A systematic review: the current status of carbapenem resistance in East Africa

Pollution by antimicrobials and antibiotic resistance genes in East Africa: Occurrence, sources, and potential environmental implications

The escalating burden of antimicrobial pollution in East Africa poses severe threats to public health, environmental integrity, and economic stability. Environmental compartments such as soil and water serve as reservoirs for these pollutants such as antimicrobials and antibiotic resistance genes, creating selective pressure that accelerates the emergence of antimicrobial resistance (AMR). These dynamic fosters the proliferation of multidrug-resistant pathogens, or "superbugs," complicating infection management and amplifying health risks in a region already challenged by inadequate healthcare and sanitation infrastructure. Furthermore, pollution by antimicrobials and antibiotic resistance genes critically disrupts ecological processes, such as nutrient cycling and organic matter degradation, diminishing soil fertility, water quality, and agricultural productivity, thereby threatening food security and overall ecological health. Current surveillance efforts, including the Global Antimicrobial Resistance and Use Surveillance System (GLASS) and the East Africa Public Health Laboratory Networking Project (EAPHLNP), have made strides in tracking AMR trends and guiding policy decisions. However, these efforts remain insufficient to address the growing crisis. This study highlights the urgent need for integrated strategies, including stringent antibiotic usage regulations, advanced wastewater treatment technologies, and comprehensive environmental surveillance. Therefore, there is a need to address the intersections of health, agriculture, and environment, to mitigate AMR and its far-reaching consequences to ensure public health safety and sustainability.

Prevalence of genes encoding carbapenem-resistance in Klebsiella pneumoniae recovered from clinical samples in Africa: systematic review and meta-analysis

BACKGROUND

The potential of Klebsiella pneumoniae (K. pneumoniae) to acquire and spread carbapenem-resistant genes is the most concerning characteristic of the bacteria. In hospitals and other healthcare settings, multidrug-resistant K. pneumoniae can be prevalent and cause severe infections, posing significant challenges to patient management. Studying genetic variants and drug-resistant mutations in pathogenic bacteria of public health importance is essential. Therefore, this study aimed to assess the overall prevalence of carbapenemase-encoding genes in K. pneumoniae across Africa.

METHODS

All studies published between January 2010, and December 2023, were retrieved from the electronic databases PubMed, Science Direct, and Scopus, as well as through the Google Scholar search engine. This systematic review and meta-analysis adhered strictly to the PRISMA guidelines. Data analysis was performed using STATA version 17. The quality of the included studies was critically evaluated using the "Joanna Briggs Institute" criteria. To evaluate heterogeneity among the studies, inverse variance (I2) tests were utilized. Subgroup analysis was conducted when heterogeneity exists among studies. To assess publication bias, we used a funnel plot and Egger's regression test. A random effects model was used to calculate the weighted pooled prevalence of genetic variants associated with carbapenem resistance in K. pneumoniae.

RESULTS

A total of 49 potential studies were included in this systematic review and meta-analysis, encompassing 8,021 K. pneumoniae isolates. Among these isolates, 2,254 (28.1%) carbapenems-resistance-conferring genes were identified. The overall pooled prevalence of carbapenemase-encoding genes in K. pneumoniae isolated from clinical specimens across Africa was found to be 34.0% (95% CI: 26.01-41.98%). Furthermore, the pooled prevalence of the carbapenemase genes blaOXA-48 and blaNDM-1 was 16.96% (95% CI: 12.17-21.76%) and 15.08% (95% CI: 9.79-20.37%), respectively. The pooled prevalence of carbapenemase genes in K. pneumoniae isolates from clinical samples across Africa increased over time, reported as 20.4%(-0.7-41.4%) for 2010-2015, 34.5% (20.2-48.8%) for 2016-2020, and 35.2% (24.8-45.5%) for 2021-2023, with heterogeneity (I2) values of 36.5%, 96.7%, and 99.3%, respectively.

CONCLUSIONS

The emergence and spread of carbapenemase-encoding genes in K. pneumoniae pose a major threat to public health. Knowledge on the genetic mechanisms of carbapenem resistance is crucial for developing effective strategies to combat these multidrug-resistant infections and reduce their impact on healthcare systems. The carbapenemase genes blaOXA-48 and blaNDM-1 were the most prevalent and showed an increasing trend over time.

Molecular epidemiology of carbapenemase-producing Enterobacteriaceae and Acinetobacter baumannii in human infections around the Red Sea

The emergence and global spread of carbapenemase-producing bacteria (CPB) is of great concern to public health. Carbapenemase enzymes, which can hydrolyse almost all β-lactams, can be readily transferred between bacterial species through recombinant plasmids, transposons, or integrons. Human infections caused by CPB have limited treatment options and are associated with high mortality rates. These enzymes are mainly identified among Enterobacteriaceae and non-fermenter bacteria such as Acinetobacter baumannii and are associated either with hospital- or community-acquired infections. Located at the crossroads of the Middle East, Europe, and Africa, the countries around the Red Sea are of interest due to their great diversity and mix of populations. This review aims to describe the epidemiology of carbapenem resistance in Enterobacteriaceae and A. baumannii around the Red Sea, with country-specific findings. In this study, we emphasise the urgent need to screen for and detect these enzymes to prevent their spread and to maintain control.

Emerging threats: Antimicrobial resistance in extended-spectrum beta-lactamase and carbapenem-resistant Escherichia coli

Antimicrobial resistance (AMR) in Escherichia coli strains, particularly those producing Extended-Spectrum Beta-Lactamase (ESBL) and Carbapenemase (CR-Ec), represents a serious global health threat. These resistant strains have been associated with increased morbidity, mortality, and healthcare costs, as they limit the effectiveness of standard antibiotic therapies. The prevalence of ESBL- and CR-Ec-producing strains continues to rise, driven by the overuse and misuse of antibiotics in healthcare and agricultural settings, and facilitated by global interconnectedness through international travel, trade, and food distribution. This review article examines the molecular mechanisms behind ESBL and CR resistance, focusing on the key genes involved in these processes, such as blaCTX-M, blaKPC, and blaNDM, and the clinical challenges posed by these strains. Additionally, the public health impact, including the spread of infections in hospital and community environments, is highlighted. The discussion emphasizes the urgent need for improved diagnostic tools, robust surveillance systems, and innovative therapeutic strategies. Emerging treatments, including phage therapy and novel antibiotic combinations, show promise in addressing these challenges and offer potential breakthroughs in combating resistant strains. Lastly, the review calls for stronger antimicrobial stewardship and policy reforms to mitigate the spread of resistant E. coli strains and protect global public health. Effective intervention at multiple levels, from diagnostics to policy, is critical to controlling the threat posed by AMR.

Clinical Predispositions, Features, and Outcomes of Infections with Carbapenem-resistant Enterobacterales among Critical Care Patients

Background

Carbapenem-resistant Enterobacterales (CRE) infections pose a significant global public health threat. We aimed to assess the risk variables, clinical characteristics, and outcomes of CRE-caused infections in criticalcare patients.

Patients and methods

This prospective study enrolled 181 adult patients infected with Enterobacterales in the intensive care unit (ICU). Patients underwent clinical assessment and monitoring throughout their ICU stay. Carbapenem resistance was identified through antibiotic susceptibility testing and multiplex molecular detection of carbapenemase-encoding genes.

Results

The mean age of patients was 67.99 ± 12.89 years, with 71.3% being males. Of 181 patients, 111 (61.3%) were found to have CRE infections, including 39 Klebsiella pneumoniae and 31 Escherichia coli isolates. The CRE isolates showed the predominance of the OXA-48 (74.8%), followed by the NewDelhi Metallobetalactamase (NDM) carbapenemase genes (20.7%). The risk factors associated with CRE infection included high sequential organ failure assessment (SOFA) score, prolonged length of stay (LOS) in ICU, prior use of broad-spectrum antimicrobials, hemodialysis, plasma exchange, and prolonged mechanical ventilation. Carbapenem-resistant Enterobacterales infections significantly required longer LOS, more need for mechanical ventilation, and exhibited lower rates of bacterial elimination than carbapenem-susceptible Enterobacterales (CSE) infections. The type of resistance gene did not significantly influence the mortality rate among CRE patients. The successful treatment of OXA-48-positive CRE showed a strong correlation with tigecycline and colistin antibiotics.

Conclusion

Carbapenem-resistant Enterobacterales infection in ICU patients was associated with adverse outcomes. Identification of high-risk patients is essential for early diagnosis and appropriate management. Therefore, it is crucial to improve infection control methods and implement antimicrobial stewardship to avoid spreading infections.

How to cite this article

Shoala ARK, Nassar Y, El-Kholy AA, Soliman NS, Abdel-Fattah A, El-Ghawaby H. Clinical Predispositions, Features, and Outcomes of Infections with Carbapenem-resistant Enterobacterales among Critical Care Patients. Indian J Crit Care Med 2025;29(1):36-44.

Gastrointestinal carriage of carbapenemase-producing enterobacterales among inpatient and outpatient children in Kenya

Gastrointestinal carriage of antimicrobial-resistant bacteria, especially carbapenemase-producing Enterobacterales (CPE), presents a critical public health threat globally. However, in many resource-constrained countries, epidemiological data on CPE is limited. Here, we assessed gastrointestinal carriage and associated factors of CPE among inpatient and outpatient children (≤ 5 years). This hospital-based cross-sectional study was conducted at Thika Level 5 Hospital in Kenya from February to June 2023. In total, 540 participants were recruited from outpatient (270) and inpatient (270) children, excluding those admitted for < 48 h and outpatients with ≤ 3 months hospitalization history. Demographic data were collected using a questionnaire, and stool or swab samples were cultured following standard microbiology methods. Automated platforms were used for isolates identification and antimicrobial susceptibility testing. Gastrointestinal carriage rate of CPE was 9.6%, 95% confidence interval (CI): 6.39-13.79% (26/270) among the inpatients and 5.9%, 95% CI: 3.42-9.45% (16/270) among the outpatients. The carbapenemase-producing Enterobacterales were predominated by multidrug-resistant Escherichia coli from inpatients (22/22, 100%) and outpatients (8/10, 80%). The colonization rate was higher among inpatients who were presenting with chills (aOR = 10.57, p = 0.008). We report a high gastrointestinal carriage of CPE among children (≤ 5 years). Strict adherence to colonization screening, and antimicrobial stewardship policies are critical to control CPE dissemination in the current study area and beyond.

Biofilm Production and Antibiogram Profiles in Escherichia coli and Salmonella

Salmonella and Escherichia coli are important enteric pathogens associated with a variety of infections. Biofilm formation and antimicrobial resistance are important characteristics making these pathogens a concern in terms of strong attachment to substrates, expression of virulence markers and difficult removal. The present study investigates the biofilm-forming ability and antibiogram patterns among E. coli and Salmonella spp. A total of 200 E. coli and 100 Salmonella isolates received at National Salmonella and Escherichia Centre were identified by biochemical testing, followed by serotyping. Biofilm production was detected by Tissue Culture Plate method. The isolates were further subjected to Antibiotic Susceptibility Testing by the Kirby-Bauer disk diffusion method. 113 (56.5%) E. coli isolates and 79 (79%) Salmonella isolates were detected as biofilm producers. A total of 114(57%)E. coli isolates and 31(31%) Salmonella isolates were found to be resistant to multiple drugs when Antibiotic Susceptibility Testing was carried out. Antibiotic resistance was found to be significantly higher in biofilm producing salmonella (p = 0.001) whereas in the case of E. coli the difference remained non-significant (p = 0.4454). The capability to produce biofilm along with acquiring high level of antimicrobial resistance in salmonella and E. coli provide enhanced survival potential in adverse environments. Therefore, it becomes a serious cause of concern for public health authorities considering the virulence of these bacteria and their association with different disease conditions and requires urgent intervention with regards to control and prevention strategies.

