Molecular epidemiology and antimicrobial susceptibility of diarrheagenic Escherichia coli isolated from children under age five with and without diarrhea in Central Ethiopia

Pathovars, occurrence, and characterization of plasmid-mediated quinolone resistance in diarrheal Escherichia coli isolated from farmers and farmed chickens in Tunisia and Nigeria

The poultry industry is a very important agricultural and industrial sector in Tunisia and Nigeria, with little information about occurrence of diarrheagenic Escherichia coli in the farmers and chickens. This study aimed to detect the prevalence of diarrheal E. coli in humans and poultry and to investigate plasmid-mediated quinolone resistance (PMQR) genes in both countries. Seventy-four isolates of E. coli were studied; nine different virulence genes were screened by PCR. Serotyping was performed only for pathotypes as well as the determining of antibiotic resistance profiles against 21 antibiotics. PMQR genes were investigated by PCR. EAEC was the most abundant pathotype (37/74; 50%) in human and chicken isolates, whereas single EHEC and EPEC (1/74, 1.35%) pathotypes were detected in Tunisia and Nigeria, respectively. About 17 (45.95%) quinolones/fluoroquinolones-resistant isolates were detected, from which the following PMQR genes were detected: aac(6')-Ib-cr (8/17, 47.05%), qepA (6/17, 35.29%), qnrA + qnrB (2/17, 11.76%), and qnrS gene (1/17, 5.88%). Our findings highlight high occurrence of EAEC pathotype in Tunisia and Nigeria, more frequent than EPEC and EHEC. Additionally, all E. coli pathotypes isolated from different sources (humans, poultry) showed resistance to several antibiotics, which are in use as therapeutic choices in Tunisia and Nigeria.

The Importance of Carbapenemase-Producing Enterobacterales in African Countries: Evolution and Current Burden

Antimicrobial resistance (AMR) is a worldwide healthcare problem. Multidrug-resistant organisms (MDROs) can spread quickly owing to their resistance mechanisms. Although colonized individuals are crucial for MDRO dissemination, colonizing microbes can lead to symptomatic infections in carriers. Carbapenemase-producing Enterobacterales (CPE) are among the most important MDROs involved in colonizations and infections with severe outcomes. This review aimed to track down the first reports of CPE in Africa, describe their dissemination throughout African countries and summarize the current status of CRE and CPE data, highlighting current knowledge and limitations of reported data. Two database queries were undertaken using Medical Subject Headings (MeSH), employing relevant keywords to identify articles that had as their topics beta-lactamases, carbapenemases and carbapenem resistance pertaining to Africa or African regions and countries. The first information on CPE could be traced back to the mid-2000s, but data for many African countries were established after 2015-2018. Information is presented chronologically for each country. Although no clear conclusions could be drawn for some countries, it was observed that CPE infections and colonizations are present in most African countries and that carbapenem-resistance levels are rising. The most common CPE involved are Klebsiella pneumoniae and Escherichia coli, and the most prevalent carbapenemases are NDM-type and OXA-48-type enzymes. Prophylactic measures, such as screening, are required to combat this phenomenon.

Enteric bacterial agents associated with diarrhea and their antimicrobial sensitivity profiles in children under 5 years from mukuru informal settlement, Nairobi, Kenya

BACKGROUND

In Kenya, diarrhoeal disease is the third leading cause of child mortality after malaria and pneumonia, accounting for nearly 100 deaths daily. We conducted a cross-sectional study in Mukuru informal settlements to determine the bacteria associated with diarrhea and their ASTs to provide data essential for implementing appropriate intervention measures.

METHODS

Diarrheagenic children (≤ 5 years) were purposively recruited from outpatient clinics of Municipal City Council, Mukuru kwa Reuben, Medical Missionaries of Mary, and Mama Lucy Kibaki Hospital, Nairobi. A total of 219 stool samples were collected between May 2021 and August 2021. Stool culture was done on MacConkey and Salmonella Shigella agar, while the recovered bacteria were identified using VITEK®2GNID and polymerase chain reaction (PCR) used for E. coli pathotyping. Antibiotic Susceptibility Testing was done using VITEK®2AST-GN83.

RESULTS

At least one bacterial organism was recovered from each of the 213 (97%) participants, with 115 (56%) participants having only one bacterial type isolated, 90 (43%) with two types of bacteria, and 2 (1%) with three types of bacteria recovered. The most predominant bacteria recovered was 85% (93/109) non-pathogenic E.coli and 15% (16/109)of pathogenic E.coli, with 2 (1%) were Enterohemorrhagic E.coli (EHEC), 6 (3%) were Enteroaggregative E.coli (EAEC), and 8 (4%) were Enteropathogenic E.coli (EPEC). Other potentially pathogenic bacteria included Enterobacter sp (27.8%), Klebsiella sp 33(11%), and Citrobacter sp 15(4.7%). Pathogenic isolates such as Salmonella 7 (2%), Proteus mirabilis 16 (6%), Providencia alcalifaciens 1 (0.3%), and Shigella 16 (4.7%) were detected. Isolates such as Pantoea spp 2(0.67%), Raoultella planticola 1(0.33%), and Kluyvera 6(2%) rarely reported but implicated with opportunistic diarrhoeal disease were also recovered. Ampicillin, cefazolin, and sulfamethoxazole-trimethoprim were the least effective antimicrobials at 64%, 57%, and 55% resistance, respectively, while meropenem (99%), amikacin (99%), tazobactam piperacillin (96%), and cefepime (95%) were the most effective. Overall, 33(21%) of all enterics recovered were multidrug-resistant.

