High prevalence of multidrug resistant Enterobacteriaceae isolated from outpatient urine samples but not the hospital environment in Bo, Sierra Leone

Evolution of copper coupons resistance in Enterobacteriaceae strains isolated from high-contact surfaces in hospital

Objective

Metallic copper alloys have gained attention recently as a cutting-edge antibacterial weapon for areas where surface hygiene is crucial. The present study aimed to assess copper coupons (99% Cu) for their potential to decrease the viability of various Enterobacteriaceae strains from inanimate hospital surfaces.

Methods

This in vitro-experimental study was conducted at the Microbiology Laboratory, Faculty of Natural and Life Sciences and Earth and Universe Sciences, University of Guelma, and Khodja Ahmed Public Hospital Establishment, Algeria, for a period of six months from January to May 2022. A total of 85 samples were collected from patient room door handles and bed rails at the government hospital in Guelma State, from which 12 enterobacterial isolates were obtained. These isolates were evaluated for susceptibility to copper and polyvinyl chloride (PVC) coupons using plate counts to determine bacterial viability after 72 hours of incubation at 37°C or room temperature (25°C). Antibiotic sensitivity testing was then carried out using a modified Kirby-Bauer disc diffusion method. Copper coupons' ability to either select for or create antibiotic resistance is also determined.

Results

Copper showed a bactericidal effect after three hours for Serratia odorifera and six hours for Escherichia coli. Whereas it was shown that within three days of selection, 83.33% of Enterobacteriaceae strains are capable of rapidly acquiring Cu resistance. Indeed, the increase in temperature reduced the effects of Cu (p<0.05; Student's t-test). Antimicrobial susceptibility testing revealed that the copper-resistant bacteria were less sensitive than their predecessors. Citrobacter freundii strains showed the highest incidence of multidrug resistance. The most significant findings included widespread resistance to beta-lactams (100%-75%) and chloramphenicol (66.67%).

Conclusion

These results suggest that prolonged copper usage may contribute to the development of antibiotic resistance, which could have significant ramifications.

Uro-pathogens: Multidrug resistance and associated factors of community-acquired UTI among HIV patients attending antiretroviral therapy in Dessie Comprehensive Specialized Hospital, Northeast Ethiopia

BACKGROUND

Urinary tract infections are common bacterial and fungal infections in humans, occurring both in the community and in immunocompromised patients in healthcare settings. Urinary tract infections have a significant health impact on HIV-infected patients. Nowadays, drug-resistant pathogens are widespread poses a serious clinical risk, and causes urinary tract infection. The common agents of bacteria and fungi that cause urinary tract infection are Escherichia coli followed by Klebsiella pneumonia, Staphylococcus saprophyticus, Enterococcus faecalis, group B streptococcus, Proteus mirabilis, Pseudomonas aeruginosa, Staphylococcus aureus and Candida. albicans. This study aimed to investigate uro-pathogen, multidrug resistance pattern of bacteria, and associated factors of community-acquired urinary tract infection among HIV-positive patients attending antiretroviral therapy in Dessie comprehensive specialized hospital, Northeast Ethiopia from February 1, 2021, to March 30, 2021.

METHODS

An institutional-based cross-sectional study was conducted at Dessie Comprehensive Specialized Hospital. Socio-demographic and clinical data were collected by using structured questionnaires from HIV patients suspected of community-acquired urinary tract infections. About 10 ml of clean-catch midstream urine was collected and inoculated into Blood agar, MacConkey, and Cysteine lactose electrolyte deficient media. Yeasts were identified by using Gram stain, germ tube test, carbohydrate fermentation, assimilation tests, and chromogenic medium. Gram stain and biochemical tests were performed to identify isolates and an antimicrobial susceptibility pattern was performed on disc diffusion techniques. Data were entered and analyzed using SPSS version 25. Both bivariate and multivariable logistic regression analysis was performed and a P value of < 0.05 with an adjusted odds ratio with their 95% confidence interval (CI) was used as statistically significant associations.

RESULTS

From the total 346 study participants, 92 (26.6%) were culture positive 75 (81.52%) were bacterial and 17 (18.48%) were fungal pathogens. From a total of 75 bacteria isolates 51(68%) were Gram-negative bacteria and the most commonly isolated bacteria were E. coli 16 (21.33%) followed by K. pneumoniae 11(14.67%) and enterococcus species 10(10.87. Of the 17 fungal isolates of fungi, 8(47.1%) were represented by C. tropicalis. Of the isolated bacteria, 61(81.3%) were resistant to three and above classes of antibiotics (drug classes). About 13 (81.3%) of E. coli, 9(81.8%) of K. pneumoniae, 8(80%) of Enterococcus species, 7 (77.8%) of P. aeruginosa, and CoNs 7(87.5%) were the most frequently exhibited three and above classes of antibiotics (multi-drug resistance). Amikacin and gentamicin were effective against Gram-negative Uro-pathogens. Participants aged>44year, female, being daily labor, being farmer, unable to read and write, patients with CD4 count of ≤ 200 cells/mm3 and CD4 count of 201-350 cells/mm3, who had chronic diabetics, patients having a history of hospitalization and who had urgency of urinations were statistically significant association with significant urinary tract infections.

CONCLUSION

The burden of community-acquired urinary tract infections among HIV patients is alarmingly increased. Therefore, behavior change communications might be considered for promoting the health status of HIV patients. Moreover, CD4 level monitoring and therapeutics selection based on microbiological culture are quite advisable for the management of urinary tract infections of HIV patients.

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.

The Antimicrobial Resistance (AMR) Rates of Enterobacterales in a Rural Hospital from the Eastern Region, Ghana: A Retrospective Study, 2022

Low- and middle-income countries bear a disproportionate burden of antimicrobial resistance and often lack adequate surveillance due to a paucity of microbiological studies. In this 2022 study, our goal was to contribute to a more precise antimicrobial treatment by understanding the prevalence of resistance in a rural environment, promoting antibiotic stewardship, and raising awareness about antimicrobial resistance. We assessed the prevalence of Multidrug-Resistant (MDR) and Extensively Drug-Resistant (XDR) Enterobacterales in clinical samples from 2905 patients being treated at Saint Dominic's Hospital, Akwatia, in the countryside of the Eastern Region, Ghana, in the year 2022. To this purpose, the samples were cultured on agar plates prepared in the laboratory using purified Oxoid™ Thermo Scientific™ agar (Thermo Fisher Scientific; Waltham, MA, USA). Cystine Lactose Electrolyte-Deficient (CLED) agar was used for urine samples, while blood agar, chocolate agar, and MacConkey agar were used for the rest of the specimens tested (HVS, blood, BFA, sputum). Antimicrobial susceptibility was determined on site using the disc diffusion method (Kirby-Bauer test). MDR bacteria accounted for more than half (53.7%) of all microorganisms tested for three or more antibiotics and 37.3% of these were XDR. Multivariate regression analysis was performed to identify risk factors associated with acquiring MDR/XDR bacteria. The results showed an increased likelihood of MDR acquisition linked to being male (OR 2.39, p < 0.001 for MDR and OR 1.95, p = 0.027 for XDR), higher age (OR 1.01, p = 0.049 for MDR), non-sputum samples (OR 0.32, p = 0.009 for MDR), and urine samples (OR 7.46, p < 0.001 for XDR). These findings emphasize the urgency for surveillance and control of antimicrobial resistance; to this end, making accurate diagnostics, studying the microorganism in question, and conducting susceptibility testing is of the utmost importance.