Diversity, Distribution, and Resistance Profiles of Bacterial Bloodstream Infections in Three Tertiary Referral Hospitals in Rwanda Between 2020 and 2022

Background: The burden of bacterial bloodstream infections (BSIs) is rapidly increasing in Africa including Rwanda. Methods: This is a retrospective study that investigates the diversity, distribution, and antimicrobial susceptibility profiles of BSI bacteria in three tertiary referral hospitals in Rwanda between 2020 and 2022. Results: A total of 1532 blood culture tests were performed for visiting patients. Overall, the proportions of Gram-negative and Gram-positive bacteria were 48.2% and 51.8, respectively. Staphylococcus aureus was the predominant species accounting for 25% of all Gram-positive BSI species, and Klebsiella species represented 41% of all Gram-negative BSI species. Antimicrobial susceptibility testing revealed that Amikacin exhibited the highest activity against Enterobacter spp., Serratia spp., and Escherichia coli in >92% of cases and Klebsiella spp. in 75.7%. Meropenem and Imipenem were highly efficacious to Salmonella spp. (100% susceptibility), Enterobacter spp. (96.2% and 91.7%, respectively), and Escherichia coli (94.7% and 95.5%, respectively). The susceptibility of Enterococcus spp., S. aureus, and Streptococcus spp. to Vancomycin was 100%, 99.5%, and 97.1%, respectively. Klebsiella spp. was highly sensitive to Colistin (98.7%), Polymyxin B (85.6%), Imipenem (84.9%), and Meropenem (78.5%). Conclusions: We recommend strengthening the implementation of integrated transdisciplinary and multisectoral One Health including AMR stewardship for the surveillance, prevention, and control of AMR in Rwanda.

A systematic review and meta-analysis of carbapenem-resistant Enterobacteriaceae in West Africa

BACKGROUND

In Africa, the problem of carbapenem-resistant Enterobacteriaceae (CRE) is aggravated by many factors. This systematic review attempted to describe the current status of the molecular epidemiology of carbapenem resistance in West Africa (WA).

METHODS

Articles published from 16 West African countries on the molecular epidemiology of carbapenem resistance were reviewed. An extensive literature search was carried out in PubMed, Scopus, Web of Science, and African Journals Online (AJOL) using specific keywords. The meta-analysis and forest plots of major pathogens and carbapenem resistance genes were done using the Open Meta-Analyst, Task Order # 2 software. The data were analysed in binary random model effects by the DerSimonian-Laird method at a 95% confidence interval.

RESULTS

Of the 431 articles found in our initial search, 60 (13.92%) were considered suitable for inclusion. Only seven of the 16 West African countries formed part of the analysis, Nigeria (23/60), Ghana (19/60), Burkina Faso (7/60), Senegal (6/60), Benin (2/60), Mali (2/60), and Togo (1/60). Also, 80% (48/60) of the studies used clinical samples, 16.67% (10/60) used environmental samples, and 3.33% (2/60) used animal samples. The average prevalence was highest in Acinetobacter baumannii (18.6%; 95% CI = 14.0-24.6, I2 = 97.9%, p < 0.001), followed by Pseudomonas aeruginosa (6.5%; 95% CI = 3.1-13.4, I2 = 96.52%, p < 0.001), Klebsiella pneumoniae (5.8%; 95% CI = 4.2-7.9, I2 = 98.06%, p < 0.001) and Escherichia coli (4.1%; 95% CI = 2.2-7.7, I2 = 96.68%, p < 0.001). The average prevalence of the blaNDM gene was 10.6% (95% CI = 7.9-14.3, I2 = 98.2%, p < 0.001), followed by 3.9% (95% CI: 1.8-8.3, I2 = 96.73%, p < 0.001) for blaVIM and 3.1% (95% CI: 1.7-5.8, I2 = 91.69%, p < 0.001) for blaOXA-48.

CONCLUSION

In West Africa, K. pneumoniae, E. coli, A. baumannii, and P. aeruginosa are the main CRE with blaNDM, blaVIM, and blaOXA-48 being the predominant carbapenem resistance genes. In view of these results, ongoing CRE surveillance combined with antimicrobial stewardship improved, laboratory detection methods, and adherence to infection control practices will be needed to control the spread of CRE.

Hospital and municipal wastewater as a source of carbapenem-resistant Acinetobacter baumannii and Pseudomonas aeruginosa in the environment: a review

The increase in the prevalence of carbapenem-resistant Gram-negative bacteria, in particular Acinetobacter baumannii (CRAB) and Pseudomonas aeruginosa (CRPA), poses a serious threat for public health worldwide. This article reviews the alarming data on the prevalence of infections caused by CRAB and CRPA pathogens and their presence in hospital and municipal wastewater, and it highlights the environmental impact of antibiotic resistance. The article describes the key role of antibiotic resistance genes (ARGs) in the acquisition of carbapenem resistance and sheds light on bacterial resistance mechanisms. The main emphasis was placed on the transfer of ARGs not only in the clinical setting, but also in the environment, including water, soil, and food. The aim of this review was to expand our understanding of the global health risks associated with CRAB and CRPA in hospital and municipal wastewater and to analyze the spread of these micropollutants in the environment. A review of the literature published in the last decade will direct research on carbapenem-resistant pathogens, support the implementation of effective preventive measures and interventions, and contribute to the development of improved strategies for managing this problem.

Antibiotic overuse, poor antimicrobial stewardship, and low specificity of syndromic case management in a cross section of men with urethral discharge syndrome in Kampala, Uganda

OBJECTIVE

High prevalence of sexually transmitted infections (STIs) combined with poor antimicrobial stewardship are drivers of STI antimicrobial resistance (AMR) especially in resource-limited settings where syndromic case management (SCM) is the norm. We characterized patterns of antibiotic use prior to clinic attendance and study enrollment in Ugandan men with urethral discharge syndrome (UDS), evaluated in-clinic prescribing, and the performance characteristics of SCM.

METHODS

Participants were recruited from government clinics participating in an existing gonococcal surveillance program in Kampala, Uganda. Questionnaires including antimicrobial use prior to attendance, prior episodes of UDS, penile swabs, and blood samples were collected. Bivariable and multivariable logistic regression models were used to estimate odds ratios (OR) for preselected factors likely to be associated with antibiotic use. In-clinic antibiotic treatment data were extracted from clinical notes, and the performance of SCM against laboratory-based STI diagnoses was evaluated.

FINDINGS

Between October 2019 and November 2020, 100(40%) of 250 men with UDS reported taking antibiotics in the 14days prior to attending the clinic. Of these 210(84%) had at least one curable STI and 20% had a reactive point-of-care HIV test. Multivariable analysis demonstrated significant associations between recent antimicrobial use and duration of UDS symptoms <6 days (OR 2.98(95%CI 1.07,8.36), p = 0.038), and sex with women only (OR 0.08(95%CI 0.01,0.82),p = 0.038). The sensitivity of SCM ranged from 80.0% to 94.4%; specificity was low between 5.6% and 33.1%. The positive predictive value of SCM ranged from 2.4(95%CI 0.7,6.0) for trichomoniasis to 63.4(95%CI 56.5,69.9) for gonorrhea.

CONCLUSION

Pre-enrollment antibiotic use was common in this population at high risk of STI and HIV. Combined with the poor specificity of SCM for male UDS, extensive antibiotic use is a likely driver of STI-AMR in Ugandan men. Interventions to improve antimicrobial stewardship and deliver affordable diagnostics to augment SCM and decrease overtreatment of STI syndromes are required.

Molecular Analysis of Carbapenem and Aminoglycoside Resistance Genes in Carbapenem-Resistant Pseudomonas aeruginosa Clinical Strains: A Challenge for Tertiary Care Hospitals

Carbapenem-resistant Pseudomonas aeruginosa (P. aeruginosa) strains have become a global threat due to their remarkable capability to survive and disseminate successfully by the acquisition of resistance genes. As a result, the treatment strategies have been severely compromised. Due to the insufficient available data regarding P. aeruginosa resistance from Pakistan, we aimed to investigate the resistance mechanisms of 249 P. aeruginosa strains by antimicrobial susceptibility testing, polymerase chain reaction for the detection of carbapenemases, aminoglycoside resistance genes, extended-spectrum beta-lactamases (ESBLs), sequence typing and plasmid typing. Furthermore, we tested silver nanoparticles (AgNPs) to evaluate their in vitro sensitivity against antimicrobial-resistant P. aeruginosa strains. We observed higher resistance against antimicrobials in the general surgery ward, general medicine ward and wound samples. Phenotypic carbapenemase-producer strains comprised 80.7% (201/249) with 89.0% (179/201) demonstrating genes encoding carbapenemases: blaNDM-1 (32.96%), blaOXA48 (37.43%), blaIMP (7.26%), blaVIM (5.03%), blaKPC-2 (1.12%), blaNDM-1/blaOXA48 (13.97%), blaOXA-48/blaVIM (1.68%) and blaVIM/blaIMP (0.56%). Aminoglycoside-modifying enzyme genes and 16S rRNA methylase variants were detected in 43.8% (109/249) strains: aac(6')-lb (12.8%), aac(3)-lla (12.0%), rmtB (21.1%), rmtC (11.0%), armA (12.8%), rmtD (4.6%), rmtF (6.4%), rmtB/aac(3)-lla (8.2%), rmtB/aac(6')-lla (7.3%) and rmtB/armA (3.6%). In total, 43.0% (77/179) of the strains coharbored carbapenemases and aminoglycoside resistance genes with 83.1% resistant to at least 1 agent in 3 or more classes and 16.9% resistant to every class of antimicrobials tested. Thirteen sequence types (STs) were identified: ST235, ST277, ST234, ST170, ST381, ST175, ST1455, ST1963, ST313, ST207, ST664, ST357 and ST348. Plasmid replicon types IncFI, IncFII, IncA/C, IncL/M, IncN, IncX, IncR and IncFIIK and MOB types F11, F12, H121, P131 and P3 were detected. Meropenem/AgNPs and Amikacin/AgNPs showed enhanced antibacterial activity. We reported the coexistence of carbapenemases and aminoglycoside resistance genes among carbapenem-resistant P. aeruginosa with diverse clonal lineages from Pakistan. Furthermore, we highlighted AgNP's potential role in handling future antimicrobial resistance concerns.

Asymptomatic gastrointestinal carriage of multidrug-resistant carbapenemase-producing Enterobacteriaceae among children under five years in a Kenyan hospital

Objectives

Asymptomatic gastrointestinal carriage of carbapenem-resistant Enterobacteriaceae (CRE) is a threat to global health in developing countries with inadequate safe drinking water, poor hygiene, and weak antimicrobial stewardship; however, epidemiological data to guide CRE infection prevention and control is limited in these settings. We assessed asymptomatic CRE and carbapenem-producing Enterobacteriaceae (CPE) fecal carriage rates and associated risk factors among hospitalized children aged under 5 years.

Methods

We adopted a cross-sectional study at Mama Lucy Kibaki Hospital in Nairobi-City County, Kenya, between June and September 2022. We collected demographic and clinical characteristics using a structured questionnaire and clinical reports and analyzed stool/rectal swab samples by standard and automated bacteriological methods.

