmonellosis is necessary. Determining a thorough evaluation of the prevalence, serotypes, and antibiotic resistance of Salmonella in humans and animals from January 1, 2010, to December 30, 2022, in Ethiopia was our goal.

Methods

To find Salmonella related articles that published in English, we used the Google Scholar and PubMed search engines. Three researchers conducted the eligible studies using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist, making sure to include the necessary keywords. If studies were duplicates, incomplete publications, or reported without an antimicrobial test were excluded. Excel 2013 was used to calculate frequencies and tabulate data.

Results

There were a total of 43 investigations from food handlers, diarrhoeic patients, and animals. The prevalence rates ranged from 1% to 10% and 1% to 13% among food handlers and diarrhoea patients, respectively. The highest prevalence was among pigs (41.6%). S. Anatum in animals and S. Typhimurium in people were the predominant serotypes. Amoxicillin and ampicillin were claimed to be 100% resistant in human studies. The highest recorded resistances for ceftriaxone and ciprofloxacin were 16.7% and 100%, respectively. Animal studies revealed that Salmonella resistances to ampicillin, streptomycin and tetracycline were 100%, 90%, 86.4%, respectively. S. Kentucky showed complete resistance to tetracycline, ampicillin, gentamicin, ciprofloxacin, and streptomycin.

Conclusion

The prevalence of Salmonella among asymptomatic food handlers, diarrheal patients and animals were high in Ethiopia. S. Typhimurium that have the zoonotic importance was presented predominantly in human study. High levels of resistances were showed to tetracycline, ampicillin and streptomycin in animal studies. Salmonellosis prevention and control techniques should be strengthened.

Occurrence of Diarrheagenic Pathogens and Their Coinfection Profiles in Diarrheic Under Five Children and Tracked Human Contacts in Urban and Rural Settings of Eastern Ethiopia

Diarrheagenic Escherichia coli, Campylobacter, Nontyphoidal Salmonella, and Shigella are common cause of childhood diarrhea in countries like Ethiopia, but data on their sources and coinfection profiles is limited. A cross sectional study was conducted from November 2021 to January 2023 to determine the prevalence, coinfection, and monthly occurrence rates of major diarrheagenic bacteria in diarrheic under five children and asymptomatic contacts at urban and rural settings in Ethiopia. A total of 345 stool samples were collected from; 262 diarrheic children visiting Hiwot Fana Hospital, Kersa, and Adelle Health Centers; and 83 caretakers and siblings through case based contact tracing. Samples were analyzed using standard laboratory procedures and the overall prevalence of enteric pathogens was 26.96%, with the highest isolation rate during the winter and peaks of 73.91% in February. The occurrence of the pathogens in children and tracked contacts was 27.86 and 24.09%, respectively. In our study, 8.53% coinfection and 23.66% single pathogen infection was recorded in diarrheic children. The study also showed 4.51 and 3.88% of diarrhea in children from urban and rural had attributed to bacterial coinfection, respectively. The most prevalent pathogen in diarrheic children was Diarrheagenic E. coli (10.31%), and followed by Campylobacter. On the other hand, Diarrheagenic E. coli was the second dominant bacteria following Shigella in the traced contacts, with prevalence of 8.43% and 9.64%, respectively. Based on the study site, the prevalence of Diarrheagenic E. coli and Nontyphoidal Salmonella was higher in children from urban than those from rural. However, the occurrence of each pathogen had no significant differences (P > .05) between settings. The high pathogens occurrence rate in the current study indicates the need for strong control strategies and better child carrying and treatment of diarrheal diseases at both urban and rural settings. Further studies on possible sources and factors attributing to the occurrence of enteric pathogens in children are also recommended.

Prevalence and Antimicrobial-Resistant Features of Shigella Species in East Africa from 2015-2022: A Systematic Review and Meta-Analysis

Background

Shigellosis is the most common cause of epidemic dysentery found worldwide, particularly in developing countries, where it causes infant diarrhea and mortality. The prevalence of Shigella species resistant to commonly used antimicrobial drugs has steadily increased. The purpose of this review is to describe the prevalence and antimicrobial resistance (AMR) characteristics of Shigella species in East Africa between 2015 and 2022.

Methods

Studies were identified using a computerized search of Medline/PubMed, Google Scholar, and Web of Science databases, with a detailed search strategy and cross-checking of reference lists for studies published between 2015 and 2022. Articles presenting data on prevalence and AMR, accessibility of the full-length article, and publication dates between 2015 and 2022 were the eligibility criteria for inclusion in the review. Original research reports written in English were considered. The heterogeneities of the studies were examined, and a meta-analysis was performed to estimate the pooled prevalence and AMR using a random effects model.

Results

The pooled prevalence of Shigella species in East Africa was 6.2% (95% CI -0.20-12.60), according to an analysis of 22 studies. Shigella species prevalence was 4.0% in Ethiopia, 14.6% in Kenya, 0.7% in Sudan, 5.2% in South Sudan, and 20.6% in Somalia. The association of Shigella infection significantly varied among the countries (p = 0.01). Among the antibiotics tested, most Shigella isolates were susceptible to ciprofloxacin, norfloxacin, nalidixic acid, and ceftriaxone. Despite the fact that the reports varied in study sites and time, Shigella species were resistant to tetracycline, ampicillin, amoxicillin, chloramphenicol, and co-trimoxazole.