Novel Starter Strain Enterococcus faecium DMEA09 from Traditional Korean Fermented Meju

The Enterococcus faecium strain DMEA09 was previously isolated from traditional Korean fermented meju. The objective of the current study was to investigate the traits of E. faecium strain DMEA09 as a starter candidate, focusing on its safety and technological properties. Regarding its safety, the DMEA09 strain was found to be sensitive to nine antibiotics (ampicillin, chloramphenicol, erythromycin, gentamicin, kanamycin, streptomycin, tetracycline, tylosin, and vancomycin) by showing lower minimum inhibitory concentrations (MICs) than the cut-off values suggested by the European Union Food Safety Authority for these nine antibiotics. However, its MIC value for clindamycin was twice as high as the cut-off value. A genomic analysis revealed that strain DMEA09 did not encode the acquired antibiotic resistance genes, including those for clindamycin. The DMEA09 strain did not show hemolysis as a result of analyzing α- and β-hemolysis. It did not form biofilm either. A genomic analysis revealed that strain DMEA09 did not encode for any virulence factors including hemolysin. Most importantly, multilocus sequence typing revealed that the clonal group of strain DMEA09 was distinguished from clinical isolates. Regarding its technological properties, strain DMEA09 could grow in the presence of 6% salt. It showed protease activity when the salt concentration was 3%. It did not exhibit lipase activity. Its genome possessed 37 putative protease genes and salt-tolerance genes for survivability under salt conditions. Consequently, strain DMEA09 shows safe and technological properties as a new starter candidate. This was confirmed by genome analysis.

Antimicrobial Resistance Patterns and Risk Factors Associated with ESBL-Producing and MDR Escherichia coli in Hospital and Environmental Settings in Lusaka, Zambia: Implications for One Health, Antimicrobial Stewardship and Surveillance Systems

Antimicrobial resistance (AMR) is a public health problem threatening human, animal, and environmental safety. This study assessed the AMR profiles and risk factors associated with Escherichia coli in hospital and environmental settings in Lusaka, Zambia. This cross-sectional study was conducted from April 2022 to August 2022 using 980 samples collected from clinical and environmental settings. Antimicrobial susceptibility testing was conducted using BD PhoenixTM 100. The data were analysed using SPSS version 26.0. Of the 980 samples, 51% were from environmental sources. Overall, 64.5% of the samples tested positive for E. coli, of which 52.5% were from clinical sources. Additionally, 31.8% were ESBL, of which 70.1% were clinical isolates. Of the 632 isolates, 48.3% were MDR. Most clinical isolates were resistant to ampicillin (83.4%), sulfamethoxazole/trimethoprim (73.8%), and ciprofloxacin (65.7%) while all environmental isolates were resistant to sulfamethoxazole/trimethoprim (100%) and some were resistant to levofloxacin (30.6%). The drivers of MDR in the tested isolates included pus (AOR = 4.6, CI: 1.9-11.3), male sex (AOR = 2.1, CI: 1.2-3.9), and water (AOR = 2.6, CI: 1.2-5.8). This study found that E. coli isolates were resistant to common antibiotics used in humans. The presence of MDR isolates is a public health concern and calls for vigorous infection prevention measures and surveillance to reduce AMR and its burdens.

Study of Plasmid-Mediated Extended-Spectrum Beta-Lactamase-Producing Clinical Strains of Enterobacteriaceae From Tabuk Region

BACKGROUND

Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae threaten infection treatment globally. This study aims to assess ESBLs-E prevalence and multidrug-resistant organisms (MDR) in clinical specimens from Tabuk, KSA.

METHODS

A cross-sectional research was carried out in March-May 2023. A collective of 90 Enterobacteriaceae isolates were identified from clinical specimens. The specimen was identified by standard methods. The Enterobacteriaceae member was screed for ESBL production by screening and confirmatory as per the Clinical and Laboratory Standards Institute (CLSI).

RESULT

E. coli was the most common isolate, followed by Proteus mirabilis and Citrobacter sp, Klebsiella oxytoca, Klebsiella pneumonia, Proteus vulgaris and Morganella morganii. Among the sample, the majority of isolates were from urine (47.8%) followed by pus (25.6%) and the least from other body fluids (6.7%). The E. coli showed the highest average antibiotic resistance (73.7%) among all the antibiotics used followed by P. mirabilis (70.4%), K. pneumoniae (70%), P. vulgaris (69.8%), M. morganii and Citrobacter (69.4% both), and K. oxytoca (68.8%). There was a 41.2% average reduction in ESBL positivity from phenotypic to confirmatory test results. The highest reduction was observed among M. morganii (66.7%) and the least was observed in E. coli (17.1%).

CONCLUSION

Most of the ESBL-producing isolates were found mainly in blood and urine samples. The most frequent ESBL-producing Enterobacteriaceae were K. pneumoniae and E. coli. The best options for treating Enterobacteriaceae that produce ESBL are Amoxicillin, Amikacin, and Cefoxitin. ESBL-producing isotopes showed a high resistance rate to cefepime and cefotaxime compared to non-ESBL producers. It is of utmost importance to implement reliable infection control measures in healthcare institutions nationwide.

Profiling of antibiotic resistance among uropathogens isolated from patients attending Kericho County Referral Hospital

Introduction

urinary tract infection (UTI) comes second after respiratory infections in most communities and hospital settings, affecting people of all ages. Frequent use of antibiotics to manage UTI has resulted in development of resistance, calling upon policymakers to fast-track and enforce policies that guide the use of antibiotics in the country. This study intended to determine the current antibiotic resistance to uropathogens among patients attending Kericho County Referral Hospital.

Methods

three hundred urine samples from eligible participants were cultured and bacteria colonies identified using biochemical tests. Antibiotic sensitivity was done using Kirby Bauer disk diffusion method on Mueller Hinton Agar. Results: the aetiological agents of UTI were Staphylococcus aureus, Enterococci faecalis, E. coli, Proteus spp and Klebsiella pneumonia. Antibiotic resistance was observed among these uropathogens to commonly used antibiotics namely; ampicillin (84.3%), azithromycin (71.9%) and augmentin (69.8%). However, there were some bacteria that were susceptible to all or some commonly used antibiotics. There was moderate resistance to norfloxacin (43%) except in Staphylococcus aureus which showed 64% resistance. The isolates showed less resistance to cefoxitine (13.2%), gentamycin (11.6%) and ciprofloxacin (10%). While most bacteria showed multiple resistance to 3 drugs, some showed resistance to at most 5 drugs tested in the study. Conclusion: this study found Staphylococcus aureus to be the predominant aetiological agent of UTI. Cefoxitine, gentamycin and ciprofloxacin are good therapeutic choices for confirmed recurrent UTI when culture results are unavailable. There is need to have regular screening of aetiological agents of UTI and their resistance to antimicrobials.

Determination of antimicrobial resistance patterns of Escherichia coli isolates from farm workers in broiler poultry production and assessment of antibiotic resistance awareness levels among poultry farmers in Lusaka, Zambia

The challenges posed by antibiotic-resistant pathogens have continued to increase worldwide, particularly in resource-limited countries. Human-livestock interactions are implicated in the complex AMR causal web. A cross-sectional study was conducted in four districts of Lusaka Province, Zambia to determine the antibiotic resistance patterns, ESBL production of E. coli isolated from stool samples of broiler poultry farm workers, and to assess poultry farmers' antibiotic resistance awareness. Sixty-six human stool samples were collected and processed for E. coli isolation, antibiotic resistance testing, and screened for ESBL production. In addition, 80 farmers were assessed for their level of awareness on antibiotic resistance. A total of 58 single E. coli isolates were obtained which showed high (87.9%) resistance to tetracycline, trimethoprim/sulfamethoxazole (48.3%), and ampicillin (46.8%); followed by nalidixic acid (19.0%), ciprofloxacin (12.1%), cefotaxime (8.6%) and chloramphenicol (5.2%). The prevalence of AMR E. coli was 67.2%, and 29.3% were MDR. Two (3.4%) isolates were identified to be ESBL producers, harboring the CTX-M gene. The study results also showed that broiler farmers were aware and knowledgeable of antibiotic resistance, although knowledge about its impact on human health was low. This study demonstrated the presence of resistant and ESBL producing E. coli among poultry farm workers.

Pilot drug and therapeutic committee programme in Sierra Leone: A descriptive mixed method study

AIMS

Irrational medicine use is a global crisis, but incidences are proportionately higher in low- and middle-income countries such as Sierra Leone. This study explores the structure, functions and challenges of drug and therapeutics committees (DTCs), an intervention towards irrational medicine use recently piloted in Sierra Leone.