Results

Asymptomatic CRE and CPE fecal carriage rate was 2.25% (6/267), with six isolates recovered, predominated by Escherichia coli (33.33%) and Enterobacter cloacae subsp dissolvens (33.33%). Third-generation cephalosporin and ciprofloxacin resistance were highest in Citrobacter farmer and E. cloacae subsp cloacae. All CRE and CPE were multidrug-resistant, and except E. cloacae subsp cloacae, were 100% colistin-resistant.

Conclusions

Asymptomatic gastrointestinal carriage of multidrug-resistant-CRE among hospitalized children under 5 years, presents a substantial public health threat. This calls for continuous surveillance including molecular characterization of isolates, to inform infection prevention and antimicrobial stewardship adherence in line with local and global plans on AMR.

Prevalence of carbapenem-resistant and extended-spectrum beta-lactamase-producing Enterobacteriaceae in a teaching hospital in Ghana

BACKGROUND

Carbapenem-resistant Enterobacteriaceae (CRE) and Extended-spectrum beta-lactamase (ESBL) production among Gram-negative Enterobacteriaceae is an increasing global challenge due to the high morbidity and mortality associated with their infections, especially in developing countries where there are little antibiotic treatment options. Despite these challenges, few studies in Ghana have described the burden of CRE. Therefore, this study aimed to determine the prevalence of carbapenem-resistant Enterobacteriaceae isolated from patients at the Cape Coast Teaching Hospital (CCTH) in the Central region of Ghana.

METHODOLOGY/PRINCIPAL FINDINGS

Enterobacteriaceae isolates were collected from April to July 2019 at the bacteriology unit of CCTH using a consecutive sampling method. Isolates were identified by standard microbiological techniques and confirmed using API 20E. Kirby Bauer disc diffusion method was used to determine the antibiogram of isolates. Isolates were also subjected to ESBL testing using the single-disc combination method. Carbapenem-resistant isolates were identified by the Kirby Bauer disc diffusion method and then examined genotypically for the presence of blaKPC-1, blaIMP-1, blaVIM-1, blaNDM-1, and blaOXA-48 genes via polymerase chain reaction (PCR). Of the 230 isolates comprising E. coli (40.9%), Citrobacter spp. (32.6%), K. pneumoniae (9.1%), P. mirabilis (6.1%), P. vulgaris (5.2%), Enterobacter spp (3.5%)., K. oxytoca (2.2%), and Serratia marcenses (0.4%). Most isolates were from urine 162(70.4%) and wound samples. The isolates showed high resistance to ampicillin 171 (74.3%) and cefuroxime 134(58.3%). The prevalence of MDR was 35.2% (81), with E. coli 40(42.6%) being the majority that exhibited MDR. Of the 230 isolates, 113(49.1%) were ESBL producers, with E. coli 54(57.5%) accounting for the majority, while Serratia marcenses was the least. Of the 13 (5.7%) CRE isolates that showed resistance towards carbapenem in the disc diffusion method, 11 showed the presence of the blaNDM-1 gene, while all isolates showed the presence of the blaOXA-48 gene.

CONCLUSION

The prevalence of carbapenem resistance and ESBL-producing Enterobacteriaceae pathogens among patients at the Cape Coast Teaching Hospital is high and alarming. Therefore, it is imperative to consider effective infection prevention and control measures should be implemented at the hospital to prevent the rapid spread of these dangerous organisms.

Carbapenem resistance in Enterobacterales from agricultural, environmental and clinical origins: South Africa in a global context

Carbapenem agents are regarded as last-resort antibiotics, however, bacterial resistance towards carbapenems has been reported in both clinical and agricultural settings worldwide. Carbapenem resistance, defined as the resistance of a bacteria towards one or more carbapenem drugs, can be mediated in either of, or a combination of, three mechanisms-although, the mechanism mediated through the production of carbapenemases (β-lactamases that are able to enzymatically degrade carbapenems) is of most significance. Of particular concern is the occurrence of carbapenemase producing Enterobacterales (CPE), with literature describing a dramatic increase in resistance globally. In South Africa, increases of carbapenemase activity occurring in Enterobacter species, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa have recently been reported. CPE can also be found in agricultural environments, as global studies have documented numerous instances of CPE presence in various animals such as pigs, cattle, seafood, horses and dogs. However, most reports of CPE occurrence in agricultural settings come from Northern America, Europe and some parts of Asia, where more extensive research has been conducted to understand the CPE phenomenon. In comparison to clinical data, there are limited studies investigating the spread of CPE in agricultural settings in Africa, highlighting the importance of monitoring CPE in livestock environments and the food chain. Further research is necessary to uncover the true extent of CPE dissemination in South Africa. This review will discuss the phenomenon of bacterial antibiotic resistance (ABR), the applications of the carbapenem drug and the occurrence of carbapenem resistance globally.

Surveillance of antimicrobial resistance in human health in Tanzania: 2016-2021

Background

Antimicrobial resistance (AMR) surveillance plays an important role in early detection of resistant strains of pathogens and informs treatments decisions at local, regional and national levels. In 2017, Tanzania developed a One Health AMR Surveillance Framework to guide establishment of AMR surveillance systems in the human and animal sectors.

Aim

We reviewed AMR surveillance studies in Tanzania to document progress towards establishing an AMR surveillance system and determine effective strengthening strategies.

Methods

We conducted a literature review on AMR studies conducted in Tanzania by searching Google Scholar, PubMed, and the websites of the Tanzania Ministry of Health and the World Health Organization for articles written in English and published from January 2012 to March 2021 using relevant search terms. Additionally, we reviewed applicable guidelines, plans, and reports from the Tanzanian Ministry of Health.

Results

We reviewed 10 articles on AMR in Tanzania, where studies were conducted at hospitals in seven of Tanzania's 26 regions between 2012 and 2019. Nine AMR sentinel sites had been established, and there was suitable and clear coordination under 'One Health'. However, sharing of surveillance data between sectors had yet to be strengthened. Most studies documented high resistance rates of Gram-negative bacteria to third-generation cephalosporins. There were few laboratory staff who were well trained on AMR.

Conclusion

Important progress has been made in establishing a useful, reliable AMR surveillance system. Challenges include a need to develop, implement and build investment case studies for the sustainability of AMR surveillance in Tanzania and ensure proper use of third-generation cephalosporins.

What this study adds

This article adds to the knowledge base of AMR trends in Tanzania and progress made in the implementation of AMR surveillance in human health sector as a contribution to the global AMR initiatives to reduce AMR burden worldwide. It has highlighted key gaps that need policy and implementation level attention.

[Epidemiological Analysis of Carbapenem-Resistant Enterobacteriaceae Strains in the Clinical Specimens of a Hospital]

Objective

To analyze the detection rate, in vitro susceptibility to antibiotics, and carbapenemase types of carbapenem-resistant Enterobacteriaceae (CRE) strains in the clinical samples of a hospital and to provide support for the prevention, control and treatment of CRE-related infections.

Methods

Clinical specimens were examined according to the operating procedures of bacteriological tests. Species identification and in vitro drug susceptibility testing were performed on the isolated strains. Carbapenemase inhibitor enhancement testing, which combined the use of 3-aminobenzeneboronic acid and ethylenediaminetetraacetic acid, was conducted to identify the types of carbapenemase in the CRE strains.

Results

In 2021, 2215 CRE strains were isolated from 157196 clinical samples collected in this hospital, presenting a detection rate of 1.4% (2215/157196). A total of 1134 non-repetitive strains of CRE were isolated from 903 patients. The main sources of samples were respiratory tract (494/1134, 43.6%), secretion (191/1134, 16.8%) and blood (173/1134, 15.3%) samples. The cases with the same CRE strain isolated from the samples of two, three and four sites accounted for 12.5%, 4.9%, and 1.1%, respectively. The most common species was Klebsiella pneumoniae (883/1134, 77.9%), followed by Enterobacter cloacae complex (107/1134, 9.4%) and Escherichia coli (96/1134, 8.5%). The rates of resistance to polymyxin B and tigecycline of different species of CRE strains were not significantly different ( P<0.05). Serine carbapenemase-producing strains, metallo-β-lactamase-producing strains, and those producing both enzymes accounted for 82.6% (809/979), 17.2% (168/979), and 0.2% (2/979), respectively.

Conclusion

CRE strains are frequently isolated from samples collected from the respiratory tract, secretion, and blood. The most common strain is serine carbapenemase-producing K. pneumoniae, which has a high resistance rate to various antimicrobial drugs, and risk factors of its associated infections deserve more attention.

Review and analysis of the overlapping threats of carbapenem and polymyxin resistant E. coli and Klebsiella in Africa

BACKGROUND

Carbapenem-resistant Enterobacterales are among the most serious antimicrobial resistance (AMR) threats. Emerging resistance to polymyxins raises the specter of untreatable infections. These resistant organisms have spread globally but, as indicated in WHO reports, the surveillance needed to identify and track them is insufficient, particularly in less resourced countries. This study employs comprehensive search strategies with data extraction, meta-analysis and mapping to help address gaps in the understanding of the risks of carbapenem and polymyxin resistance in the nations of Africa.

METHODS

Three comprehensive Boolean searches were constructed and utilized to query scientific and medical databases as well as grey literature sources through the end of 2019. Search results were screened to exclude irrelevant results and remaining studies were examined for relevant information regarding carbapenem and/or polymyxin(s) susceptibility and/or resistance amongst E. coli and Klebsiella isolates from humans. Such data and study characteristics were extracted and coded, and the resulting data was analyzed and geographically mapped.

RESULTS

Our analysis yielded 1341 reports documenting carbapenem resistance in 40 of 54 nations. Resistance among E. coli was estimated as high (> 5%) in 3, moderate (1-5%) in 8 and low (< 1%) in 14 nations with at least 100 representative isolates from 2010 to 2019, while present in 9 others with insufficient isolates to support estimates. Carbapenem resistance was generally higher among Klebsiella: high in 10 nations, moderate in 6, low in 6, and present in 11 with insufficient isolates for estimates. While much less information was available concerning polymyxins, we found 341 reports from 33 of 54 nations, documenting resistance in 23. Resistance among E. coli was high in 2 nations, moderate in 1 and low in 6, while present in 10 with insufficient isolates for estimates. Among Klebsiella, resistance was low in 8 nations and present in 8 with insufficient isolates for estimates. The most widespread associated genotypes were, for carbapenems, blaOXA-48, blaNDM-1 and blaOXA-181 and, for polymyxins, mcr-1, mgrB, and phoPQ/pmrAB. Overlapping carbapenem and polymyxin resistance was documented in 23 nations.

CONCLUSIONS

While numerous data gaps remain, these data show that significant carbapenem resistance is widespread in Africa and polymyxin resistance is also widely distributed, indicating the need to support robust AMR surveillance, antimicrobial stewardship and infection control in a manner that also addresses broader animal and environmental health dimensions.

