Antimicrobial resistance in Enterobacterales infections among children in sub-Saharan Africa: a systematic review and meta-analysis

Background

The burden of antimicrobial resistance (AMR) has been estimated to be the highest in sub-Saharan Africa (SSA). The current study estimated the proportion of drug-resistant Enterobacterales causing infections in SSA children.

Methods

We searched MEDLINE/PubMed, Embase and the Cochrane Library to identify retrospective and prospective studies published from 01/01/2005 to 01/06/2022 reporting AMR of Enterobacterales causing infections in sub-Saharan children (0-18 years old). Studies were excluded if they had unclear documentation of antimicrobial susceptibility testing methods or fewer than ten observations per bacteria. Data extraction and quality appraisal were conducted by two authors independently. The primary outcome was the proportion of Enterobacterales resistant to antibiotics commonly used in paediatrics. Proportions were combined across studies using mixed-effects logistic regression models per bacteria and per antibiotic. Between-study heterogeneity was assessed using the I2 statistic. The protocol was registered with PROSPERO (CRD42021260157).

Findings

After screening 1111 records, 122 relevant studies were included, providing data on more than 30,000 blood, urine and stool isolates. Escherichia coli and Klebsiella spp. were the predominant species, both presenting high proportions of resistance to third-generation cephalosporins, especially in blood cultures: 40.6% (95% CI: 27.7%-55%; I2: 85.7%, number of isolates (n): 1032) and 84.9% (72.8%-92.2%; I2: 94.1%, n: 2067), respectively. High proportions of resistance to other commonly used antibiotics were also observed. E. coli had high proportions of resistance, especially for ampicillin (92.5%; 95% CI: 76.4%-97.9%; I2: 89.8%, n: 888) and gentamicin (42.7%; 95% CI: 30%-56.5%; I2: 71.9%, n: 968). Gentamicin-resistant Klebsiella spp. were also frequently reported (77.6%; 95% CI: 65.5%-86.3%; I2: 91.6%, n: 1886).

Interpretation

High proportions of resistance to antibiotics commonly used for empirical treatment of infectious syndromes were found for Enterobacterales in sub-Saharan children. There is a critical need to better identify local patterns of AMR to inform and update clinical guidelines for better treatment outcomes.

Funding

No funding was received.

Molecular Characterization and Antimicrobial Resistance of Enteropathogenic Escherichia coli in Children from Ahvaz, Iran

Background: Enteropathogenic Escherichia coli (EPEC) is one of the most important pathogens among young children worldwide. Both eae and bfp genes have been used to identify EPEC strains and categorize them into typical and atypical strains. They may be an emerging pathogen in both developing and developed countries. Objectives: This study was primarily conducted to assess the epidemiology, drug resistance, and β-lactamase distribution of EPEC, as well as the detection of efa1/lifA in atypical strains. Methods: A total of 251 E. coli strains isolated from children with diarrhea were evaluated for their EPEC pathotype by PCR for the presence of eae, stx1, stx2, and bfp genes. Serogrouping with polyvalent antisera was performed to confirm EPEC strains. Atypical EPEC-containing samples were evaluated for the efa1/lifA gene. EPEC isolates were assessed to recognize the antibiotic resistance and screened to detect extended-spectrum β-lactamases (ESBLs). Results: Enteropathogenic E. coli strains were detected in 17 (6.78%) of E. coli isolates by PCR. The prevalence of typical and atypical strains was determined at 35.3% and 64.7%. All strains were completely susceptible to colistin, imipenem, and meropenem. The prevalence of blaCTX-M and blaTEM genes was calculated at 70.58% and 58.82%, respectively. Conclusions: Enteropathogenic E. coli isolates are completely sensitive to carbapenems, and precise therapeutic strategies are required to prevent the spread of these beta-lactamase genes among diarrheagenic E. coli.

Detection of the mcr-1 gene in Enteropathogenic Escherichia coli (EPEC) and Shigatoxigenic E. coli (STEC) strains isolated from broilers

ABSTRACT: Enteropathogenic Escherichia coli (EPEC) and Shigatoxigenic E. coli (STEC) strains are among the major pathotypes found in poultry and their products, which are capable of causing human enteric infections. Colistin has been claimed the drug of choice against diseases caused by multidrug-resistant Gram-negative bacteria (MDRGN) in humans. The mcr-1 gene was the first plasmidial gene that has been described to be responsible for colistin resistance and has also been detected in birds and poultry products. Our study aimed to detect the mcr-1 gene in enteropathogenic strains of E. coli in order to evaluate the resistance to colistin in broilers. The material was obtained from 240 cloacal samples and 60 broiler carcasses. The strains were isolated by the conventional bacteriological method and by the virulence genes, which characterize the enteropathogenic strains and resistance, and the samples were detected by polymerase chain reaction (PCR). Of the 213 isolated strains of E. coli, 57 (26.76%) were characterized as atypical EPEC and 35 (16.43%) as STEC. The mcr-1 gene was found in 3.5% (2/57) of the EPEC strains and 5.7% (2/35) of the STEC strains. In this study, it was possible to confirm that the mcr-1 resistance gene is already circulating in the broiler flocks studied and may be associated with the pathogenic strains.

Characterization and complete genome sequence of the virulent phage ST20 infecting Escherichia coli O165:H8

A virulent phage, named ST20, infecting Escherichia coli O165:H8 was isolated from wastewater and subjected to genomic sequencing using the Illumina HiSeq system. Genomic analysis revealed that it contains double-stranded DNA, and its complete genome consists of 44,517 nucleotides with an average GC content of 50.81%. Morphological observations showed that phage ST20 belongs to the order Caudovirales and the family Siphoviridae due to its characteristic icosahedral capsid and a long noncontractile tail. This phage was further characterized by one-step growth curve analysis and measurement of its stability at 4 °C. The study has implications for the development of potential biocontrol agents.