METHODS

A 2-phase mixed-method study design was used in this study. Firstly, a cross-sectional survey was conducted on all pharmacists who have worked for at least 1 year in DTC-piloted hospitals, using an online questionnaire to assess DTCs' structure, indicators and challenges. In phase 2, all eligible pharmacists were invited for a semistructured online interview using the WhatsApp messaging application to get deeper insights into the key issues that emerged from the survey; however, only 5 of the 7 consented to participate. MS Excel 2019 and NVivo version 12 were respectively used for data management and analysis.

RESULTS

A total of 6 survey responses and 5 interviews were included in the analysis. Participants are pharmacists from the 7 hospitals in Sierra Leone where DTC was piloted. Most DTCs are comprised of a minimum of 10 members consisting of both medical and hospital administrative staff. The main functions of DTCs are ensuring rational medicines use, monitoring and reporting adverse drug reactions. All 7 hospitals with established pilot DTCs have different subcommittees operating at varying functionality levels, ranging from effective to nonfunctional. The main challenges in DTC functions and maintenance are funding (n = 6), DTC decision implementation (n = 4), and unmotivated members (n = 4). Strategies suggested to improve DTCs at public hospitals and nationwide include resource allocation, monitoring and evaluating DTC functions and its members' capacity building.

CONCLUSION

DTCs present a compelling opportunity towards achieving rational medicines use at the hospital level in Sierra Leone. Nonetheless, the lack of funding and operational resources are significant limitations that must be noted by policymakers before expanding DTC programmes to other hospitals in Sierra Leone.

Prevalence, etiology and antibiotic resistance patterns of community-acquired urinary tract infections in Dhaka, Bangladesh

Urinary tract infection (UTI) accounts for a significant morbidity and mortality across the world and is a leading cause for antibiotic prescriptions in the community especially in developing countries. Empirical choice of antibiotics for treatment of UTI is often discordant with the drug susceptibility of the etiologic agent. This study aimed to estimate the prevalence of community-acquired UTI caused by antibiotic resistant organisms. This was a cross-sectional study where urine samples were prospectively collected from 4,500 patients at the icddr,b diagnostic clinic in Dhaka, Bangladesh during 2016–2018. Urine samples were analyzed by standard culture method and the isolated bacteria were tested for antibiotic susceptibility by using disc diffusion method and VITEK-2. Descriptive statistics were used to estimate the prevalence of community acquired UTI (CA-UTI) by different age groups, sex, and etiology of infection. Relationship between the etiology of CA-UTI and age and sex of patients was analyzed using binary logistic regression analysis. Seasonal trends in the prevalence of CA-UTI, multi-drug resistant (MDR) pathogens and MDR Escherichia coli were also analyzed. Around 81% of patients were adults (≥18y). Of 3,200 (71%) urine samples with bacterial growth, 920 (29%) had a bacterial count of ≥1.0x10⁵ CFU/ml indicating UTI. Women were more likely to have UTI compared to males (OR: 1.48, CI: 1.24–1.76). E. coli (51.6%) was the predominant causative pathogen followed by Streptococcus spp. (15.7%), Klebsiella spp. (12.1%), Enterococcus spp. (6.4%), Pseudomonas spp. (4.4%), coagulase-negative Staphylococcus spp. (2.0%), and other pathogens (7.8%). Both E. coli and Klebsiella spp. were predominantly resistant to penicillin (85%, 95%, respectively) followed by macrolide (70%, 76%), third-generation cephalosporins (69%, 58%), fluoroquinolones (69%, 53%) and carbapenem (5%, 9%). Around 65% of patients tested positive for multi-drug resistant (MDR) uropathogens. A higher number of male patients tested positive for MDR pathogens compared to the female patients (p = 0.015). Overall, 71% of Gram-negative and 46% of Gram-positive bacteria were MDR. The burden of community-acquired UTI caused by MDR organisms was high among the study population. The findings of the study will guide clinicians to be more selective about their antibiotic choice for empirical treatment of UTI and alleviate misuse/overuse of antibiotics in the community.

Patterns of Antibiotic Resistance in Enterobacteriaceae Isolates from Broiler Chicken in the West Region of Cameroon: A Cross-Sectional Study

Background. The emergence of multidrug-resistant food-borne pathogens of animal origin including Enterobacteriaceae is a growing concern. Identifying and monitoring resistance in isolates from human-related environments are of clinical and epidemiological significance in containing antimicrobial resistance. This study aimed to contribute towards the fight against antibiotic resistance and ameliorate the management/treatment of Enterobacteriaceae-linked diseases in Cameroon. Methods. Cloacal swabs from healthy broilers were enriched in buffered-peptone-water and cultured on EMB agar. Antibiotic susceptibility was tested on Mueller-Hinton-Agar by disc diffusion. Plasmid-borne genes for extended-spectrum beta lactamase (ESBL) and resistance to Quinolones (PMQR) and Aminoglycosides were detected by standard endpoint polymerase chain reaction (PCR). Results. A total of 394 isolates were identified belonging to 12 Enterobacteriaceae genera, the most prevalent were Escherichia coli (81/394 = 20.56%), Salmonella spp (74/394 = 18.78%), and Klebsiella spp (39/394 = 9.90%) respectively. Overall, 84/394 (21.32%) were ESBL producers, 164/394 (41.62%) were resistant to quinolones, 66/394 (16.75%) resistant to aminoglycosides with 44.0% (173/394) expressing MDR phenotype. Poor hygiene practice (OR 2.55, 95% CI: 1.67, 3.89, $p=0.001$ ) and rearing for >45 days, (OR = 7.98, 95% CI: 5.05, 12.6, $p=0.001$ ) were associated with increased carriage of MDR. Plasmid-borne resistance genes were detected in 76/84 (90.48%) of ESBL-producing isolates, 151/164 (92.07%) quinolone resistant isolates and 59/66 (89.39%) aminoglycoside resistant isolates with co-occurrence of two or more genes per isolate in 58/84 (69.05%) of ESBLs, 132/164 (80.49%) of quinolone resistant isolates and 28/66 (42.42%) of aminoglycoside resistant isolates. Conclusion. This study found high carriage and widespread distribution of Enterobacteriaceae with ESBL and MDR in broiler chicken in the West Region of Cameroon. Most PMQR genes in bacteria were found at levels higher than is seen elsewhere, representing a risk in the wider human community.

Culture Requests and Multi-Drug Resistance among Suspected Urinary Tract Infections in Two Tertiary Hospitals in Freetown, Sierra Leone (2017-21): A Cross-Sectional Study

In sub-Saharan Africa, there is limited information about the use of microbiology laboratory services in patients with suspected urinary tract infections (UTIs). This cross-sectional study assessed the requests for urine culture in patients with suspected UTI in two tertiary (maternal and paediatric) hospitals—Freetown and Sierra Leone, during May 2017–May 2021—and determined antimicrobial resistance (AMR) patterns among bacterial isolates. One laboratory served the two hospitals, with its electronic database used to extract information. Overall, there were 980 patients, of whom 168 (17%) had cultures requested and performed. Of these, 75 (45%) were culture positive. During 2017–2019, there were 930 patients, of whom 156 (17%) had cultures performed. During 2020–2021, when services were disrupted by the COVID-19 pandemic, there were 50 patients, of whom 12 (24%) had cultures performed. The four commonest isolates were Escherichia coli (36), Klebsiella pneumoniae (10), Staphylococcus aureus (9), and Pseudomonas spp. (6). There were high levels of AMR, especially for trimethoprim-sulfamethoxazole (47%), nalidixic acid (44%), nitrofurantoin (32%) and cefotaxime (36%). Overall, 41 (55%) bacterial isolates showed multidrug resistance, especially E. coli (58%), Pseudomonas spp. (50%), and S. aureus (44%). These findings support the need for better utilization of clinical microbiology services to guide antibiotic stewardship and monitoring of trends in resistance patterns.