Conclusion

The pooled estimate indicates high burden of Shigella infection in East Africa, as well as a high proportion of drug resistance pattern to tetracycline, ampicillin, chloramphenicol, and amoxicillin. Therefore, initiating and scale-up of performing drug susceptibility test for each shigellosis case need to be considered and strengthened.

Antimicrobial Susceptibility Patterns of Shigella Species among Children under Five Years of Age with Diarrhea in Selected Health Centers, Addis Ababa, Ethiopia

Background

Shigella and parasitic infections are common public health problems throughout the world. Shigellosis is an acute gastroenteritis infection and one of Ethiopia's most common causes of morbidity and mortality, especially in children under five. High resistance rates to commonly used antibiotic agents have been documented in different locations in Ethiopia.

Objective

This study aimed to characterize the antimicrobial features of the Shigella species isolated from children under five years of age with acute diarrhea in Addis Ababa, Ethiopia.

Methods

Using a cross-sectional study, freshly passed fecal specimens were collected for intestinal parasite and bacterial isolation. Fecal samples for bacterial identification were placed immediately in Cary-Blair media and transported to the Ethiopian Public Health Institution (EPHI) laboratory. Antimicrobial susceptibility testing (AMST) was conducted using the disk diffusion method. Data were described using descriptive statistical tools. The association of independent and dependent variables was evaluated with logistic regression. A P value ≤0.05 was considered statistically significant.

Results

The prevalence of intestinal parasites was 8.2% with seven different species. Among the 534 stool-cultured specimens, 47 (8.8%) were positive for Shigella species. Antimicrobial susceptibility testing (AMST) showed that 100%, 93.6%, 80.9%, 72.3%, and 57.5% were susceptible to norfloxacin, nalidixic acid, ciprofloxacin, gentamicin, and cefoxitin, respectively. However, 100% of the isolates were resistant to amoxicillin and erythromycin. More than 50% of the isolates were resistant to three and above antibiotics, while none of them were susceptible to all the antibiotics tested. All risk factors assessed did not show a statistically significant association with Shigella infection.

Conclusion

The high levels of antibiotic resistance observed among the commonly prescribed antibiotics are alarming. The emerging resistance to ciprofloxacin and nalidixic acid signals a severe public health threat in the management of shigellosis. Raising awareness about resistance and educating health professionals, policymakers, and the public can help improve the quality of patient care and rational antibiotic use.

Antibiotic resistance trends for common bacterial aetiologies of childhood diarrhoea in low- and middle-income countries: A systematic review

Background

Diarrhoea is the second most common cause of death among children under the age of five worldwide. The World Health Organization (WHO) recommends treating diarrhoea with oral rehydration therapy, intravenous fluids for severe dehydration, and zinc supplements. Antibiotics are only recommended to treat acute, invasive diarrhoea. Rising antibiotic resistance has led to a decrease in the effectiveness of treatments for diarrhoea.

Methods

A systematic literature review in PubMed, Web of Science, and EMBASE was conducted to identify articles relevant to antibiotic-resistant childhood diarrhoea. Articles in English published between 1990 to 2020 that described antibiotic resistance patterns of common pathogens causing childhood diarrhoea in low- and middle-income countries were included. The studies were limited to papers that categorized children as 0-5 years or 0-10 years old. The proportion of isolates with resistance to major classes of antibiotics stratified by major WHO global regions and time was determined.

Results

Quantitative data were extracted from 44 articles that met screening criteria; most focused on children under five years. Escherichia coli isolates had relatively high resistance rates to ampicillin and tetracycline in the African (AFR), American (AMR), and Eastern Mediterranean Regions (EMR). There was moderate to high resistance to ampicillin and third generation cephalosporins among Salmonella spp in the AFR, EMR, and the Western Pacific Region (WPR). Resistance rates for ampicillin, co-trimoxazole, and chloramphenicol for Shigella in the AFR started at an alarmingly high rate ( ~ 90%) in 2006 and fluctuated over time. There were limited antibiotic resistance data for Aeromonas, Yersinia, and V. cholerae. The 161 isolates of Campylobacter analysed showed initially low rates of fluoroquinolone resistance with high rates of resistance in recent years, especially in the Southeast Asian Region.

Conclusions

Resistance to inexpensive antibiotics for treatment of invasive diarrhoea in children under ten years is widespread (although data on 6- to 10-year-old children are limited), and resistance rates to fluoroquinolones and later-generation cephalosporins are increasing. A strong regional surveillance system is needed to carefully monitor trends in antibiotic resistance, future studies should include school-aged children, and interventions are needed to reduce inappropriate use of antibiotics for the treatment of community-acquired, non-invasive diarrhoea.

Registration

This systematic review was registered in Prospero (registration number CRD42020204004) in August 2020.