Prevalence of Carbapenemase and Extended-Spectrum β-Lactamase Producing Enterobacteriaceae: A Cross-Sectional Study

Enterobacteriaceae have been classified as severely drug resistant bacteria by the World Health Organization due to their extensive production and dissemination of carbapenemases (CPs) and extended-spectrum β-lactamases (ESBL). The current study was conducted with the aim to determine the prevalence of CP- and ESBL-producing Enterobacteriaceae, as well as their antibiotic susceptibility profiles. For this, a hospital-based study was conducted which included 384 participants with bacterial infections. The collection and processing of specimens was conducted per standard microbiological protocol. The samples were inoculated on agar media plates to obtain the bacterial growths, and if they were positive for any bacterial growth, the antibiotic susceptibility testing was performed using disk diffusion method to check their antibiotic susceptibility patterns. The double disc diffusion as well as carbapenem inhibition techniques were used to examine the CP enzymes. Multiplex real-time PCR technique was performed to identify three distinct genetic types of CPs that have been identified in the Enterobacteriaceae (KPC, NDM, and OXA-48). A majority of participants (58.3%) in the current study were living in urban areas. A total of 227 (59.1%) patients were hospitalized. Furthermore, 26.04% of the patients were determined to be suffering from infections with Enterobacteriaceae. Escherichia coli was the most prevalent (9.1%) isolate overall, followed by Klebsiella pneumoniae (8.07%), Acinetobacter baumannii (2.6%), Pseudomonas aeruginosa (3.1%), Enterobacter cloacae (1.3%), Proteus spp. (1.3%), and Morganella spp. (0.5%). The studied patients were suffering from urinary tract infections (48.6%), blood stream infections (32.2%), wounds infection (11.9%), and respiratory infections (7.03%), confirmed with bacterial cultures. The resistance against carbapenems was seen in 31.4% of E. coli isolates, 25.8% in K. pneumoniae, 50% in P. aeruginosa, 25% in A. baumannii, and 20% in E. cloacae isolates. Such high rates of CP- and ESBL-producing Enterobacteriaceae are alarming, suggesting high spread in the study area. It is advised to implement better infection prevention and control strategies and conduct further nationwide screening of the carriers of these pathogens. This might help in reducing the burden of highly resistant bugs.

A systematic review of the current status of carbapenem resistance in Nigeria: Its public health implication for national intervention

Carbapenem antibiotics are considered one of the most effective and the last-resort antibiotics for the treatment of infections caused by multidrug-resistant Gram-negative bacteria. However, with the advent of carbapenem resistance, it becomes obvious that quality health-care delivery will be hampered if adequate measure is not put in place. This review assessed the prevalence of carbapenem-resistant Gram-negative bacteria (CR-GNB) and also provided an up-to-date position on carbapenem resistance (CR) in Nigeria. Three electronic databases (Google Scholar, PubMed and African Journal online) were searched for relevant literatures, and 38 articles published between January 2013 and June 2022 that met the criteria for inclusion were recruited into the study. The mean prevalence of CR in Nigeria stands at 21.3%, with the southern and northern regions documenting a mean prevalence of 22.0% and 20.9%, respectively. Most of the reviewed articles were from clinical settings (81.6%), with urine samples (38.7%) constituting the most prevalent clinical sample in which CR-GNB were detected. The preponderance of phenotypic methods (55.3%) over molecular method (44.7%), particularly the use of disk diffusion test breakpoint and Modified Hodge test was documented. The most prevalent carbapenem-resistant bacteria were Escherichia coli (50.0%) and Klebsiella pneumoniae (26.3%). The blaNDM and blaVIM were the major reported carbapenemase-encoded genes, particularly among E. coli, K. pneumoniae and Pseudomonas species. This systematic review revealed a mean prevalence of CR-GNB in Nigeria that required urgent attention. Furthermore, the detection of clinically and epidemiologically important carbapenemase coding genes is of public health importance.

Prevalence and Trends of Carbapenem-Resistant Pseudomonas aeruginosa and Acinetobacter Species Isolated from Clinical Specimens at the Ethiopian Public Health Institute, Addis Ababa, Ethiopia: A Retrospective Analysis

Purpose

Carbapenem-resistant Acinetobacter species and P. aeruginosa are the leading cause of nosocomial infections. Therefore, the objective of this study was to analyze the prevalence, antimicrobial susceptibility profile, and trends of carbapenem-resistant P. aeruginosa and Acinetobacter species isolated from clinical specimens.

Patients and Methods

This retrospective study included data from Ethiopian Public Health Institute from 2017 to 2021. BD phoenix M50, Vitek 2 compact, and conventional identification methods were used to identify the organisms. The Kirby-Bauer disc diffusion, BD phoenix M50, and Vitek 2 compact methods were used to determine the antimicrobial susceptibility profiles of the isolates. Chi-square for linear trends using Epi Info was employed to test the significance of carbapenem resistance trends over time. The p-values of ≤0.05 were considered statistically significant.

Results

Following data cleaning, 7110 reports were used. Out of this, (N=185, 2.6%) and (N=142, 2%), Acinetobacter species and P. aeruginosa were isolated, respectively. Twenty-four Acinetobacter species and fourteen P. aeruginosa species were omitted because carbapenem antimicrobial agents were not tested for them. The overall prevalence of carbapenem-resistant Acinetobacter species and P. aeruginosa were 61% and 22%, respectively. The prevalence of carbapenem-resistant Acinetobacter species increased significantly from 50% in 2017 to 76.2% in 2021 (p=0.013). The trend of carbapenem-resistant P. aeruginosa was fluctuating (p=0.99). Carbapenem-resistant Acinetobacter had a lower resistance rate to amikacin (44%) and tobramycin (55%); similarly, carbapenem-resistant P. aeruginosa had a lower resistance rate to amikacin (27%) and tobramycin (47%).

Conclusion

This study revealed a high prevalence of carbapenem-resistant Acinetobacter species and P. aeruginosa, both of which showed better sensitivity to amikacin and tobramycin. Furthermore, Acinetobacter species showed a statistically significant increasing trend in carbapenem resistance.

Prevalence of colonization with multidrug-resistant bacteria in communities and hospitals in Kenya

We estimated the prevalence of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE), carbapenem-resistant Enterobacterales (CRE), and methicillin-resistant Staphylococcus aureus (MRSA) in communities and hospitals in Kenya to identify human colonization with multidrug-resistant bacteria. Nasal and fecal specimen were collected from inpatients and community residents in Nairobi (urban) and Siaya (rural) counties. Swabs were plated on chromogenic agar to presumptively identify ESCrE, CRE and MRSA isolates. Confirmatory identification and antibiotic susceptibility testing were done using the VITEK®2 instrument. A total of 1999 community residents and 1023 inpatients were enrolled between January 2019 and March 2020. ESCrE colonization was higher in urban than rural communities (52 vs. 45%; P = 0.013) and in urban than rural hospitals (70 vs. 63%; P = 0.032). Overall, ESCrE colonization was ~ 18% higher in hospitals than in corresponding communities. CRE colonization was higher in hospital than community settings (rural: 7 vs. 1%; urban: 17 vs. 1%; with non-overlapping 95% confidence intervals), while MRSA was rarely detected (≤ 3% overall). Human colonization with ESCrE and CRE was common, particularly in hospitals and urban settings. MRSA colonization was uncommon. Evaluation of risk factors and genetic mechanisms of resistance can guide prevention and control efforts tailored to different environments.

Dissemination of Antibiotic Resistance Genes Among Patients with Diarrhea - Freetown, Sierra Leone, 2018

What is already known about this topic?

Antibiotic resistance (AR) is a serious public health threat worldwide. However, the AR and antibiotic resistance genes (ARGs) data from West Africa, especially from Sierra Leone, are limited.

What is added by this report?

The study revealed ARGs' common dissemination, and multiplex antibiotic resistance genes in one sample. Genes bla _NDM and bla _{OXA -48-like} were first discovered in Sierra Leone.

What are the implications for public health practice?

Basic information is provided for AR research and surveillance and highlights that effective AR surveillance among diarrhea patients is necessary for Sierra Leone and West Africa.

Antibiotic resistomes and their chemical residues in aquatic environments in Africa

The aquatic environment is a hotspot for the transfer of antibiotic resistance to humans and animals. Several reviews have put together research efforts on the presence and distribution of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antibiotic chemical residue (ACRs) in food, hospital wastewater, and even in other aquatic environments. However, these reports are largely focused on data from developed countries, while data from developing countries and especially those in Africa, are only marginally discussed. This review is the first effort that distills information on the presence and distribution of ARGs and ACRs in the African aquatic environments (2012-2021). This review provides critical information on efforts put into the study of ARB, ARGs, and ACRs in aquatic environments in Africa through the lens of the different sub-regions in the continent. The picture provided is compared with those from some other continents in the world. It turns out that the large economies in Africa (South Africa, Nigeria, Tunisia, Kenya) all have a few reports of ARB and ARGs in their aquatic environment while smaller economies in the continent could barely provide reports of these in their aquatic environment (in most cases no report was found) even though they have some reports on resistomes from clinical studies. Interestingly, the frequency of these reports of ARB and ARGs in aquatic environments in Africa suggests that the continent is ahead of the South American continent but behind Europe and Asia in relation to providing information on these contaminants. Common ARGs found in African aquatic environment encode resistance to sulfonamide, tetracycline, β-lactam, and macrolide classes of antibiotics. The efforts and studies from African scientists in eliminating ARB and ARGs from the aquatic environment in Africa are also highlighted. Overall, this document is a ready source of credible information for scientists, policy makers, governments, and regional bodies on ARB, ARGs, and ACRs in aquatic environments in Africa. Hopefully, the information provided in this review will inspire some necessary responses from all stakeholders in the water quality sector in Africa to put in more effort into providing more scientific evidence of the presence of ARB, ARGs, and ACRs in their aquatic environment and seek more efficient ways to handle them to curtail the spread of antibiotic resistance among the population in the continent. This will in turn, put the continent on the right path to meeting the United Nations Sustainable Development Goals #3 and #6, which at the moment, appears to be largely missed by most countries in the continent.

Multidrug-Resistant Bacteria: Their Mechanism of Action and Prophylaxis

In the present scenario, resistance to antibiotics is one of the crucial issues related to public health. Earlier, such resistance to antibiotics was limited to nosocomial infections, but it has now become a common phenomenon. Several factors, like extensive development, overexploitation of antibiotics, excessive application of broad-spectrum drugs, and a shortage of target-oriented antimicrobial drugs, could be attributed to this condition. Nowadays, there is a rise in the occurrence of these drug-resistant pathogens due to the availability of a small number of effective antimicrobial agents. It has been estimated that if new novel drugs are not discovered or formulated, there would be no effective antibiotic available to treat these deadly resistant pathogens by 2050. For this reason, we have to look for the formulation of some new novel drugs or other options or substitutes to treat such multidrug-resistant microorganisms (MDR). The current review focuses on the evolution of the most common multidrug-resistant bacteria and discusses how these bacteria escape the effects of targeted antibiotics and become multidrug resistant. In addition, we also discuss some alternative mechanisms to prevent their infection as well.

Genomic evaluation of novel Kenyan virulent phage isolates infecting carbapenemase-producing Klebsiella pneumoniae and safety determination of their lysates in Balb/c mice

This study aimed to evaluate the genomic features of novel Kenyan virulent phage isolates infecting carbapenemase-producing Klebsiella pneumoniae and to determine the safety of their lysates using mice model in a preclinical study. The genomics showed that the Klebsiella phages vB_KpM_CPRSA and vB_KpM_CPRSB belonged to the genus Slopekvirus with a similarity index of less than 92% compared to the most closest relative species. Their genomes did not contain antimicrobial resistance and toxin genes. Then endotoxin levels in the Klebsiella phage lysates were statistically significant (p value ˃ 0.05). The serum activities of aspartate aminotransferase, alanine aminotransferase and urea in the group of balb/c mice injected with bacteriophage lysates through the intravenous route were higher compared to that of the intranasal route. Unexpectedly, there was mild congestion of the central veins of kidneys and liver without damage to renal tubules and hepatocytes and a lack of physical discomfort and pain in the mice. Our study isolated and characterised Klebsiella phages against carbapenem-resistant K. pneumoniae, which are promising therapeutic agents for the treatment of respiratory tract infections using the topical mode of administration as the preferred route of bacteriophage delivery.