Antimicrobial resistance trend of bacterial uropathogens at the university of Gondar comprehensive specialized hospital, northwest Ethiopia: A 10 years retrospective study

Urinary tract infection and antimicrobial resistance remains the major problem, with significant health and socioeconomic burden, particularly in developing countries. This infection is commonly caused by Gram-negative bacteria, principally by Escherichia coli. So, this study aimed to determine bacterial isolates and antimicrobial resistance trend among patients with urinary tract infection at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia. A retrospective study was conducted from January 1^st to February 28^th. A ten years (2010–2019) record of urine culture results, the biochemical test and antimicrobial susceptibility test results of isolates were collected from the medical microbiology laboratory register using a checklist. Data quality was checked, entered, and analyzed using SPSS version 23. We have presented results through descriptive tables and graphs. The overall prevalence of urinary tract infection among 4441 patients was 24.1%. Escherichia coli (37.7%), Klebsiella pneumoniae (11.4%), and Staphylococcus aureus (9.1%) were the predominant uropathogens. The infection rate was nearly similar across both sexes but highest in the age group above 60 years. Above 75% of Gram-negative isolates were resistant to ampicillin (92.5%), amoxicillin-clavulanate (80.1%), tetracycline (79.3%), cefuroxime (79.2%), and Trimethoprim-sulfamethoxazole (78.3%). Over 2/3 of Gram-positive isolates also showed increased resistance to tetracycline (84.8%) and penicillin (71.6%). Moreover, more than 44% of the isolates were multidrug-resistant (MDR). We have seen an inconsistent trend of antimicrobial resistance, with an overall resistance rate of above 50%. In conclusion, the overall prevalence of urinary tract infection was high and elderly patients were most affected. More than 70% of both Gram positive and gram-negative isolates were resistant to penicillin, ampicillin, amoxicillin-clavulanate, tetracycline, cefuroxime, Trimethoprim-sulfamethoxazole. Above than 44% of the isolates were multidrug-resistant (MDR). The increasing rate of antimicrobial resistance calls for routine diagnosis and antimicrobial susceptibility testing. A prospective multicenter study indicating the status of resistance should be encouraged.

The Five Ds of Outpatient Antibiotic Stewardship for Urinary Tract Infections

Urinary tract infections (UTI) are one of the most common indications for antibiotic prescriptions in the outpatient setting. Given rising rates of antibiotic resistance among uropathogens, antibiotic stewardship is critically needed to improve outpatient antibiotic use, including in outpatient clinics (primary care and specialty clinics) and emergency departments. Outpatient clinics are in general a neglected practice area in antibiotic stewardship programs, yet most antibiotic use in the United States is in the outpatient setting. This article provides a comprehensive review of antibiotic stewardship strategies for outpatient UTI in the adult population, with a focus on the "five Ds" of stewardship for UTI, including right diagnosis, right drug, right dose, right duration, and de-escalation. Stewardship interventions that have shown success for improving prescribing for outpatient UTI are discussed, including diagnostic stewardship strategies, such as reflex urine cultures, computerized decision support systems, and modified reporting of urine culture results. Among the many challenges to achieving stewardship for UTI in the outpatient setting, some of the most important are diagnostic uncertainty, increasing antibiotic resistance, limitations of guidelines, and time constraints of stewardship personnel and front-line providers. This article presents a stewardship framework, built on current evidence and expert opinion, that clinicians can use to guide their own outpatient management of UTI.

Clinical Specimens are the Pool of Multidrug- resistant Pseudomonas aeruginosa Harbouring oprL and toxA Virulence Genes: Findings from a Tertiary Hospital of Nepal

The multidrug- or extensively drug-resistant (MDR/XDR) Pseudomonas aeruginosa carrying some virulence genes has become a global public health threat. However, in Nepal, there is no existing report showing the prevalence of oprL and toxA virulence genes among the clinical isolates of P. aeruginosa. Therefore, this study was conducted for the first time in the country to detect the virulence genes (oprL and toxA) and antibiotic susceptibility pattern of P. aeruginosa. A total of 7,898 clinical specimens were investigated following the standard microbiological procedures. The antibiotic susceptibility testing was examined by the modified disc diffusion method, and virulence genes oprL and toxA of P. aeruginosa were assessed using multiplex PCR. Among the analyzed specimens, 87 isolates were identified to be P. aeruginosa of which 38 (43.68%) isolates were reported as MDR. A higher ratio of P. aeruginosa was detected from urine samples 40 (45.98%), outpatients' specimens 63 (72.4%), and in patients of the age group of 60–79 years 36 (41.37%). P. aeruginosa was more prevalent in males 56 (64.36%) than in female patients 31 (35.63%). Polymyxin (83.90%) was the most effective antibiotic. P. aeruginosa (100%) isolates harboured the oprL gene, while 95.4% of isolates were positive for the toxA gene. Identification of virulence genes such as oprL and toxA carrying isolates along with the multidrug resistance warrants the need for strategic interventions to prevent the emergence and spread of antimicrobial resistance (AMR). The findings could assist in increasing awareness about antibiotic resistance and suggest the judicious prescription of antibiotics to treat the patients in clinical settings of Nepal.

Antimicrobial Resistance and Molecular Characterization of Citrobacter spp. Causing Extraintestinal Infections

Objectives

This prospective study was carried out to investigate molecular characteristics and antimicrobial susceptibility patterns of Citrobacter spp. from extraintestinal infections.

Methods

Forty-six clinical Citrobacter spp. isolates were isolated from hospital patients with extraintestinal infections and analyzed by multilocus sequence typing (MLST) using seven housekeeping genes. Antimicrobial susceptibility testing was performed by disk diffusion method according to the Clinical and Laboratory Standards Institute (CLSI) recommendations. Adhesion and cytotoxicity to HEp-2 cells were assessed.

Results

The 46 clinical Citrobacter spp. isolates were typed into 38 sequence types (STs), 9 of which belonged to four clonal complexes (CCs). None of the isolates shared the same ST or CCs with isolates from other countries or from other parts of China. Over half of the isolates were multidrug-resistant (MDR), with 17/26 C. freundii, 5/6 C. braakii, and 3/14 C. koseri isolates being MDR. Moreover, four isolates were carbapenem resistant with resistance to imipenem or meropenem. Among eight quinolone resistant C. freundii, all had a mutation in codon 59 (Thr59Ile) in quinolone resistance determining region of the gyrA gene. Only a small proportion of the isolates were found to be highly cytotoxic and adhesive with no correlation to sample sources.

Conclusions

There was a diverse range of Citrobacter isolates causing extraintestinal infections and a high prevalence of MDR.

High Levels of Antibiotic Resistance Patterns in Two Referral Hospitals during the Post-Ebola Era in Free-Town, Sierra Leone: 2017-2019

The Post-Ebola era (2017–2019) presented an opportunity for laboratory investments in Sierra Leone. US CDC supported the Ministry of Health and Sanitation to establish a microbiological unit for routine antimicrobial sensitivity testing in two referral (pediatric and maternity) hospitals in Freetown. This study describes resistance patterns among patients’ laboratory samples from 2017 to 2019 using routine data. Samples included urine, stool, cerebrospinal fluid, pus-wound, pleural fluid, and high vaginal swabs. Selected Gram-positive and Gram-negative bacterial isolates were tested for antimicrobial susceptibility. Of 200 samples received by the laboratory, 89 returned positive bacterial isolates with urine and pus-wound swabs accounting for 75% of positive isolates. The number of positive isolates increased annually from one in 2017 to 42 in 2018 and 46 in 2019. Resistance of the cultures to at least one antibiotic was high (91%), and even higher in the pediatric hospital (94%). Resistance was highest with penicillin (81%) for Gram-positive bacteria and lowest with nitrofurantoin (13%). Gram-negative bacteria were most resistant to ampicillin, gentamycin, streptomycin, tetracycline, cephalothin and penicillin (100%) and least resistant to novobiocin (0%). Antibiotic resistance for commonly prescribed antibiotics was high in two referral hospitals, highlighting the urgent need for antimicrobial stewardship and access to reserve antibiotics.

Multidrug-Resistant and Carbapenemase-Producing Enterobacteriaceae in Addis Ababa, Ethiopia

Background

The emergence and spread of multi-drug resistant (MDR) bacteria have become a public health problem in recent years. For the last many years, carbapenem antibiotics have been used successfully to treat infections caused by MDR Enterobacteriaceae. However, recently, Enterobacteriaceae producing carbapenemases have emerged, which confer broad resistance to most β-lactam antibiotics including carbapenems. Therefore, this study is aimed at determining the magnitude of MDR and carbapenemase-producing Enterobacteriaceae (CPE) isolated from various clinical specimens in Addis Ababa, Ethiopia.