Prevalence of enteric bacterial pathogens in diarrheic under-five children and their association with the nutritional status in Bahir Dar Zuria District, Northwest Ethiopia

BACKGROUND

Diarrheal disease is one of the leading causes of child mortality in low and middle-income countries. Low nutritional status and bacterial infections contribute to growth deficiency and death in children. But there is a gap in identifying the bacterial etiology of diarrheal diseases and their association with the nutritional status of under-five children. This study aimed to determine the bacterial etiology of diarrheal diseases and their association with the nutritional status of diarrheic under-five children.

METHODS

A cross-sectional study was carried out from February 2021 to March 2022 at seven Health Centers in Bahir Dar Zuria district, Ethiopia. A total of 196 diarrheic under-five children visiting the health centers were included in the study. Stool samples were collected from each child for the isolation of Salmonella, Shigella, and E.coli O157:H7. The demographic characteristics and symptoms of children were obtained from parents/guardians. The weight, height, and age of each child were recorded and anthropometric indices were determined by WHO Anthro version 3.2.2 software. The association between bacterial prevalence and the nutritional status of children was analyzed by SPSS version 26 software using Binary logistic regression. All analyses were conducted at a 95% confidence interval and significant association was determined using a p-value < 0.05.

RESULTS

Of the total children included in the study, 13.1% had either E.coli O157:H7, Shigella, or Salmonella. Watery diarrhea and fever were the most clinical characteristics observed in children who are positive for enteric bacteria. The prevalence of stunted, underweight, and wasted was 56.6%, 24.4%, and 13.2% respectively. Children with wasting were significantly associated with Salmonella detection (OR = 7.2, CI, 1.38-38.1, P = 0.02) whereas stunted and underweight were not associated with bacterial prevalence.

CONCLUSION

Overall, the prevalence of bacterial pathogens in the study area is high. Stunting, wasting, and being underweight are important nutritional deficits of diarrheic under-five children in the study site. Further studies targeting possible sources of bacteria and determinants of malnutrition in children are suggested. Health sectors found in the district should increase their effort to enhance good nutritional practice through health education and treatment of malnourished children by the provision of micronutrients.

Prevalence, antimicrobial resistance pattern, and associated factors of Salmonella and Shigella among under five diarrheic children attending public health facilities in Debre Markos town, Northwest Ethiopia

Background

Under five children are at risk of diarrhea-associated morbidity and mortality. Salmonella and Shigella are major causes of diarrhea in under-five children, especially in developing countries. This study aimed to assess the prevalence, antimicrobial resistance pattern, and associated factors of Salmonella and Shigella among under-five diarrheic children in Debre Markos town public health facilities.

Methods

A cross-sectional study was conducted at public health facilities in Debre Markos town using a consecutive convenient sampling technique. Data on socio-demographic and associated factors were collected using a structured questionnaire. Salmonella serovars and Shigella species were identified using MacConkey, Xylose Lysine Deoxycholate, Salmonella Shigella agar, and biochemical tests. The antimicrobial resistance pattern was determined by using the modified Kirby-Bauer disk diffusion technique.

Results

The overall prevalence of Salmonella and Shigella was 11.7% (26/222; 95% CI = 7.2-17.5%). Isolated Salmonella serovars showed a higher rate of resistance (85.7%, 6/7) for both Ampicillin and Amoxicillin/Clavulanic acid while Shigella isolates showed a higher resistance rate to Amoxicillin/Clavulanic acid (78.9%, 15/19) and Ampicillin (73.7%, 14/19). The overall multidrug resistance (MDR) rate of Salmonella and Shigella isolates was 88.5% (23/26). Parent/guardian educational status ≤ elementary school (AOR = 3.783; 95% CI = 1.28-11.19; P = 0.016), presence of two or more under-five children in the family (AOR = 8.999; 95% CI = 2.93-27.69; P < 0.001), unimproved source of drinking water (AOR = 5.010; 95% CI = 1.56-16.10; P = 0.007), the habit of storing cooked foods for later use (AOR = 3.199; 95% CI = 1.07-9.54; P = 0.037), attendance of the child at social gatherings (AOR = 5.387; 95% CI = 1.78-16.35; P = 0.003), and infrequent child fingernail trimming (every ≥ 2 weeks; AOR = 4.693; 95% CI = 1.47-14.94; P = 0.009) showed statistically significant association with the prevalence of culture-confirmed Salmonella and Shigella isolates.

Conclusion

The prevalence of culture-confirmed Salmonella and Shigella isolates was significantly high in the study area. Salmonella and Shigella isolates exhibited a high rate of MDR pattern. Parent/guardian education level below the elementary school, the presence of two or more under-five children in the family, using unimproved water source, a habit of storing cooked food, and infrequent fingernail trimming were independent predictors of culture-confirmed Salmonella and Shigella. Therefore, besides public health measures, regular surveillance of the prevalence and antimicrobial resistance pattern of Salmonella and Shigella should be routinely practiced in the study setting.