CONCLUSION

The study documented different bacteria potentially implicated with childhood diarrhea that were not limited to E. coli, Shigella, and Salmonella, as previously observed in Kenya. The strains were resistant to the commonly used antibiotics, thus narrowing the treatment options for diarrheal disease.

Molecular Characterization of Hetero-Pathogenic and Diarrheagenic Escherichia coli Pathotypes in Diarrheic Children under Five Years and Exposure Environment in Ogun State, South-West Nigeria

BACKGROUND

Diarrheagenic Escherichia coli (DEC) is one of the most common etiological agents of moderate-to-severe diarrhea in Low- and Middle-Income Countries (LMICs). Therefore, determining the source(s) of DEC in index cases and exposure environment is important for developing a prevention strategy. The current study aims to investigate the prevalence of DEC among children under 5 years and their exposure environment in Ogun State, Nigeria.

METHODS

Samples from 228 diarrheic children and their exposure environment were collected and screened for E. coli. Bio-chemically compatible distinct colonies were molecularly characterized using a 7-virulence-gene multiplex PCR with virulence factors (VFs) indicative of four pathotypes of E. coli: enterotoxigenic (ETEC), verotoxigenic (VTEC), enteropathogenic (EPEC), and enteroinvasive (EIEC). Representative pathotypes were subjected to antimicrobial susceptibility and over-expressed efflux pump assays.

RESULTS

One or more VFs typical of specific pathotypes were detected in 25.9% (59/228) diarrhea cases consisting of ETEC (21.5%) and EPEC (0.4%), while hetero-pathogenic pathotypes were found in 4.0% of cases. Of the food sources, 27.9% (101/362) were positive for DEC, of which ETEC accounted for 21.0%, VTEC 1.9%, EPEC 0.6%, EIEC 0.6%, and hetero-pathogenic pathotypes were 3.9%. Furthermore, ETEC was the only pathotype detected in the wastewater (4/183). Interestingly, the consumption of street-vended foods was the most significant (p = 0.04) risk factor for DEC infection in the study area. A total of 73.3% of selected DEC pathotypes showed resistance to antimicrobials, while 27.5% demonstrated over-expression of efflux pump activity.

CONCLUSION

The high prevalence of ETEC across all sources and the occurrence of hetero-pathogenic DEC in diarrheic children and food sources emphasizes the importance of establishing a better strategy for the control and prevention of diarrhea among children in low- and medium-income households.

Distribution of ß-Lactamase Genes Among Multidrug-Resistant and Extended-Spectrum ß-Lactamase-Producing Diarrheagenic Escherichia coli from Under-Five Children in Ethiopia

Purpose

Escherichia coli strains that produce extended-spectrum ß-lactamase (ESBL) and carbapenemase are among the major threats to global health. The objective of the present study was to determine the distribution of ß-lactamase genes among multidrug-resistant (MDR) and ESBL-producing Diarrheagenic E. coli (DEC) pathotypes isolated from under-five children in Ethiopia.

Patients and Methods

A cross-sectional study was conducted in Addis Ababa and Debre Berhan, Ethiopia. It was a health-facility-based study and conducted between December 2020 and August 2021. A total of 476 under-five children participated in the study. DEC pathotypes were detected by conventional Polymerase Chain Reaction (PCR) assay. After evaluating the antimicrobial susceptibility profile of the DEC strains by disk diffusion method, confirmation test was done for ESBL and carbapenemase production. ß-lactamase encoding genes were identified from phenotypically ESBLs and carbapenemase positive DEC strains using PCR assay.

Results

In total, 183 DEC pathotypes were isolated from the 476 under-five children. Seventy-nine (43%, 79/183) MDR-DEC pathotypes were identified. MDR was common among enteroaggregative E. coli (EAEC) (58%, 44/76), followed by enterotoxigenic E. coli (ETEC) (44%, 17/39)) and enteroinvasive E. coli (EIEC) (30%, 7/23). Phenotypically, a total of 30 MDR-DEC pathotypes (16.4%, 30/183) were tested positive for ESBLs. Few ETEC (5.1%, 2/39) and EAEC (2.6%, 2/76) were carbapenemase producers. The predominant β-lactamase genes identified was blaTEM (80%, 24/30) followed by blaCTX-M (73%, 22/30), blaSHV (60%, 18/30), blaNDM (13%, 4/30), and blaOXA-48 (13%, 4/30). Majority of the ß-lactamase encoding genes were detected in EAEC (50%) and ETEC (20%). Co-existence of different β-lactamase genes was found in the present study.

Conclusion

The blaTEM, blaCTX-M, blaSHV, blaNDM, and blaOXA-48, that are associated with serious and urgent threats globally, were detected in diarrheagenic E. coli isolates from under-five children in Ethiopia. This study also revealed the coexistence of the β-lactamase genes.