Methods

A cross-sectional study was conducted from January to April 2018. A total of 312 Enterobacteriaceae isolates were identified from various clinical specimens. The Phoenix automated system (BD Phoenix100) was used for bacterial identification and antimicrobial susceptibility testing. Potential carbapenemase producers were confirmed by the modified carbapenem inactivation test, and KPC, MBL, and OXA-48 were phenotypically characterized by the disk diffusion method. The data obtained were entered and analyzed using SPSS version 20 software. Descriptive statistics, chi square, bivariate and multivariable logistic regression analyses were performed. P value ≤ 0.05 with corresponding 95% confidence interval was considered for statistical significance.

Results

A total of 312 Enterobacteriaceae were recovered. Of these isolates, 68.6% were MDR and 2.6% were CPE with different classes including OXA-48 1.6% (5/312), MBL 0.6% (2/312), and KPC and OXA-48 0.3% (1/312). The predominant bacterial isolates were E. coli 72.4% (226/312) followed by K. pneumoniae 13.8% (43/312). The antibiotic resistance rates of CPE isolates were significantly higher than other MDRE including ampicillin (100% versus 77.6%), cefoxitin (75% versus 20.6%), and piperacillin/tazobactam (50% versus 13.1%).

Conclusion

In this study, a relatively higher prevalence of MDR was observed, and the highest resistance was recorded against ampicillin, amoxicillin with clavulanic acid, and sulfamethoxazole-trimethoprim. Detection of CPE is important for implementing appropriate antimicrobial therapy and in controlling the spread of the infection. Furthermore, continuous screening and investigations, including genotypic characterization of CPE, are required for the prevention and control of the spread of antimicrobial-resistant pathogens.

Microbial Profile and Antibiogram Pattern Analysis of Skin and Soft Tissue Infections at a Tertiary Care Center in South India

Skin and soft tissue infections (SSTIs) are the most common type of infection globally and also in India. Periodic evaluation of data on microbial profiling and antibiogram trend analysis is mandatory for creating a timely empirical treatment guideline and a proper antimicrobial cycling plan. In the current study, retrospective analysis of the data from 3,570 samples collected from suspected SSTI over one year was performed. Analysis was done on the clinical condition, causative agent/s identified and their antimicrobial susceptibility according to the standard guidelines. Seventy-three percent of samples yielded positive growth, with majority being unimicrobial infections. Gram-negative bacteria (GNB) were more commonly associated with infections from in-patients while Gram-positive cocci (GPC) were seen among out-patients. More than 70% of isolates among GNB were found susceptible to Carbapenems, piperacillin-tazobactam, amikacin and chloramphenicol. Among GPC, maximum sensitivity was seen to glycopeptides, linezolid followed by chloramphenicol, tetracycline, clindamycin and amikacin. Unusual resistance patterns like Penicillin resistant Ampicillin sensitive Enterococcus faecalis (PRASEF)strains, Multidrug resistance (MDR) and Extended drug resistance (XDR) were higher among Enterococci spp, MRSA, Acinetobacter spp and Klebsiella spp. Resistance to penicillin and cephalosporin drugs were high among GNB and GPC. Carbapenems, aminoglycosides, glycopeptides and broad-spectrum antibiotics are found sensitive and potential choices for empirical therapy. As prevalence of MDR and XDR strains were high and the trend analysis shows likelihood of few of the first and second line drugs becoming sensitive in future, we conclude that continued analysis of bacterial profiling and AMR pattern analysis among SSTI is essential.

Isolation and characterization of human pathogenic multidrug resistant bacteria associated with plastic litter collected in Zanzibar

Plastic pollution is a growing problem, not at least in areas where poor waste management results in direct pollution of coastal zones, such as South Asia and regions in Africa. In addition to the effect on ecosystems and their related services, plastic pollution may also affect human health indirectly as vectors for infectious disease. As plastic offers a suitable surface for the attachment of biofilm forming bacteria, it may contribute to disease outbreaks and antimicrobial resistance. To investigate the role of plastic litter as potential vectors for pathogenic bacteria, we collected plastic litter from four rural sites in Zanzibar, and isolated adhered bacteria. Isolates were short-read sequenced for further molecular analysis. This revealed that collected plastic litter was associated with diverse bacterial species, including human pathogens Citrobacter freundii, Klebsiella pneumoniae and Vibrio cholerae. Furthermore, most isolates were found to be multidrug resistant. Our findings confirm that plastic litter, serve as novel reservoir for human multidrug resistant pathogenic bacteria that combined with poor sanitation and waste handling, may lead to transmission of infectious diseases and antimicrobial resistance. These findings add a new level to the environmental challenges with plastic pollution; the potential health risk associated with exposure to plastic litter.

The magnitude of extended-spectrum beta-lactamase- producing Enterobacteriaceae from clinical samples in Ethiopia: a systematic review and meta-analysis

BACKGROUND

The rapid spread of resistance among extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is a serious problem around the world. It results in serious clinical complications in humans and has become a global threat. Therefore, this systematic review and meta-analysis was aimed to estimate the pooled prevalence of ESBL-producing Enterobacteriaceae in different clinical samples in Ethiopia.

METHODS

A systematic search was conducted on PubMed, Web of Science, Embase, Google Scholar and the Cochrane Library. All identified observational studies reporting the prevalence of ESBL-producing Enterobacteriaceae from clinical samples in Ethiopia were included. Four authors independently extracted data and analysed using R software version 3.6.1 and STATA statistical software version 13. A random-effects model was computed to estimate the pooled prevalence of ESBL-producing Enterobacteriaceae in Ethiopia.

RESULTS

Of 142 articles reviewed, 14 studies that fulfilled the inclusion criteria were included in the meta-analysis. The pooled prevalence of ESBL-producing Enterobacteriaceae in the different clinical specimens in Ethiopia was 49 % (95 % CI: 39, 60). Klebsiella pneumoniae was the leading ESBL-producing Enterobacteriaceae followed by Escherichia coli and Acinetobacter baumannii with a prevalence of 74, 67 and 60 %, respectively. ESBL-producing isolates showed a high rate of resistance to cefotaxime, ceftriaxone, ceftazidime, Amoxicillin clavulanic acid (AMC), ampicillin and aztreonam. The better options for the treatment of ESBL-producing Enterobacteriaceae are amikacin and Imipenem.

CONCLUSION

The magnitude of ESBL-producing Enterobacteriaceae in different clinical samples in Ethiopia is alarmingly high and represents a threat to human health. Hence, a coordinated effort needs to be implemented for the prevention and control of these Enterobacteriaceae .

Extended-spectrum Beta-lactamase and AmpC beta-lactamases producing gram negative bacilli isolated from clinical specimens at International Clinical Laboratories, Addis Ababa, Ethiopia

BACKGROUND

Extended spectrum Beta-lactamases (ESBLs) and AmpC beta-lactamases (AmpC) are the common enzymes produced by gram negative bacilli, which are their main mechanisms of resistance to all generations of cephalosporins. Hence, this study aimed to determine the magnitude of ESBLs and AmpC producing gram negative bacilli (GNB) isolated from clinical specimens at International clinical Laboratories in Addis Ababa, Ethiopia.

METHODS

A cross sectional study was conducted from January to May 2018. From different clinical specimens, 338 GNB were isolated and characterized. Bacterial species identification, antimicrobial susceptibility testing and screening for ESBLs and AmpC production were performed using Phoenix automated system (BD phoenix100). ESBLs production was confirmed using a combination disc method. All Cefoxitin resistant and confirmed ESBLs producing GNB were confirmed for AmpC beta-lactamases production by AmpC confirmatory Neo-Sensitabs discs (ROSCO tablet). Data were analyzed using SPSS version 20 software.

RESULTS

E. coli 66.0% (224/338) followed by K. pneumoniae 12.1% (41/338) were GNB most frequently isolated. The overall magnitude of ESBLs producing GNB was 38.8% (131/338) and the extent of AmpC beta-lactamase producing GNB was 2.4% (8/338). Majority of ESBLs and AmpC beta-lactamases producing GNB were isolated from urine specimens 47.5% (116/338). Ampicillin (75.4%), amoxicillin with clavulanic acid (64.0%) and sulfamethoxazole-trimethoprim (55.6%) were most the antibiotics to which resistance was most commonly found. The multidrug resistance (MDR) level of GNB was 74.0% (250/338). Of ESBLs and AmpC beta-lactamases producing GNB, 99.3% were MDR (p < 0.05).