Prevalence and drug resistance patterns of Gram-negative enteric bacterial pathogens from diarrheic patients in Ethiopia: A systematic review and meta-analysis

Background

Diarrhoea is the leading cause of morbidity and mortality in the world particularly in developing countries and among vulnerable groups of the population. Gram-negative enteric bacterial pathogens (GNEBPs) are a group of organisms that reside mainly in the intestine and induce diarrhoea. Antimicrobial agents are usually the part of their treatment regimen. The therapeutic effect of antimicrobials is hindered by the emergence and spread of drug-resistant strains. The information regarding the prevalence and antimicrobial resistance patterns of GNEBPs in Ethiopia is limited and found in a scattered form.

Objectives

This study was designed to determine the pooled prevalence and drug resistance patterns of GNEBPs by meta-analysis of data from diarrhoeic patients in Ethiopia.

Method

A comprehensive literature search was conducted through internet searches using Google Scholar, PubMed, Science Direct, HINARI databases, and reference lists of previous studies. Published articles were included in the study based on priorly set inclusion and exclusion criteria. Results were presented in the forest plot, tables, and figures with a 95% confidence interval (CI). The inconsistency index (I²) test statistics was used to assess heterogeneity across studies. The pooled prevalence estimate of GNEBPs and their drug resistance patterns were computed by a random-effects model. Software for Statistics and Data Science (STATA) version 14 statistical software was used for the analysis.

Result

After removing those articles which did not fulfil the inclusion criteria, 43 studies were included in the analysis. Studies were conducted in 8 regions of the country and most of the published articles were from the Amhara region (30.23%) followed by Oromia (18.60%) and Southern Nations, Nationalities, and Peoples’ region (SNNP) (18.60%). The pooled prevalence of GNEBPs was 15.81% (CI = 13.33–18.29). The funnel plot indicated the presence of publication bias. The pooled prevalence of GNEBPs in Addis Ababa, Amhara, SNNP, and Oromia regions were 20.08, 16.67, 12.12, and 11.61%, respectively. The pooled prevalence was 14.91, 18.03, and 13.46% among studies conducted from 2006–2010, 2011–2015, and 2016–2021, respectively and it was the highest (20.35%) in children having age less than or equal to 15 years. The pooled prevalence of Escherichia coli, Campylobacter spp., Shigella spp., and Salmonella enterica were 19.79, 10.76, 6.24, and 5.06%, respectively. Large proportions (60–90%) of the isolates were resistant to ampicillin, amoxicillin, tetracycline, and trimethoprim-sulphamethoxazole. The pooled prevalence of multidrug resistance (MDR) was 70.56% (CI = 64.56–76.77%) and MDR in Campylobacter spp., Shigella spp., E. coli, and S. enterica. were 80.78, 79.08, 78.20, and 59.46%, respectively.

Conclusion

The pooled estimate showed a high burden of GNEBPs infections and a high proportion of drug resistance characters to commonly used antimicrobial agents in Ethiopia. Therefore, performing drug susceptibility tests, establishing an antimicrobial surveillance system and confirmation by molecular techniques are needed.

Prevalence and epidemiological distribution of selected foodborne pathogens in human and different environmental samples in Ethiopia: a systematic review and meta-analysis

Bacterial Foodborne Pathogens (FBP) are the commonest cause of foodborne illness or foodborne diseases (FBD) worldwide. They contaminate food at any stages in the entire food chain, from farm to dining-table. Among these, the Diarrheagenic Escherichia coli (DEC), Non typhoidal Salmonella (NTS), Shigella spp. and Campylobacter spp. are responsible for a large proportion of illnesses, deaths; and, particularly, as causes of acute diarrheal diseases. Though existing studies indicate the problem may be severe in developing countries like Ethiopia, the evidence is commonly based on fragmented data from individual studies. A review of published and unpublished manuscripts was conducted to obtain information on major FBP and identify the gaps in tracking their source attributions at the human, animal and environmental interface. A total of 1753 articles were initially retrieved after restricting the study period to between January 2000 and July 2020. After the second screening, only 51 articles on the humans and 43 on the environmental sample based studies were included in this review. In the absence of subgroups, overall as well as human stool and environmental sample based pooled prevalence estimate of FBP were analyzed. Since, substantial heterogeneity is expected, we also performed a subgroup analyses for principal study variables to estimate pooled prevalence of FBP at different epidemiological settings in both sample sources. The overall random pooled prevalence estimate of FBP (Salmonella, pathogenic Escherichia coli (E. coli), Shigella and Campylobacter spp.) was 8%; 95% CI: 6.5-8.7, with statistically higher (P <  0.01) estimates in environmental samples (11%) than in human stool (6%). The subgroup analysis depicted that Salmonella and pathogenic E. coli contributed to 5.7% (95% CI: 4.7-6.8) and 11.6% (95% CI: 8.8-15.1) respectively, of the overall pooled prevalence estimates of FBD in Ethiopia. The result of meta-regression showed, administrative regional state, geographic area of the study, source of sample and categorized sample size all significantly contributed to the heterogeneity of Salmonella and pathogenic E. coli estimates. Besides, the multivariate meta- regression indicated the actual study year between 2011 and 2015 was significantly associated with the environmental sample-based prevalence estimates of these FBP. This systematic review and meta-analysis depicted FBP are important in Ethiopia though majority of the studies were conducted separately either in human, animal or environmental samples employing routine culture based diagnostic method. Thus, further FBD study at the human, animal and environmental interface employing advanced diagnostic methods is needed to investigate source attributions of FBD in one health approach.