Mining of Thousands of Prokaryotic Genomes Reveals High Abundance of Prophages with a Strictly Narrow Host Range

Phages and prophages are one of the principal modulators of microbial populations. However, much of their diversity is still poorly understood. Here, we extracted 33,624 prophages from 13,713 complete prokaryotic genomes to explore the prophage diversity and their relationships with their host. Our results reveal that prophages were present in 75% of the genomes studied. In addition, Enterobacterales were significantly enriched in prophages. We also found that pathogens are a significant reservoir of prophages. Finally, we determined that the prophage relatedness and the range of genomic hosts were delimited by the evolutionary relationships of their hosts. On a broader level, we got insights into the prophage population, identified in thousands of publicly available prokaryotic genomes, by comparing the prophage distribution and relatedness between them and their hosts.

IMPORTANCE Phages and prophages play an essential role in controlling their host populations either by modulating the host abundance or providing them with genes that benefit the host. The constant growth in next-generation sequencing technology has caused the development of powerful computational tools to identify phages and prophages with high precision. Making it possible to explore the prophage populations integrated into host genomes on a large scale. However, it is still a new and under-explored area, and efforts are still required to identify prophage populations to understand their dynamics with their hosts.

Formulation of phage cocktails and evaluation of their interaction with antibiotics in inhibiting carbapenemase-producing Klebsiella pneumoniae in vitro in Kenya

Background

The development of alternative control measures, such as phage therapy or adjunctive therapy, is urgently needed to manage the dissemination of carbapenemase-producing Klebsiella pneumoniae.

Objective

This study aimed to evaluate the therapeutic potential of formulated phage cocktails and their interaction with select antibiotics in inhibiting the growth of carbapenemase-producing K. pneumoniae clinical isolate in vitro in Kenya.

Methods

The study was conducted from February 2021 to October 2021 at the Institute of Primate Research, Nairobi, Kenya. Phage cocktails were formulated based on the morphology and biological properties of precipitated Klebsiella phages. The efficacy of individual bacteriophages and phage cocktails as well as their combination with antibiotics were determined for their inhibitory activity on carbapenemase-producing K. pneumoniae (KP20).

Results

The precipitated bacteriophages were members of Myoviridae, Siphoviridae and Podoviridae. Regarding the evaluation of the phage cocktails, the absorbances at 600 nm of the bacterial culture treated with the two-phage cocktail (2φ MA) ranged from 0.173 to 0.246 at 16 h and 20 h whereas it peaked from 2.116 to 2.190 for the positive control. Moreover, the results of the adjunctive therapy showed that the optical density at 600 nm of the bacterial culture treated with 2φ MA was 0.186 at 24 h post-incubation time while it was 0.099 with the bacterial culture treated with imipenem in combination with 2φ MA.

Conclusion

This study demonstrated that the two-phage cocktail in combination with imipenem was able to synergistically delay the increase in carbapenemase-producing K. pneumoniae growth in vitro.

Antimicrobial Resistance Rates and Surveillance in Sub-Saharan Africa: Where Are We Now?

Introduction

Although antimicrobials have traditionally been used to treat infections and improve health outcomes, resistance to commonly used antimicrobials has posed a major challenge. An estimated 700,000 deaths occur globally every year as a result of infections caused by antimicrobial-resistant pathogens. Antimicrobial resistance (AMR) also contributes directly to the decline in the global economy. In 2019, sub-Saharan Africa (SSA) had the highest mortality rate (23.5 deaths per 100,000) attributable to AMR compared to other regions.

Methods

We searched PubMed for articles relevant to AMR in pathogens in the WHO-GLASS list and in other infections of local importance in SSA. In this review, we focused on AMR rates and surveillance of AMR for these priority pathogens and some of the most encountered pathogens of public health significance. In addition, we reviewed the implementation of national action plans to mitigate against AMR in countries in SSA.

Results and Discussion

The SSA region is disproportionately affected by AMR, in part owing to the prevailing high levels of poverty, which result in a high burden of infectious diseases, poor regulation of antimicrobial use, and a lack of alternatives to ineffective antimicrobials. The global action plan as a strategy for prevention and combating AMR has been adopted by most countries, but fewer countries are able to fully implement country-specific action plans, and several challenges exist in many settings.

Conclusion

A concerted One Health approach will be required to ramp up implementation of action plans in the region. In addition to AMR surveillance, effective implementation of infection prevention and control, water, sanitation, and hygiene, and antimicrobial stewardship programs will be key cost-effective strategies in helping to tackle AMR.

Causative organisms and antimicrobial susceptibility in jaundiced infants with significant bacteriuria

BACKGROUND

Jaundice may be one of the first signs of urinary tract infection (UTI) in infants. The most common pathogen is Escherichia coli. Currently recommended antibiotic treatment for neonatal UTI is ampicillin and an aminoglycoside. Recently, increasing ampicillin and gentamicin resistance in strains of E. coli has been isolated. The aim of this study was to determine causative organisms and antimicrobial susceptibility in jaundiced infants with significant bacteriuria (SB).

METHODS

We evaluated admitted afebrile, asymptomatic infants younger than 1-month old with hyperbilirubinemia (total bilirubin >15 mg/dl) requiring phototherapy between January 2011 and December 2015. A total of 615 asymptomatic jaundiced infants were enrolled. Urinalysis and urine cultures were performed on all jaundiced infants. A urine culture was defined as SB if a single pathogen with more than 105-colony forming units per milliliter (CFU/ml) by sterile urinary collection bag or 104 CFU/ml by catheterization was isolated.

RESULTS

A total of 88 (14.3%) of 615 asymptomatic jaundiced infants had positive urinary culture. E coli was the most common cultured bacteria (40 cases, [45.5%]). Enterococcus faecalis was the second most common bacteria (17 cases, [19.3%]). Seven cases (8.0%) of Streptococcus agalactiae and six cases (6.8%) of Klebsiella pneumoniae were also identified. Ampicillin sensitivity was found in 22.5% of E. coli infections, gentamicin sensitivity was found in 84.2%, and extended-spectrum β-lactamases were found in 7.5%.

CONCLUSION

E. coli was the most common causative organism for infants with SB. We suggest modifying current empiric antibiotics by changing gentamicin to amikacin for neonatal Gram-negative bacterial infections.

Emergence of High Prevalence of Extended-Spectrum Beta-Lactamase and Carbapenemase Producing Acinetobacter Species and Pseudomonas aeruginosa Among Hospitalized Patients at Dessie Comprehensive Specialized Hospital, North-East Ethiopia

Background

The emergence of extended spectrum beta lactamase and carbapenemase production of Acinetobacter and Pseudomonas aeruginosa is a great concern and major cause of nosocomial infections due to its ability to production of extended spectrum beta lactamase and carbapenemase enzymes.

Objective

To assess Emergence of high prevalence of extended-spectrum beta-lactamase and Carbapenemase producing Acinetobacter species and Pseudomonas aeruginosa among hospitalized patients at Dessie Comprehensive Specialized Hospital, North-East Ethiopia.

Materials and Methods

A hospital-based cross-sectional study was conducted from February–August 2021 at Dessie Referral Hospital in the North eastern Ethiopia. A total of 423 clinical samples taken from admitted patients. Clinical specimens were collected aseptically and inoculated on blood agar and MacConkey agar media. Antimicrobial susceptibility test, ESBL and carbapenemase production were performed as CLSI guideline. The data were entered into the Epi-data and imported to Statistical Package for Social Science version 25. P value of <0.05 with odds ratio and 95% confidence interval was considered as statistically significant.

Results

Out of 423 clinical specimens 17.7% (75/423) were culture positive nosocomial infection. The proportions of nosocomial infection were higher in blood stream followed by wound infection which accounted 24.6%, 20.8%, respectively. Overall, 32/75 (42.7%) and 19/75 (25.3%) patients had infection with ESBL and CP producing bacterial infection. P. aeruginosa was the most predominant isolated bacteria 46/75 (52.9%). The overall multidrug resistance rate of the isolated bacteria was 88% (66/75). The majority of highest resistance rate was Piperacillin tazobactam 50 (66.7%) and Aztreonam 26 (56.5%), respectively, while least resistance rate was Amikacin 27 (36%).

Conclusion

The incidence rates of ESBL, carbapenemase production and antimicrobial resistant Acinetobacter species and P. aeruginosa infections are high. Therefore, treatment should be based on culture and antimicrobial test result and minimize the use of antibiotics empirically.

Phyto-Mediated Copper Oxide Nanoparticles for Antibacterial, Antioxidant and Photocatalytic Performances

The greatest challenge of the current generation and generations to come is antimicrobial resistance, as different pathogenic bacteria have continuously evolved to become resistant to even the most recently synthesized antibiotics such as carbapenems. Resistance to carbapenems limits the therapeutic options of MDR infections as they are the only safe and effective drugs recommended to treat such infections. This scenario has complicated treatment outcomes, even to the commonest bacterial infections. Repeated attempts to develop other approaches have been made. The most promising novel therapeutic option is the use of nanomaterials as antimicrobial agents. Thus, this study examined the efficacy of Camellia sinensis extract (CSE) and Prunus africana bark extract (PAE) green synthesized Copper oxide nanoparticles (CuONPs) against carbapenem-resistant bacteria. Furthermore, the photocatalytic and antioxidant activities of CuONPs were evaluated to determine the potential of using them in a wide range of applications. CuONPs were biosynthesized by CSE and PAE. UV vis spectroscopy, X-ray Diffraction (XRD), Dynamic light scattering (DLS), Fourier Transform Infrared spectroscopy (FTIR), and Scanning Electron Microscopy (SEM) were used to characterize the nanoparticles. CuONPs susceptibility tests were carried out by the agar well diffusion method. The photocatalytic and antioxidant activities of the CuONPs were determined by the methylene blue and DPPH free radical scavenging assays, respectively. UV vis absorbance spectra registered surface plasmon resonance peaks between 272 and 286 nm, confirming the presence of CuONPs. The XRD array had nine strong peaks at 2θ values typical of CuONPs. FTIR spectra exhibited bands associated with organic functional groups confirming capping and functionalization of the CuONPs by the phytochemicals. DLS analysis registered a net zeta potential of +12.5 mV. SEM analysis revealed that the nanoparticles were spherical and clustered with a mean diameter of 6 nm. Phytosynthesized CuONPs exhibited the highest growth suppression zones of 30 mm with MIC ranging from 30 to 125 μg/ml against MDR bacteria. Furthermore, the CuONPs achieved a methylene blue dye photocatalysis degradation efficiency of 85.5% and a free radical scavenging activity of 28.8%. PAE and CSE successfully bio-reduced copper ions to the nanoscale level with potent antimicrobial, photocatalysis, and antioxidant activities.