CONCLUSION

The high magnitude of ESBLs and AmpC beta-lactamases producing GNB calls the needs of strong intervention to minimize further occurrence and spread of such GNB. More importantly, the MDR level was high which suggests continuous monitoring & reviewing of antimicrobial policy in hospitals and the country at large.

Fecal Carriage Rate of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae Among Apparently Health Food Handlers in Dilla University Student Cafeteria

BACKGROUND

The rapid spread of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae among food handlers is a public health concern and has become a serious world threat. Klebsiella pneumoniae and Escherichia coli are the predominant ESBL-producing Enterobacteriaceae. This study aimed to assess the magnitude of ESBL producing K. pneumoniae and E. coli isolated from the stool of food handlers in the Dilla University Student Cafeteria.

METHODS

A cross-sectional study was conducted from November to September 2018/2019. A total of 220 stool samples were cultured on MacConkey agar and a series of biochemical tests were performed for the identification of bacterial species. Double-disk synergy method was used for the detection of ESBL-producing strains.

RESULTS

The rate of fecal carriage of E. coli and K. pneumoniae among the food handlers of the current study was 66.4%, of which 81.5% was E. coli, while 18.5% was K. pneumoniae. Of the total bacterial isolates, 25.3% were confirmed to be positive for ESBL production, of which 19.9% was E. coli, while 5.5% was K. pneumoniae. ESBL-producing fecal carriage showed high resistance to aztreonam, cefotaxime, ceftriaxone, cefuroxime, and ceftazidime, with resistance rates ranging from 88% to 100%, while the lowest resistance rate was observed against imipenem accounted <26.3%. In this study, 91.9% of ESBL-producers were co-resistant to β-lactams antibiotics plus at least one of the non-β-lactam antibiotics. ESBL carriers were more common among food handlers who used antibiotics repeatedly, drunk unpasteurized milk, and ate raw meat.

CONCLUSION

The magnitude of ESBL-producing E. coli and K. pneumoniae fecal carriage is alarmingly high and a threat to human health. MDR to third-generation cephalosporins and non-β-lactam antibiotics is more common among ESBL producers. Detecting ESBL-producing organisms has a remarkable importance in clinical decision-making. Hence, a coordinated effort should be implemented for the prevention and control of the disease.

Epidemiology and prevalence of extended-spectrum β-lactamase- and carbapenemase-producing Enterobacteriaceae in humans, animals and the environment in West and Central Africa

Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) and carbapenemase-producing Enterobacteriaceae (CPE) are widespread. Here we used the 'One Health' approach to determine knowledge gaps on ESBL-E and CPE in West and Central Africa. We searched all articles on ESBL-E and CPE in these African regions published in PubMed, African Journals Online and Google Scholar from 2000 onwards. Among the 1201 articles retrieved, we selected 165 studies (West Africa, 118; Central Africa, 47) with data from 22 of the 26 West and Central Africa countries. Regarding the settings, 136 articles focused only on humans (carriage and/or infection), 6 articles on humans and animals, 13 on animals, 1 on humans and the environment, 8 on the environment and 1 on humans, animals and environments. ESBL-E prevalence ranged from 11-72% in humans and 7-79% in aquatic environments (wastewater). In animals, ESBL-E prevalence hugely varied: 0% in cattle, 11-36% in chickens, 20% in rats, 21-71% in pigs and 32-75% in dogs. The bla_CTX-M-15 gene was the predominant ESBL-encoding gene and was associated with plasmids of incompatibility groups F, H, K, Y, N, I1 and R. CPE were studied only in humans. Class B metallo-β-lactamases (NDM) and class D oxacillinases (OXA-48 and OXA-181) were the most common carbapenemases. Our results show major knowledge gaps, particularly on ESBL and CPE in animals and the environment, that might limit antimicrobial resistance management in these regions. The results also emphasise the urgent need to improve active surveillance programmes in each country and to support antimicrobial stewardship.

Acquisition of Plasmid-Mediated Colistin Resistance Gene mcr-1 in Escherichia coli of Livestock Origin in Bangladesh

Aims: To investigate plasmid-borne colistin resistance mechanism (plasmid-mediated colistin resistance [mcr-1]) in Escherichia coli of human, veterinary, and environmental origin in Bangladesh. Materials and methods: A total of 810 samples were collected from different sources. Isolation and identification of E. coli was performed using classical bacteriology and then tested for antimicrobial susceptibility. Colistin-resistant isolates were further analyzed for mcr-1 gene using PCR. Minimum inhibitory concentration (MIC) was determined using microbroth dilution technique. After sequencing of mcr-1 gene, phylogenetics was conducted to see the relationship with other mcr-1 gene sequences. Results: A total of 358 E. coli were isolated from 810 samples of humans, animals, environment, and food in Bangladesh. Of them 49 (15.9%) isolates were phenotypically resistant to colistin and 254 (70.9%) were resistant to multiple antimicrobials. mcr-1 gene was detected in three E. coli isolates of poultry source. For the three mcr-1 positive isolates the MIC of colistin sulfate was 4, 8, and 128 μg/mL. Gene sequencing of two of the three mcr-1 positive isolates and phylogenetic analysis showed close similarities of one isolate to other mcr-1 sequences available at GenBank while the other appeared to have evolved locally. Conclusion: First-ever report on circulation of mcr-1 E. coli of livestock origin in Bangladesh.

Evolution of antibiotic cross-resistance and collateral sensitivity in Staphylococcus epidermidis using the mutant prevention concentration and the mutant selection window

In bacteria, evolution of resistance to one antibiotic is frequently associated with increased resistance (cross-resistance) or increased susceptibility (collateral sensitivity) to other antibiotics. Cross-resistance and collateral sensitivity are typically evaluated at the minimum inhibitory concentration (MIC). However, these susceptibility changes are not well characterized with respect to the mutant prevention concentration (MPC), the antibiotic concentration that prevents a single-step mutation from occurring. We measured the MIC and the MPC for Staphylococcus epidermidis and 14 single-drug resistant strains against seven antibiotics. We found that the MIC and the MPC were positively correlated but that this correlation weakened if cross-resistance did not evolve. If any type of resistance did evolve, the range of concentrations between the MIC and the MPC tended to shift right and widen. Similar patterns of cross-resistance and collateral sensitivity were observed at the MIC and MPC levels, though more symmetry was observed at the MIC level. Whole-genome sequencing revealed mutations in both known-target and nontarget genes. Moving forward, examining both the MIC and the MPC may lead to better predictions of evolutionary trajectories in antibiotic-resistant bacteria.

Implementation of antimicrobial stewardship programmes in African countries: a systematic literature review

OBJECTIVE

Antimicrobial stewardship is one of the strategic objectives of the WHO global action plan on antimicrobial resistance. This paper sought to review the extent of implementation of antimicrobial stewardship programmes (ASPs) in African countries and the reported outcomes.

METHODS

We searched five electronic databases, including PubMed, Scopus, Cochrane library, African Journal Online, CINAHL and Google scholar for papers published between 1990 and March 2019. We combined the names of countries in the five regions of Africa with antimicrobial stewardship terms. Studies of any design, employing any stewardship strategies were included. The quality of included studies was assessed using the National Heart, Lung and Blood Institute (NHLBI) quality assessment tool for before and after studies.

RESULTS

Of 1752 titles identified, 13 studies met the criteria for inclusion. Seven of the studies were conducted in South Africa, three in Kenya and one each in Sudan, Tanzania and Egypt. Eleven studies were of high quality with low risk of bias. The included studies mainly assessed the outcome using process measures and these were associated with improved compliance with antibiotic guidelines, appropriateness of prescribing, reduction in antibiotic use and cost savings. Decrease in rate of surgical site infections and nonsignificant change in mortality and 30-day readmission rate were reported in two studies respectively.