Complete genome analysis of the newly isolated Shigella sonnei phage vB_SsoM_Z31

This work describes the characterization and genome annotation of the newly isolated lytic phage vB_SsoM_Z31 (referred to as Z31), isolated from wastewater samples collected in Dalian, China. Transmission electron microscopy revealed that phage Z31 belongs to the family Myoviridae, order Caudovirales. This phage specifically infects Shigella sonnei, Shigella dysenteriae, and Escherichia coli. The genome of the phage Z31 is an 89,355-bp-long dsDNA molecule with a G+C content of 38.87%. It was predicted to contain 133 ORFs and encode 24 tRNAs. No homologs of virulence factor genes or antimicrobial resistance genes were found in this phage. Based on the results of nucleotide sequence alignment and phylogenetic analysis, phage Z31 was assigned to the genus Felixounavirus, subfamily Ounavirinae.

Magnitude, risk factors and antimicrobial susceptibility pattern of Shigella and Salmonella, among children with diarrhea in Southern Ethiopia: A Cross-sectional Study

Objective:

This study was aimed at identifying Shigella and Salmonella infection, their antibiotic susceptibility pattern and associated risk factors among children with diarrhea who attended Alamura Health Center.

Method:

A facility-based cross-sectional study was conducted on 263 children aged below 14 years with diarrhea. A structured questionnaire was used to collect socio-demographic and clinical data after obtaining the necessary consent from their parents or caretakers. The culture and sensitivity tests were performed using the standard operating procedure of the microbiology laboratory.

Results:

Accordingly, 20/263 (7.6%), 95% confidence interval: 4.4%–11.4% Shigella and 1/263 (0.38%), 95% confidence interval: 0.0%–1.1% Salmonella were isolated. Shigella dysenteriae was dominant 11 (4.2%), followed by Shigella spp. 9 (3.42%) and Salmonella typ 1 (0.38%). The isolates showed 71.4% overall resistance to ampicillin and 61.9% for augmentin and tetracycline, whereas 95.2% of the isolates were sensitive to ciprofloxacin, 85.9% to ceftriaxone and ceftazidime, 81% to gentamycin, 76.2% to chloramphenicol, 66.7% to cefuroxime and 52.4% to cotrimoxazole. The habit of washing hands after toilet use for a while (adjusted odds ratio: 235.1, 95% confidence interval: 20.9–2643.3, p < 0.000) and storing cooked food in an open container for later use (adjusted odds ratio: 36.44, 95% confidence interval: 5.82–228.06, p < 0.000) showed a statistically significant association.

Conclusion:

High level of Shigella and single Salmonella was isolated. Ampicillin, augmentin and tetracycline were resistant and ciprofloxacin, ceftriaxone, ceftazidime, gentamycin, chloramphenicol, cefuroxime and cotrimoxazole were relatively sensitive. Hand-washing after defecation for some time and storing of foods for later use in an open container were statistically associated. Therefore, to alleviate this infection, the concerned body should focus on imparting health education for hand-wash after defecation and storing food in a closed container for later use is mandatory.

Prevalence, Risk Factors, and Antibiogram of Nontyphoidal Salmonella from Beef in Ambo and Holeta Towns, Oromia Region, Ethiopia

Background

Salmonella has been recognized as a major cause of food-borne illness associated with the consumption of food of animal origin. The present cross-sectional study was conducted from December 2017 to May 2018 in Ambo and Holeta towns to assess the prevalence, risk factors, and antimicrobial susceptibility patterns of nontyphoidal Salmonella isolates from raw beef samples from abattoirs, butchers, and restaurants in Ambo and Holeta towns, Oromia region, Ethiopia.

Methods

A total of 354 beef samples were collected from abattoirs, butchers, and restaurants. Salmonella isolation and identification were carried out using standard bacteriological methods recommended by the International Organization for Standardization. Antimicrobial susceptibility testing was performed using the disk diffusion method. Besides, a structured questionnaire was used to collect sociodemographic data and potential risk factors for contamination of meat. Chi-square tests and logistic regression were used for data analyses.

Results

Of the total 354 meat samples examined, 20 (5.7%, 95% confidence interval (CI): 3.5–8.6) were positive for Salmonella. Two serotypes belonging to S. typhimurium (11 isolates) and I:4,5,12: i:- (9 isolates) were identified. The Salmonella detection rate in abattoirs, butchers, and restaurants was 4.2% (5/118), 8.5% (10/118), and 4.2% (5/118), respectively. The antimicrobial susceptibility test showed that 40%, 30%, and 20% of the Salmonella isolates were resistant to azithromycin, amoxicillin, and ceftriaxone, respectively. The odds of Salmonella isolation when meat handlers are illiterate were 7.8 times higher than those when they are educated to the level of secondary and above (P=0.032). Similarly, the likelihood of Salmonella isolation was 6.3 and 7.6 times higher among workers of butcher and restaurants, respectively, who had no training (P=0.003) and no knowledge (P=0.010) on food safety and hygiene.

