Antibiogram Signatures of Some Enterobacteria Recovered from Irrigation Water and Agricultural Soil in two District Municipalities of South Africa

Prevalence of extended-spectrum β-lactamase producing Enterobacterales in Africa's water-plant-food interface: A meta-analysis (2010–2022)

Background

Multidrug-resistant extended-spectrum β-lactamase (ESBL)-producing Enterobacterales is regarded as a critical health issue, yet, surveillance in the water-plant-food interface remains low, especially in Africa.

Objectives

The objective of the study was to elucidate the distribution and prevalence of antimicrobial resistance in clinically significant members of the Enterobacterales order isolated from the water-plant-food interface in Africa.

Methods

A literature search was conducted using six online databases according to the PRISMA guidelines. All available published studies involving phenotypic and genotypic characterization of ESBL-producing Enterobacterales from water, fresh produce or soil in Africa were considered eligible. Identification and characterization methods used as well as a network analysis according to the isolation source and publication year were summarized. Analysis of Escherichia coli, Salmonella spp. and Klebsiella pneumoniae included the calculation of the multiple antibiotic resistance (MAR) index according to isolation sources and statistical analysis was performed using RStudio.

Results

Overall, 51 studies were included for further investigation. Twelve African countries were represented, with environmental AMR surveillance studies predominantly conducted in South Africa. In 76.47% of the studies, occurrence of antimicrobial resistant bacteria was investigated in irrigation water samples, while 50.98% of the studies included fresh produce samples. Analysis of bacterial phenotypic antimicrobial resistance profiles were reported in 94.12% of the studies, with the disk diffusion method predominantly used. When investigating the MAR indexes of the characterized Escherichia coli, Klebsiella pneumoniae and Salmonella spp., from different sources (water, fresh produce or soil), no significant differences were seen across the countries. The only genetic determinant identified using PCR detection in all the studies was the blaCTX − M resistance gene. Only four studies used whole genome sequence analysis for molecular isolate characterization.

Discussion

Globally, AMR surveillance programmes recognize ESBL- and carbapenemase-producing Enterobacterales as vectors of great importance in AMR gene dissemination. However, in low- and middle-income countries, such as those in Africa, challenges to implementing effective and sustainable AMR surveillance programmes remain. This review emphasizes the need for improved surveillance, standardized methods and documentation of resistance gene dissemination across the farm-to-fork continuum in 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.

A study on drinking water quality in different income groups of Vizianagaram region of India

Portable clean water consumption is the basic right of every individual. The major global concern is water pollution which can cause mortality. Change in physicochemical characteristics in drinking water is not only a pollution problem, but the presence of antibiotic-resistant microbes is also a significant issue. The study was carried out to assess the physicochemical and microbiological quality of the reservoir, municipality-supplied water, and bottled water. A total of 100 samples were collected from different income classes (higher, medium, and low) groups. The experiments were carried out based on the guidelines of APHA. In the present study, 40% of samples have been found to be contaminated with bacteria such as Escherichia coli, Vibrio cholerae, and Enterobacter aerogenes. Moreover, these bacteria also showed antibiotic resistance to certain drugs. The percentage of isolated bacterial strains was resistant to amoxicillin and ampicillin antibiotics. The statistical analysis of the Chi-square test states that there is a significant correlation between E. coli and other microbes (p ≤ 0.5). This study gives a piece of baseline information about the prevalence of antibiotic-resistant bacteria and focuses on the improvement of water from purification before reaching the consumer.

Genetic Characterization of Enterobacter hormaechei Co-Harboring blaNDM-1 and mcr-9 Causing Upper Respiratory Tract Infection

Purpose

With the spread of multiple drug-resistant bacteria, bla_NDM-1 and mcr-9 have been detected in various bacteria worldwide. However, the simultaneous detection of bla_NDM-1 and mcr-9 in Enterobacter hormaechei has been rarely reported. This study identified an E. hormaechei strain carrying both bla_NDM-1 and mcr-9. We investigated the genetic characteristics of these two resistance genes in detail, elucidating various potential mechanisms by which they may be transmitted.

Methods

Bacterial genomic features and possible origins were assessed by whole-genome sequencing (WGS) with Illumina and PacBio platforms and phylogenetic analysis. Subsequent investigations were performed, including antimicrobial susceptibility testing and multilocus sequence typing (MLST).