Emergence of High Prevalence of Extended-Spectrum Beta-Lactamase and Carbapenemase-Producing Enterobacteriaceae Species among Patients in Northwestern Ethiopia Region

Background. World Health Organization identified some Enterobacteriaceae as superbugs because of their high production and spread of extended-spectrum beta-lactamases (ESBL) and carbapenemases. Moreover, their resistance against commonly prescribed antibiotics left few choices of drugs to treat infection. This study is aimed at determining the magnitude of ESBL and carbapenemase-producing Enterobacteriaceae pathogens and their antimicrobial resistance pattern. Materials and Methods. A hospital-based cross-sectional study was carried out from February to April 2019 in the Northwestern Ethiopia region. A total of 384 patients presumptive for bacterial infections were conveniently enrolled in the study. Specimens were collected and processed following standard bacteriological procedures. Drug susceptibility tests were performed using disk diffusion technique. ESBL and carbapenemase enzymes were tested by double disk diffusion and modified carbapenem inhibition methods, respectively. The data obtained were analyzed using SPSS version 22 software, and descriptive statistics were summarized in tables and graphs. Results. Out of 384 clinical specimens processed 100 (26%) were culture positive for Enterobacteriaceae. The proportion of Enterobacteriaceae infection was relatively higher among in-patients 86 (32.6%) than out-patients 14 (11.7%). Overall, Escherichia coli 35 (9.1%) was the leading isolate followed by Klebsiella pneumoniae 31 (8.1%). Klebsiella pneumoniae 15 (15.6%) was the most frequent isolate from bloodstream infection and is the leading isolate from intensive care unit patients 15 (38.3%). Overall, 44 (44%) of Enterobacteriaceae were extended-spectrum beta-lactamase producers. Among them, Citrobacter spp. was the leading one 4 (80%) followed by Enterobacter cloacae 6 (60%) and K. pneumoniae 18 (58.1%). Furthermore, 6 (6%) of Enterobacteriaceae were carbapenemase-producers, in which 5 (50%) of E. cloacae and 3 (9.7%) of K. pneumoniae had highest percentage. Conclusions. ESBL and carbapenemase-producing isolates of Enterobacteriaceae are alarmingly spreading in the study area. Thus, improving the infection prevention strategy and further screening at the national level is recommended to develop the optimal use of antibiotics.

Prevalence and characterization of antimicrobial resistance among gram-negative bacteria isolated from febrile hospitalized patients in central Ethiopia

BACKGROUND

Infectious diseases are among the leading causes of death in many low-income countries, such as Ethiopia. Without reliable local data concerning causative pathogens and antimicrobial resistance, empiric treatment is suboptimal. The objective of this study was to characterize gram-negative bacteria (GNB) as pathogens and their resistance pattern in hospitalized patients with infections in central Ethiopia.

METHODS

Patients ≥ 1 year of age with fever admitted to the Asella Referral and Teaching Hospital from April 2016 to June 2018 were included. Blood and other appropriate clinical specimens were collected and cultured on appropriate media. Antibiotic susceptibility testing (AST) was performed using the Kirby-Bauer method and VITEK® 2. Species identification and detection of resistance genes were conducted using MALDI-ToF MS (VITEK® MS) and PCR, respectively.

RESULTS

Among the 684 study participants, 54.2% were male, and the median age was 22.0 (IQR: 14-35) years. Blood cultures were positive in 5.4% (n = 37) of cases. Among other clinical samples, 60.6% (20/33), 20.8% (5/24), and 37.5% (3/8) of swabs/pus, urine and other body fluid cultures, respectively, were positive. Among 66 pathogenic isolates, 57.6% (n = 38) were GNB, 39.4% (n = 26) were gram-positive, and 3.0% (n = 2) were Candida species. Among the isolated GNB, 42.1% (16/38) were Escherichia coli, 23.7% (9/38) Klebsiella pneumoniae and 10.5% (4/38) Pseudomonas aeruginosa. In total, 27/38 gram-negative isolates were available for further analysis. Resistance rates were as follows: ampicillin/sulbactam, 92.6% (n = 25); cefotaxime, 88.9% (n = 24); ceftazidime, 74.1% (n = 20); cefepime, 74.1% (n = 20); gentamicin, 55.6% (n = 15); piperacillin/tazobactam, 48.1% (n = 13); meropenem, 7.4% (n = 2); and amikacin, 3.7% (n = 1). The bla_NDM-1 gene was detected in one K. pneumoniae and one Acinetobacter baumannii isolate, which carried an additional bla_OXA-51 gene. The ESBL enzymes were detected in 81.5% (n = 22) of isolates as follows: TEM, 77.2% (n = 17); CTX-M-1 group, 68.2% (n = 15); SHV group, 27.3% (n = 6); and CTX-M-9 group, 9.1% (n = 2). Based on the in vitro antimicrobial susceptibility results, empiric treatment initiated in 13 of 18 (72.2%) patients was likely ineffective.

CONCLUSION

We report a high prevalence of ESBL-producing bacteria (81.5%) and carbapenem resistance (7.4%), with more than half of GNB carrying two or more ESBL enzymes resulting in suboptimal empiric antibiotic therapy. These findings indicate a need for local and national antimicrobial resistance surveillance and the strengthening of antimicrobial stewardship programs.

The current state of immunization against Gram-negative bacteria in children: a review of the literature

PURPOSE OF REVIEW

Gram-negative bacteria (GNB) are a major cause of infection worldwide and multidrug resistance in infants and children. The major pathogens include Klebsiella pneumoniae, Escherichia coli, Enterobacter spp., Pseudomonas aeruginosa and Acinetobacter baumannii. With new antibiotic options limited, immunization is likely to play a critical role in prevention. This review discusses their epidemiology, the current state of vaccine research and potential immunization strategies to protect children. A comprehensive review of the literature, conference abstracts along with web searches was performed to identify current and investigational vaccines against the major GNB in children.

RECENT FINDINGS

Phase I--III vaccine trials have been undertaken for the major Gram-negative bacteria but not in infants or children. E. coli is a common infection in immune-competent children, including neonatal sepsis. Several vaccines are in late-phase clinical trials, with some already licensed for recurrent urinary tract infections in women. Klebsiella spp. causes community-acquired and hospital-acquired infections, including sepsis in neonates and immunocompromised children although no vaccine trials have extended beyond early phase 2 trials. P. aeruginosa is a common pathogen in patients with cystic fibrosis. Phase 1--3 vaccine and monoclonal antibody trials are in progress, although candidates provide limited coverage against pathogenic strains. Enterobacter spp. and A. baumannii largely cause hospital-acquired infections with experimental vaccines limited to phase 1 research.

SUMMARY

The current immunization pipelines for the most prevalent GNB are years away from licensure. Similar to incentives for new antibiotics, global efforts are warranted to expedite the development of effective vaccines.

Novel chromosomal insertions of ISEcp1-blaCTX-M-15 and diverse antimicrobial resistance genes in Zambian clinical isolates of Enterobacter cloacae and Escherichia coli

Background

The epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types. bla_CTX-M genes, encoding CTX-M-type ESBLs, are usually found on plasmids, but chromosomal location is becoming common. Given that bla_CTX-M-harboring strains often exhibit multidrug resistance (MDR), it is important to investigate the association between chromosomally integrated bla_CTX-M and the presence of additional antimicrobial resistance (AMR) genes, and to identify other relevant genetic elements.

Methods

A total of 46 clinical isolates of cefotaxime-resistant Enterobacteriaceae (1 Enterobacter cloacae, 9 Klebsiella pneumoniae, and 36 Escherichia coli) from Zambia were subjected to whole-genome sequencing (WGS) using MiSeq and MinION. By reconstructing nearly complete genomes, bla_CTX-M genes were categorized as either chromosomal or plasmid-borne.

Results

WGS-based genotyping identified 58 AMR genes, including four bla_CTX-M alleles (i.e., bla_CTX-M-14, bla_CTX-M-15, bla_CTX-M-27, and bla_CTX-M-55). Hierarchical clustering using selected phenotypic and genotypic characteristics suggested clonal dissemination of bla_CTX-M genes. Out of 45 bla_CTX-M gene-carrying strains, 7 harbored the gene in their chromosome. In one E. cloacae and three E. coli strains, chromosomal bla_CTX-M-15 was located on insertions longer than 10 kb. These insertions were bounded by ISEcp1 at one end, exhibited a high degree of nucleotide sequence homology with previously reported plasmids, and carried multiple AMR genes that corresponded with phenotypic AMR profiles.

Conclusion

Our study revealed the co-occurrence of ISEcp1-bla_CTX-M-15 and multiple AMR genes on chromosomal insertions in E. cloacae and E. coli, suggesting that ISEcp1 may be responsible for the transposition of diverse AMR genes from plasmids to chromosomes. Stable retention of such insertions in chromosomes may facilitate the successful propagation of MDR clones among these Enterobacteriaceae species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-021-00941-8.

Multidrug resistance pattern of Acinetobacter species isolated from clinical specimens referred to the Ethiopian Public Health Institute: 2014 to 2018 trend anaylsis

BACKGROUND

Acinetobacter species have been a leading cause of nosocomial infections, causing significant morbidity and mortality over the entire world including Ethiopia. The most important features of A. baumannii are its ability to persist in the hospital environment and rapidly develop resistance to a wide variety of antibiotics. This study aimed to determine trend of antimicrobial resistance in Acinetobacter species over a five years period.

METHOD

A retrospective data regarding occurrence and antimicrobial resistance of Acinetobacter species recovered from clinical specimens referred to the national reference laboratory was extracted from microbiology laboratory data source covering a time range from 2014 to 2018. Socio-demographic characteristics and laboratory record data was analyzed using SPSS 20.

RESULTS

A total of 102 strains of Acinetobacter species were analyzed from various clinical specimens. Majority of them were from pus (33.3%) followed by blood (23.5%), urine (15.6%) and body fluid (11.7%). Significant ascending trends of antimicrobial resistance was shown for meropenem (12.5% to 60.7%), ceftazidime (82.1% to 100%), ciprofloxacin (59.4% to 74.4%), ceftriaxone (87.1% to 98.6%), cefepime (80.0% to 93.3%) and pipracillin- tazobactam (67.8% to 96.3%). However, there was descending trend of antimicrobial resistance for tobramycin (56.5% to 42.8%), amikacin (42.1% to 31.4%) and trimethoprim-sulfamethoxazole (79.0 to 68.2%). The overall rate of carbapenem non-susceptible and multidrug resistance rates in Acinetobacter species were 56.7% and 71.6%.respectively.

CONCLUSION

A five year antimicrobial resistance trend analysis of Acinetobacter species showed increasing MDR and resistance to high potent antimicrobial agents posing therapeutic challenge in our Hospitals and health care settings. Continuous surveillance and appropriate infection prevention and control strategies need to be strengthened to circumvent the spread of multidrug resistant pathogens in health care facilities.

Carbapenem-Resistant Enterobacteriaceae-Implications for Treating Acute Leukemias, a Subgroup of Hematological Malignancies

Acute leukemias (AL) are a group of aggressive malignant diseases associated with a high degree of morbidity and mortality. Patients with AL are highly susceptible to infectious diseases due to the disease itself, factors attributed to treatment, and specific individual risk factors. Enterobacteriaceae presence (e.g., Klebsiella pneumonia and Escherichia coli) is a frequent cause of bloodstream infections in AL patients. Carbapenem-resistant Enterobacteriaceae (CRE) is an emerging health problem worldwide; however, the incidence of CRE varies greatly between different regions. Carbapenem resistance in Enterobacteriaceae is caused by different mechanisms, and CRE may display various resistance profiles. Bacterial co-expression of genes conferring resistance to both broad-spectrum β-lactam antibiotics (including carbapenems) and other classes of antibiotics may give rise to multidrug-resistant organisms (MDROs). The spread of CRE represents a major treatment challenge for clinicians due to lack of randomized clinical trials (RCTs), a limited number of antibiotics available, and the side-effects associated with them. Most research concerning CRE infections in AL patients are limited to case reports and retrospective reviews. Current research recommends treatment with older antibiotics, such as polymyxins, fosfomycin, older aminoglycosides, and in some cases carbapenems. To prevent the spread of resistant microbes, it is of pivotal interest to implement antibiotic stewardship to reduce broad-spectrum antibiotic treatment, but without giving too narrow a treatment to neutropenic infected patients.