Conclusions

The study showed widespread multidrug-resistant Salmonella isolates in the study areas. Therefore, raw meat consumption and indiscriminate use of antimicrobial drugs should be discouraged. Provision of food safety education for meat handlers and further surveillance of antimicrobial-resistant isolates are suggested.

Prevalence and antimicrobial resistance patterns of Salmonella isolates in human stools and animal origin foods in Ethiopia: A systematic review and meta-analysis

OBJECTIVE

Foodborne diseases caused by non-typhoid Salmonella and the emergence of antimicrobial resistance remain as a public health challenge, especially in developing countries. The current study aimed to estimate the pooled prevalence and the antimicrobial resistance patterns of non-typhoid Salmonella in Ethiopia.

METHODS

Literature search was conducted from major electronic databases and indexing services. Both published and unpublished studies addressing the prevalence and antimicrobial resistance profiles of Salmonella in Ethiopia from 2010 to 2020 and those studies reported sample size and the numbers of isolates/number of positive samples were included in the study. Data were extracted using format prepared in Microsoft Excel. The identified data were exported to EndNote to remove duplicated studies, then after the remained articles were screened using title, abstract, and full text to identify studies that meet the inclusion criteria and finally appraised for methodological validity using JBI guideline. The pooled prevalence of Salmonella and its drug resistance pattern was computed by a random-effects model. I2 test statistic was used to test heterogeneity across studies. The presence of publication bias was evaluated using the Begg's and Egger's tests.

RESULTS

A total of 49 eligible articles, 33 of them on human stools, 15 of them on animal origin foods, and one both on human stools and animal origin foods, were included in the study. The pooled prevalence of Salmonella among human stools and animal origin foods in Ethiopia was 4.8% (95% CI: 3.9, 5.9) and 7.7% (95% CI: 5.6, 10.4), respectively. The subgroup analysis detected high pooled prevalence, 7.6% (95% CI: 5.3, 10.7) among outpatients and low, 3.7% (95% CI: 2.6, 5.1) in food handlers. The pooled resistant level of Salmonella was 80.6% (95% CI 72.6, 86.7) for ampicillin and 63.5% (95% CI 53.7, 72.4) for tetracycline. Low pooled resistance pattern was reported in ciprofloxacin, 8.7% (95% CI 5.6, 13.3) and ceftriaxone 12.2% (95% CI 7.9, 18.3). There was some sort of publication bias.

CONCLUSION

High pooled prevalence of Salmonella among human stools and animal origin foods which were 4.8% and 7.7% respectively, and high Salmonella resistance, >72% to ampicillin and tetracycline were detected in Ethiopia. Antimicrobial stewardship efforts and infection control strategies are required to mitigate this major public health concern.

Prevalence of Escherichia coli in Under-Five Children with Diarrhea in Ethiopia: A Systematic Review and Meta-Analysis

Diarrhea remains as a high health burden, especially to children in low-income countries including Ethiopia. Diarrheagenic Escherichia coli have been commonly associated as bacterial pathogens causing diarrheal disease among children. This systemic review and meta-analysis was intended to determine the pooled prevalence of Escherichia coli in under-five children with diarrhea in Ethiopia. A comprehensive search in PubMed, Google Scholar, ScienceDirect, ResearchGate, and Google search engine and manual searching were done for this systematic review and meta-analysis. The eligibility criteria for selecting studies were studies involving under-five children with diarrhea in Ethiopia, published articles, cross-sectional studies, and articles reported in English. The study was conducted based on the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) checklist. The data analysis was done using STATA 16.0 software. Cochran's Q-test and I 2 statistics were used for the assessment of heterogeneity. The random-effect model was used to estimate the pooled prevalence of Escherichia coli. A total of 797 articles were initially retrieved, and finally, 11 studies met the eligibility criteria and were included in the final meta-analysis. The pooled prevalence of Escherichia coli was 25% (95% CI: 9, 41). The pooled prevalence was varied by region, detection method, and sample size. The high prevalence emphasizes that Escherichia coli is a potential pathogen in under-five children with diarrhea in Ethiopia.

Antibiotic resistance patterns of Staphylococcus aureus, Escherichia coli, Salmonella, Shigella and Vibrio isolated from chicken, pork, buffalo and goat meat in eastern Nepal

Objective

Food-borne pathogens are a major cause of illnesses, death and expenses. Their occurrence in meat and other food is considered a global health problem. The burden of food-borne disease is increasing due to antimicrobial resistance which represents a greater risk of treatment failure. However, very little is known about the antibiotic resistance profile of food-borne pathogens in Nepal. This study was conducted to examine the antibiotic resistance profile of common food-borne bacterial pathogens isolated from raw meat sold in Nepal. A total of 83 meat samples were collected from the market and analyzed.