CONCLUSION

Findings of this review show the paucity of data on implementation of ASPs in African countries. Although the continent is faced with challenges which impact on effective implementation of ASPs, the successes reported in the included studies show that other African countries can implement these programmes.

Antimicrobial resistance of Enterobacter cloacae complex isolates from the surface of muskmelons

The increasing antimicrobial resistance (AMR) among pathogenic and opportunistic pathogenic microorganisms is one of the main global public health problems. The consumption of food contaminated with such bacteria (ARB), especially of raw products, might result in the direct acquisition of ARB and in a spread of resistant bacteria along the food chain. The aim of the study was to characterize the antimicrobial susceptibility of potentially extended spectrum β-lactamase (ESBL) producing or AmpC resistant Enterobacteriaceae isolated from the surface of 147 muskmelons from wholesale and retail. A phenotypic analysis was carried out by using minimum inhibitory concentration (MIC) test strips for ESBL detection and MIC susceptibility plates against 14 antimicrobials. Furthermore, ESBL genes, sul-genes and plasmid-mediated AmpC resistance were analyzed by real-time PCR. Additionally, a further insight in the AmpC resistance of isolates of the Enterobacter cloacae complex (ECC) was obtained by analyzing the sequence of the ampC regulatory region (n = 15). A total of 73 potentially resistant Enterobacteriaceae were isolated from 56 muskmelons. Of these, 15 isolates of the ECC were suspicious for ESBL/AmpC resistance, and eleven thereof were positive for the AmpC family EBC. Phenotypic analysis showed diminished susceptibility against "critically" and "highly important" antimicrobials, according to the WHO classification. Furthermore, divergence in the ampC regulatory region was detected between the 15 isolates. These findings highlight the important role that raw produce might play in the transmission of antimicrobial resistances along the food chain.

Extended-spectrum beta-lactamase production and multi-drug resistance among Enterobacteriaceae isolated in Addis Ababa, Ethiopia

Background

The global emergence and spread of extended-spectrum beta-lactamases (ESBLs) producing Enterobacteriaceae have been threatening the ability to treat an infection. Hence, this study aimed to determine the prevalence of ESBL-producing and multi-drug resistance (MDR) Enterobacteriaceae (ESBLs-E) from different clinical specimens in Addis Ababa, Ethiopia.

Methods

A cross-sectional study was conducted from January 1 to May 30, 2017. A total of 426 Enterobacteriaceae isolates were identified from clinical specimens. The isolates were collected from four laboratories. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method on Muller Hinton agar (MHA). All Enterobacteriaceae were screened for ESBLs production using cefotaxime and ceftazidime as per CLSI guideline. Each ESBL screening positive Enterobacteriaceae were confirmed by a combination disk test (CDT). Data were entered and analyzed by using SPSS version-20.

Result

The most frequent Enterobacteriaceae were E. coli 228 (53.5%) and K. pneumoniae 103 (24.1%). The magnitude of ESBLs-E was 57.7% (246/426). The highest frequencies of ESBLs-E were observed in blood specimesns (84.4%) and the highest ESBLs production was observed in K. pneumoniae (85.4%). The highest resistance level was seen to sulfamethoxazole-trimethoprim (77.0%), amoxicillin with clavulanic acid (71.6%), cefotaxime (62.2%), cefepime (60.3%) and ceftazidime (60.8%). The overall magnitude of multi-drug resistance (MDR) level was 68.3%. Of ESBLs-E, 96.3% of them were MDR (P < 0.001).

Conclusion

There was a high prevalence of ESBLs-E and MDR isolate in Addis Ababa. Most of ESBLs-E was isolated primarily in blood and urine. The highest ESBLs production was observed among K. pneumoniae. Hence, strong infection control strategies must be implemented in hospital settings of the country.

Predominance of CTX-M Type Extended Spectrum β-lactamase (ESBL) Producers Among Clinical Isolates of Enterobacteriaceae in a Tertiary Care Hospital, Kathmandu, Nepal

Background:

ESBL problem is increasing worldwide and only limited studies on genes of ESBL are performed in Nepal.

Objectives:

We aimed to focus on the molecular detection of plasmid-mediatedblaTEM,blaSHVandblaCTX-Mgenes among the ESBL producing Enterobacteriaceae from different clinical samples.

Methods:

A total of 550 clinical samples were processed and organisms of Enterobacteriaceae were identified using standard microbiological process. ESBL producers were screened and confirmed using modified Kirby Bauer disc diffusion method by CLSI guidelines. Plasmids extracted from the confirmed ESBL positives were the template for PCR.blaSHV,blaTEMandblaCTX-Mgenes were amplified using specific primers of respective genes by uniplex PCR. The presence of these genes was confirmed by gel electrophoresis.

Results:

Among 550 different clinical samples 343 (62.36%) were culture positive. Of which, 157 (45.57%) belonged to Enterobacteriaceae.Escherichia coli(45.9%) was predominant. Of these 33.2% (52/157) isolates ESBL positive. ESBL-E. coli(52.8%) were prevalent. All ESBL positive organisms were sensitive to imipenem. Of confirmed ESBL positives, 34.6% harboringblaTEMgene, 30.8% harboringblaSHVgene andblaCTX-Mgenes were present in all ESBL producers. Twenty-eightout of 52 (53.9%) isolates harbored multipleblagenes, the most common combination beingblaCTX-M+blaTEM(21.2%).

Conclusion:

We report 100% plasmid mediated CTX-M genotype among ESBL producers which might indicate rapid dissemination ofblaCTX-Mgenes from the community to the patients. Besides, there is a need for regular monitoring of antibiotic resistance in the country and de-escalate the use of antibiotics so as to preserve the antibiotics for future generation.

Escherichia hermannii Infections in Humans: A Systematic Review

Eshcerichia hermannii is a member of the Enterobacteriaceae, first described in 1982 and reclassified as a distinct species in the Escherichia genus after identifying biochemical and genomic differences from E. coli. It is a rare cause of human infections and is supposed to be a co-infector rather than an autonomous cause of infection. The aim of this systematic review was to record and evaluate all available evidence regarding human infections by E. hermannii. A systematic review of PubMed (through 21 December 2018) for studies providing epidemiological, clinical, and microbiological information, as well as treatment data and outcomes of E. hermannii infections was performed. A total of 16 studies, containing data of 17 patients, were eventually included in the analysis. The most common E. hermannii infections were bacteremias, urinary tract, and central nervous system infections. The complication rate, like the occurrence of sepsis, was high. Cephalosporins and aminoglycosides were the most common agents used for treatment. This systematic review describes bacterial infections by E. hermannii and provides information on the epidemiology, clinical presentation, antibiotic resistance, treatment, and outcomes associated with these infections.

Genetic Diversity, Multidrug Resistance, and Virulence of Citrobacter freundii From Diarrheal Patients and Healthy Individuals

Objectives:Citrobacter freundii is a frequent cause of nosocomial infections and a known cause of diarrheal infections, and has increasingly become multidrug resistant (MDR). In this study, we aimed to determine the genetic diversity, the antimicrobial resistance profiles and in vitro virulence properties of C. freundii from diarrheal patients and healthy individuals. Methods: 82 C. freundii isolates were obtained from human diarrheal outpatients and healthy individuals. Multilocus Sequence Typing (MLST) of seven housekeeping genes was performed. Antimicrobial susceptibility testing was carried out using the disk diffusion method according to the Clinical and Laboratory Standards Institute (CLSI) recommendations. Adhesion and cytotoxicity to HEp-2 cells were assessed. PCR and sequencing were used to identify bla_CTX-M, bla_SHV, bla_TEM, qnrA, qnrB, qnrS, qnrC, qnrD, aac(6')-Ib-cr, and qepA genes. Results: The 82 C. freundii isolates were divided into 76 sequence types (STs) with 65 STs being novel, displaying high genetic diversity. Phylogenetic analysis divided the 82 isolates into 5 clusters. All 82 isolates were sensitive to imipenem (IPM), but resistant to one or more other 16 antibiotics tested. Twenty-six isolates (31.7%) were multidrug resistant to three or more antibiotic classes out of the 10 distinct antibiotic classes tested. Five MDR isolates, all of which were isolated from 2014, harbored one or more of the resistance genes, bla_TEM-1, bla_CTX-M-9, aac(6')-Ib-cr, qnrS1, qnrB9, and qnrB13. All 11 qnrB-carrying C. freundii isolates belonged to cluster 1, and one C. freundii isolate carried a new qnrB gene (qnrB92). Six isolates showed strong cytotoxicity to HEp-2 cells, one of which was multidrug resistant. Conclusions:C. freundii isolates from human diarrheal outpatients and healthy individuals were diverse with variation in sequence types, antibiotic resistance profiles and virulence properties.