Prevalence of pathogenic Klebsiella pneumoniae based on PCR capsular typing harbouring carbapenemases encoding genes in Uganda tertiary hospitals

BACKGROUND

Klebsiella pneumoniae is an opportunistic pathogen that has been implicated as one of commonest cause of hospital and community acquired infections. The K. pneumoniae infections have considerably contributed to morbidity and mortality in patients with protracted ailments. The capacity of K. pneumoniae to cause diseases depends on the presence of an array virulence factors. Coexistence and expression of virulence factors and genetic determinants of antibiotic resistance complicates treatment outcomes. Thus, emergence of pathogenic MDR K. pneumoniae poses a great threat to the healthcare system. However, the carriage of antibiotic resistance among pathogenic K. pneumoniae is yet to be investigated in Uganda. We sought to investigate the carbapenem resistance profiles and pathogenic potential based on capsular serotypes of K. pneumoniae clinical isolates.

METHODS

This was a cross sectional study involving use of archived Klebsiella pneumoniae isolates collected between January and December, 2019 at four tertiary hospitals in Uganda. All isolates were subject to antimicrobial susceptibility assays to determine phenotypic antibiotic resistance, pentaplex PCR to detect carbapenemases encoding genes and heptaplex PCR to identify capsular serotypes K1, K2, K3, K5, K20, K54 and K57.

RESULTS

The study found an overall phenotypic carbapenem resistance of 23.3% (53/227) and significantly higher genotypic resistance prevalence of 43.1% (98/227). Over all, the most prevalent gene was blaOXA-48-like (36.4%), followed by blaIMP-type (19.4%), blaVIM-type (17.1%), blaKPC-type (14.0%) and blaNDM-type (13.2%). blaVIM-type and blaOXA-48-like conferred phenotypic resistance in all isolates and 38.3% of isolates that harbored them respectively. Capsular multiplex PCR revealed that 46.7% (106/227) isolates were pathogenic and the predominantly prevalent pathotype was K5 (18.5%) followed by K20 (15.1%), K3 (7.1%), K2 (3.1%) and K1 (2.2%). Of the 106 capsular serotypes, 37 expressed phenotypic resistance; thus, 37 of the 53 carbapenem resistant K. pneumoniae were pathogenic.

CONCLUSION

The high prevalence of virulent and antibiotic resistant K. pneumoniae among clinical isolates obtained from the four tertiary hospital as revealed by this study pose a great threat to healthcare. Our findings underline the epidemiological and public health risks and implications of this pathogen.

Detection of diverse carbapenem and multidrug resistance genes and high-risk strain types among carbapenem non-susceptible clinical isolates of target gram-negative bacteria in Kenya

Carbapenem-resistant gram-negative bacteria are an increasingly significant clinical threat globally. This risk may be underestimated in Kenya as only four carbapenemase genes in three bacterial species have been described. The study aimed to understand the antibiotic resistance profiles, genes, sequence types, and distribution of carbapenem-resistant gram-negative bacteria from patients in six hospitals across five Kenyan counties by bacterial culture, antibiotic susceptibility testing, and whole-genome sequence analysis. Forty-eight, non-duplicate, carbapenem non-susceptible, clinical isolates were identified across the five counties (predominantly in Nairobi and Kisii): twenty-seven Acinetobacter baumannii, fourteen Pseudomonas aeruginosa, three Escherichia coli, two Enterobacter cloacae, and two Klebsiella pneumoniae. All isolates were non-susceptible to β-lactam drugs with variable susceptibility to tigecycline (66%), minocycline (52.9%), tetracycline (29.4%), and levofloxacin (22.9%). Thirteen P. aeruginosa isolates were resistant to all antibiotics tested. Eleven carbapenemase genes were identified: blaNDM-1, blaOXA-23, -58, -66, -69, and -91 in A. baumannii (STs 1, 2, 164 and a novel ST1475), blaNDM-1 in E. cloacae (STs 25,182), blaNDM-1, blaVIM-1and -6, blaOXA-50 in P. aeruginosa (STs 316, 357, 654, and1203), blaOXA-181, blaNDM-1 in K. pneumoniae (STs 147 and 219), and blaNDM-5 in E. coli (ST164). Five A. baumannii isolates had two carbapenemases, blaNDM-1, and either blaOXA-23 (4) or blaOXA-58 (1). AmpC genes were detected in A. baumannii (blaADC-25), E. cloacae (blaDHA-1 and blaACT-6, 16), and K. pneumoniae (blaCMY). Significant multiple-drug resistant genes were the pan-aminoglycoside resistance16srRNA methyltransferase armA, rmtB, rmtC, and rmtF genes. This study is the first to report blaOXA-420, -58, -181, VIM-6, and blaNDM-5 in Kenyan isolates. High-risk STs of A. baumannii (ST1475, ST2), E. cloacae ST182, K. pneumoniae ST147, P. aeruginosa (ST357, 654), and E. coli ST167, ST648 were identified which present considerable therapeutic danger. The study recommends urgent carbapenem use regulation and containment of high-risk carbapenem-resistant bacteria.

Phenotypic Detection of Carbapenem-Resistant Gram-Negative Bacilli from a Clinical Specimen in Sidama, Ethiopia: A Cross-Sectional Study

BACKGROUND

Carbapenem-resistant gram-negative bacteria are an emergent source of both community-acquired and healthcare-associated infection that poses a substantial hazard to public health. This study aimed to conclude the magnitude of carbapenem resistance gram-negative bacteria from a clinical specimen at Hawassa University Comprehensive Specialized Hospital.

METHODS

A hospital-based cross-sectional study was accompanied from February 13 to June 7, 2020, in which consecutive patients with 103 gram-negative bacteria were encompassed. The isolates included were 54 urine, 17 blood, 17 pusses, 4 cerebrospinal fluid (CSF), 3 aspirates, 3 effusions, 2 stools, 2 ear discharges, and 1 nasal swab. A semi-structured questionnaire was used to gather socio-demographic data from the attendant and clinical data from the patient's chart. Patients admitted in any wards and visited outpatients department were included for the study if gram-negative bacteria was identified for those who accepted the consent. A routine manual culture, Gram's staining and biochemical tests used to identify the bacteria. Antibiotic susceptibility was determined for twelve antibiotics including cotrimoxazole, ceftazidime, meropenem, gentamycin, chloramphenicol, ampicillin, ciprofloxacin, cefotaxime, cefuroxime, nitrofurantoin, piperacillin-tazobactam, and amikacin using the Kirby-Bauer disc diffusion method. Modified carbapenem inactivation (mCIM) method was used to determine carbapenem resistance using meropenem disk as per the recommendation of Clinical and Laboratory Standards Institute guideline. Statistical package for social science software version 21 was used for data entry and analysis. The odds ratio at 95% confidence interval (CI) and p-value <0.05 were taken as a statistically significant association.

RESULTS

Generally, 111 gram-negative bacteria were identified from 103 patients. Of 111 isolates, thirteen isolates (nine resistance and four intermediates) were identified in disk diffusion testing for meropenem. Of this, 10 isolates were carbapenemases producer with the overall rates of 9% in the Modified carbapenem inactivation method (mCIM). Pseudomonas spp. 3 (30.0%), E. coli, K. pneumonia, Acinetobacter spp. each two (20.0%), and K. oxytoca 1 (10.0%) were identified as carbapenemases positive. The rates of the multidrug, extensive, pan drug were 86.5, 43.3, and 1.8, respectively. Ampicillin 94 (97.9%), followed by cefuroxime 52 (91.2%), cefotaxime 94 (88.7%), cotrimoxazole 58 (88.1%), ceftazidime 40 (83.3%), ciprofloxacin 47 (77.1%), nitrofurantoin 35 (70.0%), gentamycin 71 (65.7%), with high level of resistance. However, piperacillin-tazobactam 41 (48.8%), chloramphenicol 25 (47.2%), meropenem 13 (11.7%), and amikacin 9 (8.5%) were with low rates of resistance. In this study, there were no variables statically associated with carbapenem resistance that is p > 0.05.

CONCLUSION

Our study showed that carbapenem-resistant gram-negative bacilli are 9% in the study area. Our finding signposts that ampicillin, cefuroxime, cefotaxime, cotrimoxazole, ceftazidime, ciprofloxacin, nitrofurantoin, and gentamycin with a high rate of resistance >50%. However, piperacillin-tazobactam, chloramphenicol, meropenem, and amikacin were at low rates of resistance. Therefore, a measure should be taken to contain carbapenem resistance gram-negative bacteria in the study area. Further, study with better method needs to be conducted to conclude the real scenario of carbapenem resistance.

Elevated Level of Imipenem-Resistant Gram-Negative Bacteria Isolated from Patients Attending Health Centers in North Gondar, Ethiopia

Background

The frequent identification of resistant bacteria in hospitals constantly presents antimicrobial therapy with a challenge. Imipenem, once considered an extremely powerful antibiotic against multidrug-resistant bacterial infections, is losing its effectiveness. Its use in empirical therapy with inadequate or nonexistent antimicrobial stewardship programs has further triggered bacterial resistance in low-income countries. Therefore, this study aimed at identifying imipenem-resistant Gram-negative bacteria from patients who were referred to health centers in North Gondar, Ethiopia.

Methods

A total of 153 sputum samples were used to isolate Gram-negative bacteria. The isolates, which were resistant to imipenem, were identified by standard biochemical tests and 16S rRNA sequencing. The Kirby-Bauer disk diffusion method was used to determine the sensitivity or resistance of the isolate to diverse antimicrobial agents.

Results

The study identified 79 imipenem-resistant bacterial isolates from eight genera with clinically relevant microorganisms, including Acinetobacter baumannii (20.77%), Klebsiella pneumoniae (19.48%), Pseudomonas aeruginosa (16.88%), and Serratia marcescens (14.28%). Overall, imipenem-resistant bacterial isolates were detected in 31 samples (20.26%). Additionally, a remarkably high level of resistance to most antibiotics was observed among isolates of Klebsiella pneumoniae and Acinetobacter baumannii. Gentamycin is the most active antibiotic against many of the isolates, while β-lactams appear to be less effective.

Conclusion

The study indicated that many Gram-negative bacteria were resistant to imipenem with parallel resistances to other antimicrobials. Hence, the prescription of imipenem within the region should be according to the antibiotic resistance profiles of the multi-drug resistant bacteria.