Results

The prevalence of Staphylococcus aureus, Escherichia coli, Salmonella, Shigella, and Vibrio were 68%, 53%, 35%, 6%, and 6% respectively. The resistance of Salmonella was most frequently observed to amoxicillin (100%), tetracycline (24%), chloramphenicol (11%), and nalidixic acid (11%). S. aureus was resistant to amoxicillin (100%) followed by tetracycline (63%), nalidixic acid (17%), and cefotaxime (13%) respectively. Vibrio isolates resisted amoxicillin (100%), tetracycline (40%) and chloramphenicol (20%). Shigella expressed the highest resistance to amoxicillin (100%), followed by chloramphenicol (80%), tetracycline (60%) and nalidixic acid (20%). E. coli exhibited the highest resistance to amoxicillin (100%), followed by tetracycline (93%), nalidixic acid (25%) and cefotaxime (19%).

Prevalence and antimicrobial susceptibility patterns of Salmonella and Shigella isolates among children aged below five years with diarrhea attending Robe General Hospital and Goba Referral Hospital, South East Ethiopia

BACKGROUND

Diarrheal diseases are responsible for high level of morbidity and mortality, particularly in children below 5 years. Salmonella and Shigella spp. are pathogenic microbes responsible for the major diarrheal associated mortality. The purpose of this study was to determine the prevalence, factors associated with Salmonella and Shigella isolates infections and their antimicrobial susceptibility patterns among diarrheic children aged below 5 years attending BRGH and GRH, Ethiopia.

METHODS

A health institution based cross-sectional study was conducted from April to July 2016. One stool samples was collected from 422 diarrheic children under the ages of five and were cultured on to Hektoen Enteric (HE) and Salmonella-Shigella agar. Isolation identification of the Salmonella and Shigella isolates were conducted using standard bacteriological methods. Antibiotic susceptibility was done by Kirby-Bauer disk diffusion method. The isolates were defined as multidrug resistant if it was resistant to two or more antimicrobial agents. Descriptive statistics were employed and logistic regression models were constructed to determine factors associated with Shigella/Salmonella prevalence.

RESULTS

The prevalence of Salmonella and Shigella isolates were 6.9 and 4.3%, respectively. Children aged between 1 to 3 years were significantly associated with Salmonella infection [AOR = 19.08, 95% CI (2.68-135.86)]. The odd of prevalence of Salmonella/Shigella isolates was significantly associated with absence of latrine, absence of hand washing after latrine, and in unimmunized children in adjusted odd ratio. Unimproved water sources and hand washing before meal had also higher odd of prevalence although the difference was not significant. All Salmonella and Shigella isolates were resistant to amoxicillin (100%). In addition, all Shigella isolates were completely resistant to chloramphenicol, and tetracycline, and were multidrug resistant. However, all Salmonella and Shigella isolates were susceptible to ciprofloxacin and ceftriaxone.

CONCLUSION

There was a relatively low prevalence of Salmonella and Shigella species in the study areas and were significantly associated with lack of personal hygiene and environmental sanitation. There were also higher drug resistance and multidrug resistant pattern. Personal hygiene and environmental sanitation, including access to latrine and supply of safe drinking water are suggested. Checking susceptibilities of Shigella and Salmonella isolates causing diarrhea is also suggested.

Antibiotic Use and Resistance Pattern in Ethiopia: Systematic Review and Meta-Analysis

BACKGROUND

In the last decades, medicines have had an unprecedented positive effect on health, leading to reduced mortality and disease burden and consequently to an improved quality of life. The rapid and ongoing spread of antimicrobial-resistant organisms threatens our ability to successfully treat a growing number of infectious diseases. In the absence of the development of new generations of antibiotic drugs, appropriate use of existing antibiotics is needed to ensure the long-term availability of effective treatment for bacterial infections. Irrational use of antibiotics is an ongoing global public health problem that deserves more attention. This review is conducted to evaluate the prevalence of inappropriate antibiotic utilization and resistance to antibiotics in Ethiopia.

METHODS

Electronic search in PubMed/MEDLINE and Google was used to find published literature with reference lists of relevant articles searched manually. Titles and abstracts were initially screened for eligibility. The full texts of articles judged to be eligible were reviewed if they meet the inclusion criteria. Data were extracted on important variables like the sample size, region of the study, the inappropriate antibiotic use, bacterial detection rate, multidrug resistance pattern, and more other variables. Microsoft Excel was used for data extraction. Quantitative analysis was performed using STATA version 11.

RESULTS

The electronic searches identified 193 articles of which 33 were found eligible. The random-effects model was used to provide point estimates (with 95% confidence interval (CI)) of bacterial detection rate, inappropriate antibiotic use, and multidrug resistance rate to account for heterogeneity. The pooled bacteria detection rate was 29.1 with 95% CI (16.6-41.7). The pooled prevalence of multidrug resistant strains identified was 59.7% (95% CI: 43.5-75.9). The pooled estimate of inappropriate antibiotic use was 49.2% (95% CI: 32.2-66.2). The pooled proportion of self-antibiotic prescription was 43.3% (95% CI: 15.7-70.9). Other reasons for inappropriate antibiotic use included a wrong indication, wrong duration, improper route of administration, use of leftover antibiotics from a family member, and immature discontinuation of antibiotics.