Results

We isolated an E. hormaechei strain DY1901 carrying both bla_NDM-1 and mcr-9 from the sputum sample. Susceptibility testing showed that the isolate was multidrug-resistant. Multiple antibiotic resistance genes and virulence genes are widely distributed in DY1901. S1-PFGE, Southern blotting, and plasmid replicon typing showed that DY1901 carried four plasmids. The plasmid carrying mcr-9 was 259Kb in size and belonged to IncHI2, while the plasmid carrying bla_NDM-1 was 45Kb in length and belonged to IncX3.

Conclusion

The E. hormaechei strain isolated in this study has a broad antibiotic resistance spectrum, posing a challenge to clinical treatment. Plasmids carrying mcr-9 are fusion plasmids, and those taking NDM are widely disseminated in China, suggesting that we should conduct routine genomic surveillance on such plasmids to curb the spread of drug-resistant bacteria in the region.

Estimating the Risk of Acute Gastrointestinal Disease Attributed to E. coli O157:H7 in Irrigation Water and Agricultural Soil: A Quantitative Microbial Risk Assessment

Introduction: The occurrence of E. coli O157:H7 in the agricultural environment poses a serious threat to public health. The primary aim was to estimate the probability of illness caused by E. coli O157:H7 in irrigation water and agricultural soil niches. Methods: The Quantitative Microbial Risk Assessment was used and the risks were characterized using the Monte Carlo simulation with 10,000 iterations. Results: The mean levels of E. coli O157:H7 in the irrigation water and agricultural soil samples was 1.328 × 103 CFU/100 mL (Range: 0.00 to 13.000 × 103 CFU/100 mL) and 2.482 × 103 CFU/g (Range: 0.167 × 103 to 16.333 × 103 CFU/g), respectively. The risk of infection in humans exposed to this water and soil was 100%. In addition, a high risk of acute diarrheal disease was estimated at 25.0 × 10−2 for humans exposed to contaminated water and/or soil. Summary: These results exceeded the WHO diarrheal disease risk standard of 1.0 × 10−3. These findings demonstrated a high probability of acute gastrointestinal disease among humans exposed to E. coli O157:H7 in irrigation water and agricultural soil samples collected from the study sites representing a huge public health threat.

Whole Genome Sequencing of Extended-Spectrum- and AmpC- β-Lactamase-Positive Enterobacterales Isolated From Spinach Production in Gauteng Province, South Africa

The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase- (AmpC) producing Enterobacterales in irrigation water and associated irrigated fresh produce represents risks related to the environment, food safety, and public health. In South Africa, information about the presence of ESBL/AmpC-producing Enterobacterales from non-clinical sources is limited, particularly in the water-plant-food interface. This study aimed to characterize 19 selected MDR ESBL/AmpC-producing Escherichia coli (n=3), Klebsiella pneumoniae (n=5), Serratia fonticola (n=10), and Salmonella enterica (n=1) isolates from spinach and associated irrigation water samples from two commercial spinach production systems within South Africa, using whole genome sequencing (WGS). Antibiotic resistance genes potentially encoding resistance to eight different classes were present, with bla CTX-M-15 being the dominant ESBL encoding gene and bla ACT-types being the dominant AmpC encoding gene detected. A greater number of resistance genes across more antibiotic classes were seen in all the K. pneumoniae strains, compared to the other genera tested. From one farm, bla CTX-M-15-positive K. pneumoniae strains of the same sequence type 985 (ST 985) were present in spinach at harvest and retail samples after processing, suggesting successful persistence of these MDR strains. In addition, ESBL-producing K. pneumoniae ST15, an emerging high-risk clone causing nosocomical outbreaks worldwide, was isolated from irrigation water. Known resistance plasmid replicon types of Enterobacterales including IncFIB, IncFIA, IncFII, IncB/O, and IncHI1B were observed in all strains following analysis with PlasmidFinder. However, bla CTX-M-15 was the only β-lactamase resistance gene associated with plasmids (IncFII and IncFIB) in K. pneumoniae (n=4) strains. In one E. coli and five K. pneumoniae strains, integron In191 was observed. Relevant similarities to human pathogens were predicted with PathogenFinder for all 19 strains, with a confidence of 0.635-0.721 in S. fonticola, 0.852-0.931 in E. coli, 0.796-0.899 in K. pneumoniae, and 0.939 in the S. enterica strain. The presence of MDR ESBL/AmpC-producing E. coli, K. pneumoniae, S. fonticola, and S. enterica with similarities to human pathogens in the agricultural production systems reflects environmental and food contamination mediated by anthropogenic activities, contributing to the spread of antibiotic resistance genes.