Tracking Antimicrobial Resistance Determinants in Diarrheal Pathogens: A Cross-Institutional Pilot Study

Infectious diarrhea affects over four billion individuals annually and causes over a million deaths each year. Though not typically prescribed for treatment of uncomplicated diarrheal disease, antimicrobials serve as a critical part of the armamentarium used to treat severe or persistent cases. Due to widespread over- and misuse of antimicrobials, there has been an alarming increase in global resistance, for which a standardized methodology for geographic surveillance would be highly beneficial. To demonstrate that a standardized methodology could be used to provide molecular surveillance of antimicrobial resistance (AMR) genes, we initiated a pilot study to test 130 diarrheal pathogens (Campylobacter spp., Escherichia coli, Salmonella, and Shigella spp.) from the USA, Peru, Egypt, Cambodia, and Kenya for the presence/absence of over 200 AMR determinants. We detected a total of 55 different determinants conferring resistance to ten different categories of antimicrobials: genes detected in ≥ 25 samples included bla_TEM, tet(A), tet(B), mac(A), mac(B), aadA1/A2, strA, strB, sul1, sul2, qacEΔ1, cmr, and dfrA1. The number of determinants per strain ranged from none (several Campylobacter spp. strains) to sixteen, with isolates from Egypt harboring a wider variety and greater number of genes per isolate than other sites. Two samples harbored carbapenemase genes, bla_OXA-48 or bla_NDM. Genes conferring resistance to azithromycin (ere(A), mph(A)/mph(K), erm(B)), a first-line therapeutic for severe diarrhea, were detected in over 10% of all Enterobacteriaceae tested: these included >25% of the Enterobacteriaceae from Egypt and Kenya. Forty-six percent of the Egyptian Enterobacteriaceae harbored genes encoding CTX-M-1 or CTX-M-9 families of extended-spectrum β-lactamases. Overall, the data provide cross-comparable resistome information to establish regional trends in support of international surveillance activities and potentially guide geospatially informed medical care.

High rate of extended-spectrum beta-lactamase-producing gram-negative infections and associated mortality in Ethiopia: a systematic review and meta-analysis

Background

Extended-spectrum beta-lactamase (ESBL)-producing Gram-negative bacteria have become a serious threat to global health. Their rapid spread is associated with high mortality due to ineffective antibiotic treatment. To date a regular surveillance of multidrug-resistant (MDR) pathogens in Ethiopia is not established. For this report, published data regarding ESBL-producing bacteria in different health facilities of Ethiopia were reviewed.

Methods

This study collates data from published information on the rates and clinical implications of infection with ESBL-producing Gram-negative bacteria in Ethiopia. A systematic literature search was conducted using PubMed, PubMed Central, Medline, Science Direct and Google scholar from October 2018 to March 2019. Eligible studies were identified by applying quality criteria. The pooled proportion of ESBL-producing Gram-negative bacteria was estimated based on a random effect model. The publication bias and the variation in proportion estimates attributed to heterogeneity were assessed.

Results

Fourteen studies with relevant data were included in the review. In total, 1649 Gram-negative bacteria isolated from 5191 clinical samples were included. The pooled proportion estimate of ESBL-producing Gram-negative bacteria was 50% (95% CI: 47.7–52.5%. Data showed a high level of heterogeneity (I² = 95%, P <  0.01). ESBL rates varied by species; 65.7% (263/400) in Klebsiella spp., 48.4% (90/186) in Salmonella spp., and 47.0% (383/815) in E. coli. ESBL-encoding genes were reported in 81 isolates: 67 isolates harbored the CTX-M-1 group and 14 isolates TEM. The mortality associated with infections by bacteria resistant to third generation cephalosporins has rarely been investigated. However, two studies reported a mortality of 33.3% (1/3) and 100% (11/11).

Conclusions

In this meta-analysis, the pooled prevalence of ESBL-producing pathogens is alarmingly high. Data on mortality rates is scarce. This highlights the need for establishing and upgrading clinical microbiology laboratories in Ethiopia for routine antibiotic susceptibility testing and extended surveillance of multidrug resistance.

Genetic diversity and risk factors for the transmission of antimicrobial resistance across human, animals and environmental compartments in East Africa: a review

Background

The emergence and spread of antimicrobial resistance (AMR) present a challenge to disease control in East Africa. Resistance to beta-lactams, which are by far the most used antibiotics worldwide and include the penicillins, cephalosporins, monobactams and carbapenems, is reducing options for effective control of both Gram-positive and Gram-negative bacteria. The World Health Organization, Food and Agricultural Organization and the World Organization for Animal Health have all advocated surveillance of AMR using an integrated One Health approach. Regional consortia also have strengthened collaboration to address the AMR problem through surveillance, training and research in a holistic and multisectoral approach. This review paper contains collective information on risk factors for transmission, clinical relevance and diversity of resistance genes relating to extended-spectrum beta-lactamase-producing (ESBL) and carbapenemase-producing Enterobacteriaceae, and Methicillin-resistant Staphylococcus aureus (MRSA) across the human, animal and environmental compartments in East Africa.

Main body

The review of the AMR literature (years 2001 to 2019) was performed using search engines such as PubMed, Scopus, Science Direct, Google and Web of Science. The search terms included ‘antimicrobial resistance and human-animal-environment’, ‘antimicrobial resistance, risk factors, genetic diversity, and human-animal-environment’ combined with respective countries of East Africa. In general, the risk factors identified were associated with the transmission of AMR. The marked genetic diversity due to multiple sequence types among drug-resistant bacteria and their replicon plasmid types sourced from the animal, human and environment were reported. The main ESBL, MRSA and carbapenem related genes/plasmids were the ^blaCTX-Ms (45.7%), SCCmec type III (27.3%) and IMP types (23.8%), respectively.

Conclusion

The high diversity of the AMR genes suggests there may be multiple sources of resistance bacteria, or the possible exchange of strains or a flow of genes amongst different strains due to transfer by mobile genetic elements. Therefore, there should be harmonized One Health guidelines for the use of antibiotics, as well as regulations governing their importation and sale. Moreover, the trend of ESBLs, MRSA and carbapenem resistant (CAR) carriage rates is dynamic and are on rise over time period, posing a public health concern in East Africa. Collaborative surveillance of AMR in partnership with regional and external institutions using an integrated One Health approach is required for expert knowledge and technology transfer to facilitate information sharing for informed decision-making.

The Existence of High Bacterial Resistance to Some Reserved Antibiotics in Tertiary Hospitals in Tanzania: A Call to Revisit Their Use

Background

Antibiotic resistance poses burden to the community and health-care services. Efforts are being made at local, national and global level to combat the rise of antibiotic resistance including antibiotic stewardship. Surveillance to antibiotic resistance is of importance to aid in planning and implementing infection prevention and control measures. The study was conducted to assess the resistance pattern to cefepime, clindamycin and meropenem, which are reserved antibiotics for use at tertiary hospitals in Tanzania.

Methods

A hospital-based antibiotic resistance surveillance was conducted between July and November 2019 at Muhimbili National Hospital and Bugando Medical Center, Tanzania. All organisms isolated were identified based on colony morphology, Gram staining and relevant biochemical tests. Antibiotic susceptibility testing was performed on Muller-Hinton agar using Kirby-Bauer disc diffusion method. Antibiotic susceptibility was performed according to the protocol by National Committee for Clinical Laboratory Standards.

Results

A total of 201 clinical samples were tested in this study. Urine (39.8%, n=80) and blood (35.3%, n=71) accounted for most of the collected samples followed by pus (16.9%, n=34). The bacterial resistance to clindamycin, cefepime and meropenem was 68.9%, 73.2% and 8.5%, respectively. About 68.4% Staphylococcus aureus isolates were resistant to clindamycin whereby 56.3%, 75.6%, 93.8% and 100% of the tested Escherichia coli, Klebsiella spp, Pseudomonas aeruginosa and Enterobacter cloacae, respectively, were cefepime resistant. About 8.5% of isolated Klebsiella spp were resistant and 6.4% had intermediate susceptibility to meropenem. Also, Pseudomonas aeruginosa was resistant by 31.2% and 25% had intermediate susceptibility to meropenem.

Conclusion

The bacterial resistance to clindamycin and cefepime is high and low in meropenem. Henceforth, culture and susceptibility results should be used to guide the use of these antibiotics. Antibiotics with low resistance rate should be introduced to the reserve category and continuous antibiotic surveillance is warranted.

Urban and agricultural soils in Southern California are a reservoir of carbapenem-resistant bacteria

Carbapenems are last‐resort β‐lactam antibiotics used in healthcare facilities to treat multidrug‐resistant infections. Thus, most studies on identifying and characterizing carbapenem‐resistant bacteria (CRB) have focused on clinical settings. Relatively, little is still known about the distribution and characteristics of CRBs in the environment, and the role of soil as a potential reservoir of CRB in the United States remains unknown. Here, we have surveyed 11 soil samples from 9 different urban or agricultural locations in the Los Angeles–Southern California area to determine the prevalence and characteristics of CRB in these soils. All samples tested contained CRB with a frequency of <10 to 1.3 × 10⁴ cfu per gram of soil, with most agricultural soil samples having a much higher relative frequency of CRB than urban soil samples. Identification and characterization of 40 CRB from these soil samples revealed that most of them were members of the genera Cupriavidus, Pseudomonas, and Stenotrophomonas. Other less prevalent genera identified among our isolated CRB, especially from agricultural soils, included the genera Enterococcus, Bradyrhizobium, Achromobacter, and Planomicrobium. Interestingly, all of these carbapenem‐resistant isolates were also intermediate or resistant to at least 1 noncarbapenem antibiotic. Further characterization of our isolated CRB revealed that 11 Stenotrophomonas, 3 Pseudomonas, 1 Enterococcus, and 1 Bradyrhizobium isolates were carbapenemase producers. Our findings show for the first time that both urban and agricultural soils in Southern California are an underappreciated reservoir of bacteria resistant to carbapenems and other antibiotics, including carbapenemase‐producing CRB.

Antibiotic resistance in patients with clinical features of healthcare-associated infections in an urban tertiary hospital in Sierra Leone: a cross-sectional study

Background

Available data on antibiotic resistance in sub-Saharan Africa is limited despite its increasing threat to global public health. As there is no previous study on antibiotic resistance in patients with clinical features of healthcare-associated infections (HAIs) in Sierra Leone, research is needed to inform public health policies. Our study aimed to assess antibiotic resistance rates from isolates in the urine and sputum samples of patients with clinical features of HAIs.

Methodology

We conducted a cross-sectional study of adult inpatients aged ≥18 years at Connaught Hospital, an urban tertiary care hospital in Freetown between February and June 2018.

Results

Over the course of the study, we enrolled 164 patients. Risk factors for HAIs were previous antibiotic use (93.3%), comorbidities (58.5%) and age (≥65 years) (23.9%). Of the 164 samples, 89.6% were urine. Bacterial growth was recorded in 58.8% of cultured specimens; the type of specimen was an independent predictor of bacterial growth (p < 0.021). The most common isolates were Escherichia coli and Klebsiella pneumoniae; 29.2% and 19.0% in urine samples and 18.8% and 31.3% in sputum samples, respectively.

The overall resistance rates were 58% for all extended-spectrum beta-lactamase (ESBL)-producing organisms, 13.4% for carbapenem-resistant non-lactose fermenting gram-negative bacilli, 8.7% for carbapenem-resistant Acinetobacter baumannii (CRAB) and 1.3% for carbapenem-resistant Enterobacteriaceae (CRE). There were no carbapenem-resistant P. aeruginosa (CRPA) isolates but all Staphylococcus aureus isolates were methicillin-resistant S. aureus.

Conclusion

We demonstrated a high prevalence rate of ESBL-producing organisms which are a significant burden at the main tertiary hospital in Sierra Leone. Urgent action is needed to strengthen microbiological diagnostic infrastructure, initiate surveillance on antibiotic resistance and develop and implement policy framework on antibiotic stewardship.