CONCLUSION AND RECOMMENDATIONS

Inappropriate antibiotic use is a huge problem in Ethiopia, and many bacteria were resistant to commonly used antibiotics and similarly, multidrug-resistant bacterial strains are numerous. Appropriate antibiotic use should be ensured by prohibiting over-the-counter sale of antibiotics and strengthening antimicrobial stewardship.

Prevalence of Shigella species and its drug resistance pattern in Ethiopia: a systematic review and meta-analysis

BACKGROUND

Shigella species are a major cause of dysentery and may attribute for death worldwide. Currently antibiotic resistance became the critical challenges for management of infectious disease. The aim was to conduct a systematic review and meta-analysis of Shigella species and its drug resistance pattern in Ethiopia.

METHODS

A comprehensive literature search was conducted through internet searches using database of MEDLINE, PubMed, Google scholar, EMBASE, HINARI, Cochrane Library and reference lists of previous prevalence studies from January 1999 to November 2018. Results were presented in forest plot, tables and figures with 95% CI. The Cochrane Q test and I2 test statistic were used to test heterogeneity across studies. The Pooled estimate of Shigella species and its drug resistance pattern was computed by a random effects model.

RESULTS

The pooled prevalence of Shigella species in Ethiopia was 6.6% (95% CI 4.7-8.8). In the subgroup analysis, the highest prevalence was observed among patients in Health facility (8.5%, 95% CI 6.2-11.5) whereas the lowest prevalence was observed in Community based studies (1.6%, 95% CI 0.8-3.4). In addition, Shigella species were highly resistant to ampicillin, amoxicillin, erythromycin and multi-drug resistant (MDR) with the pooled resistance proportions of 83.1% (95% CI 75.7-88.6), 84.1% (95% CI 75.6-90.1), 86.5% (95% CI 70.9-94.4) and 83.2% (95% CI 77.1-87.9), respectively. On the other hand, comparably low resistance pattern was reported for ciprofloxacin 8.9% (95% CI 6.0-12.8), ceftriaxone 9.3% (95% CI 3.9-20.5), and norfloxacin 8.2% (95% CI 3.8-16.6) and gentamycin 17.3% (95% CI 11.2-25.9). Subgroup analyses indicated that study years were associated with a decreasing Shigella prevalence over time (p = 0.002).

CONCLUSION

The pooled estimate showed high burden of Shigella infection and its high proportion of drug resistance pattern to ampicillin, amoxicillin and erythromycin in Ethiopia. Therefore, initiating and scale up of performing drug susceptibility test for each shigellosis case, educate the community and health care providers on appropriate use of antibiotics need to be considered and strengthened.

Resistance profile of clinically relevant bacterial isolates against fluoroquinolone in Ethiopia: a systematic review and meta-analysis

Background

Fluoroquinolones are among the most frequently utilized antibacterial agents in developing countries like Ethiopia. Ciprofloxacin has become the most prescribed drug within this class and remains as one of the top three antibacterial agents prescribed in Ethiopia. However, several studies indicated that there is a gradual increase of antibacterial resistance. Therefore, this meta-analysis aimed to quantitatively estimate the prevalence of ciprofloxacin resistance bacterial isolates in Ethiopia.

Methods

Literature search was conducted from electronic databases and indexing services including EMBASE (Ovid interface), PubMed/MEDLINE, Google Scholar, Science Direct and WorldCat. Data were extracted with structured format prepared in Microsoft Excel and exported to STATA 15.0 software for the analyses. Pooled estimation of outcomes was performed with DerSimonian-Laird random-effects model at 95% confidence level. Degree of heterogeneity of studies was presented with I² statistics. Publication bias was conducted with comprehensive meta-analysis version 3 software and presented with funnel plots of standard error supplemented by Begg’s and Egger’s tests. The study protocol has been registered on PROSPERO with reference number ID: CRD42018097047.

Results

A total of 37 studies were included for this study. The pooled prevalence of resistance in selected gram-positive bacterial isolates against ciprofloxacin was found to be 19.0% (95% confidence interval [CI]: 15.0, 23.0). The degree of resistance among Staphylococcus aureus, Coagulase negative Staphyloccoci (CoNS), Enterococcus faecalis and Group B Streptococci (GBS) was found to be 18.6, 21.6, 23.9, and 7.40%, respectively. The pooled prevalence of resistance in gram-negative bacteria was about 21.0% (95% CI: 17, 25). Higher estimates were observed in Neisseria gonorrhea (48.1%), Escherichia coli (24.3%) and Klebsiella pneumonia (23.2%). Subgroup analysis indicated that blood and urine were found to be a major source of resistant S. aureus isolates. Urine was also a major source of resistant strains for CoNS, Klebsiella and Proteus species.

Conclusion

Among gram-positive bacteria, high prevalence of resistance was observed in E. faecalis and CoNS whereas relatively low estimate of resistance was observed among GBS isolates. Within gram-negative bacteria, nearly half of isolates in N. gonorrhoea were found ciprofloxacin resistant. From enterobacteriaceae isolates, K. pneumonia and E. coli showed higher estimates of ciprofloxacin resistance.

Electronic supplementary material

The online version of this article (10.1186/s40360-018-0274-6) contains supplementary material, which is available to authorized users.