Antimicrobial resistance among clinically relevant bacterial isolates in Accra: a retrospective study

Objective

The aim of this study was to determine the antimicrobial resistance pattern of bacterial isolates from different specimens at various hospitals and private diagnostic service laboratories in Ghana.

Results

A retrospective data of culture and sensitivity test results from 2016 were extracted from the microbiology record book of six laboratories in Accra, Ghana. The data included type of clinical specimen, sex of patient, name of bacterial isolate and antibiotic resistance profile. A total of 16.6% (n = 10,237) resistant isolates were obtained, however, the proportions of resistant isolates varied significantly between laboratories. High resistance towards tetracycline, ampicillin, cotrimoxazole and cephalosporins, but low towards amoxiclav and aminoglycosides, was observed. This study identified E. coli and Staphylococcus species as the major resistant bacteria from clinical specimen in Accra and the highest prevalence of the isolates was found in urine specimens in all six laboratories (69.1%, n = 204; 52.6%, n = 36; 52.3%, n = 350; 37.9%, n = 298; 53%, n = 219; 62.1%, n = 594) and in female patients (81.4, 50 and 69.5%). Regular surveillance and local susceptibility pattern analysis is extremely important in selecting the most appropriate and effective antibiotic for the treatment of bacterial infections.

Electronic supplementary material

The online version of this article (10.1186/s13104-018-3377-7) contains supplementary material, which is available to authorized users.

Gene cassettes of class I integron-associated with antimicrobial resistance in isolates of Citrobacter spp. with multidrug resistance

BACKGROUND AND OBJECTIVES

Integrons play a major role in the transmission and accumulation of resistance factors in multidrug resistant bacteria. This study was aimed to evaluate the gene cassettes of class I integron and antimicrobial resistance in isolates of Citrobacter with multidrug resistance (MDR).

MATERIALS AND METHODS

Ninety isolates of Citrobacter spp. were collected from the largest hospital in Kermanshah, Iran. Antimicrobial resistance patterns were determined using disc diffusion method. The class I integron were detected by PCR. The integrase positive isolates were further analyzed for the presence of gene cassettes using 5' and 3' conserved sequences (CSs) primers and PCR products were sequenced. The data were analyzed using the chi-square test.

RESULTS

Of 90 Citrobacter isolates, 46 (51.1%) were multidrug resistant. Class I integron and gene cassettes were determined in 30 isolates (65.2%). Gene cassettes were found which contained genes encoded resistance to aminoglycosides and trimethoprim and a putative gene. Gene cassettes of dfrA12-orfF-aadA2, dfrA1-aadA1, aadA1 and dfrA15-aadA2 were also found in Citrobacter isolates.

CONCLUSION

Our results indicate there is a high frequency of class I integron among multi-drug resistant strains of Citrobacter isolated from clinical settings. A high frequency of class I integron associated gene cassettes, in particular dfr and aadA, present in MDR strains of Citrobacter. This data indicates an important role of integrons in the creation and transmission of MDR strains in health care centers.

Community-acquired Lower Urinary Tract Infections: Etiology, Antimicrobial Resistance, and Treatment Results in Female Patients

Background/Purpose:

Most community-acquired urinary tract infections (UTIs) are usually treated empirically. The knowledge of antibiotic resistance patterns of the microorganisms causing UTI is essential for defining the empirical treatment.

Objective:

The aim of the present study is to determine the distribution of bacterial strains isolated from lower UTIs and their resistance patterns against commonly used antimicrobial agents and treatment results in female patients.

Subjects and Methods:

This is a retrospective analysis of medical case records of 90 female patients with lower UTI for a period of 4 years from January 2013 to December 2016 in a tertiary care hospital in the Trakya region of Turkey.

Results:

The most common causative agent was Escherichia coli (66.6% of cases) followed by Klebsiella pneumoniae (16.6%). Fosfomycin was the most active agent against E. coli (resistant isolates: 5.5%), followed by nitrofurantoin (resistant isolates: 7.4%). Extended-spectrum beta-lactamases (ESBLs) production was observed in 29 (32.2%) isolates (22 in E. coli, 6 in K. pneumoniae, and 1 in Enterobacter spp.). The antimicrobial resistance rates among ESBL-producing E. coli isolates for trimethoprim-sulfamethoxazole, ciprofloxacin, fosfomycin, and nitrofurantoin were 77.7%, 72.7%, 13.6%, and 18.2%, respectively (P < 0.05). The estimated microbiological eradication rates for nitrofurantoin and fosfomycin were 89.7% and 83.8%, respectively.

Conclusions:

The results of the present study indicate that nitrofurantoin and fosfomycin may be considered for empirical therapy of lower UTIs in Trakya region of Turkey.

Antimicrobial Resistance and Cytotoxicity of Citrobacter spp. in Maanshan Anhui Province, China

Objectives:Citrobacter spp. especially Citrobacter freundii, is frequently causing nosocomial infections, and increasingly becoming multi-drug resistant (MDR). In this study, we aimed to determine the genetic diversity and relationships of Citrobacter spp. from diarrheal patients and food sources, their antimicrobial resistance profiles and in vitro virulence properties.

Methods: Sixty two Citrobacter isolates, including 13 C. freundii, 41 C. youngae and eight C. braakii isolates, were obtained from human diarrheal patients and food sources. Multilocus Sequence Typing (MLST) of seven housekeeping genes and antimicrobial susceptibility testing using the broth microdilution method according to CLSI recommendations were carried out. Adhesion and cytotoxicity to HEp-2 cells were performed. PCR and sequencing were used to identify bla_CTX−M, bla_SHV, bla_TEM and qnr genes.

Results: The 62 isolates were divided into 53 sequence types (STs) with all STs being novel, displaying high genetic diversity. ST39 was a predominant ST shared by 5 C. youngae strains isolated from four foods and a diarrheal patient. All isolates were resistant to cefoxitin, and sensitive to imipenem, meropenem and amikacin. The majority of Citrobacter isolates (61.3%) were MDR of three or more antibiotics out of the 22 antibiotics tested. Two C. freundii isolates each carried the bla_TEM−1 gene and a variant of qnrB77. Three Citrobacter isolates each carried qnrS1 and aac(6')-Ib-cr genes. Seven isolates that showed strong cytotoxicity to HEp-2 cells were MDR.

Conclusions:Citrobacter spp. from human and food sources are diverse with variation in virulence properties and antibiotic resistance profiles. Food may be an important source of Citrobacter species in transmission to humans. C. freundii and C. youngae are potential foodborne pathogens.

Finished Genome Sequence of the Highly Multidrug-Resistant Human Urine Isolate Citrobacter freundii Strain SL151

Citrobacter freundii is a Gram-negative opportunistic pathogen that is increasingly being recognized as a causative agent of hospital-acquired urinary tract infections and an important reservoir of antimicrobial resistance determinants. In this report, we describe the finished genome sequence of C. freundii strain SL151, a highly multidrug-resistant human urine isolate.

Prevalence of Quinolone Resistance in Enterobacteriaceae from Sierra Leone and the Detection of qnrB Pseudogenes and Modified LexA Binding Sites

A collection of 74 Enterobacteriaceae isolates found in Bo, Sierra Leone, were tested for quinolone antibiotic susceptibility and resistance mechanisms. The majority of isolates (62%) were resistant to quinolones, and 61% harbored chromosomal gyrA and/or parC mutations. Plasmid-mediated quinolone resistance genes were ubiquitous, with qnrB and aac(6')-Ib-cr being the most prevalent. Mutated LexA binding sites were found in all qnrB1 genes, and truncated qnrB pseudogenes were found in the majority of Citrobacter isolates.