A snapshot survey of antimicrobial resistance in food-animals in low and middle-income countries

A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs

BACKGROUND

Members of the Klebsiella pneumoniae species complex (KpSC) are opportunistic pathogens that cause severe and difficult-to-treat infections. KpSC are common in non-human niches, but the clinical relevance of these populations is disputed.

METHODS

In this study, we analysed 3255 whole-genome sequenced isolates from human, animal and marine sources collected in Norway between 2001 and 2020. We used population genomics in a One Health context to assess the diversity of strains, genes and other clinically relevant genetic features within and between sources. We further explored niche-enriched traits using genome-wide association studies and investigated evidence of spillover and connectivity across the KpSC populations from the three niches.

RESULTS

We found that the KpSC populations in different niches were distinct but overlapping. Overall, there was high genetic diversity both between and within sources, with nearly half (49%) of the genes in the accessory genome overlapping the ecological niches. Further, several sublineages (SLs) including SL17, SL35, SL37, SL45, SL107 and SL3010 were common across sources. There were few niche-enriched traits, except for aerobactin-encoding plasmids and the bacteriocin colicin a, which were associated with KpSC from animal sources. Human infection isolates showed the greatest connectivity with each other, followed by isolates from human carriage, pigs, and bivalves. Nearly 5% of human infection isolates had close relatives (≤22 substitutions) amongst animal and marine isolates, despite temporally and geographically distant sampling of these sources. There were limited but notable recent spillover events, including the movement of plasmids encoding the virulence locus iuc3 between pigs and humans.

CONCLUSIONS

Our large One Health genomic study highlights that human-to-human transmission of KpSC is more common than transmission between ecological niches. Still, spillover of clinically relevant strains and genetic features between human and non-human sources does occur and should not be overlooked. Infection prevention measures are essential to limit transmission within human clinical settings and reduce infections. However, preventing transmission that leads to colonisation, e.g. from direct contact with animals or via the food chain, could also play an important role in reducing the KpSC disease burden.

One Health Approach: Antibiotic Resistance Among Enterococcal Isolates in Dairy Farms in Selangor

BACKGROUND/OBJECTIVES

Antibiotic resistance is a growing public health concern. The One Health approach is essential in addressing antibiotic (AR) resistance. Therefore, this study aimed to determine AR among enterococcal isolates in dairy farms across various domains based on the emerging dairy industry.

METHODS

A total of 208 enterococcal isolates from the workers = 70, milk = 76, and environment = 62 of eight dairy farms in Selangor, Malaysia, were used in this study. The bacterial identification and antibiotic susceptibility testing (AST) were conducted utilising the Vitek-2 system.

RESULTS

Approximately 28% of the isolates exhibited susceptibility to all tested antibiotics. A relatively higher proportion of isolates demonstrated resistance to tetracycline, which was followed by erythromycin. The multidrug resistance (MDR) and multiple antibiotic resistance (MAR) index were low in this study.

CONCLUSIONS

The studied dairy farms exhibited lower AR, MDR, and MAR index values. Nevertheless, ongoing surveillance is essential due to the recent expansion of the dairy farming industry.

Gene profile of virulence, antimicrobial resistance and action of enterocins in Campylobacter species isolated from broiler carcasses

Campylobacteriosis is among the most reported zoonoses in the world, caused by species of Campylobacter, this disease is characterized by gastroenteritis in humans. The main species involved is Campylobacter jejuni, followed by Campylobacter coli. Contaminated chicken meat is often identified as an important source of infection related to human cases and Brazil is the largest exporter of chicken meat in the world, which makes the characterization of brazilian isolates crucial for the establishment of control measures. The objective was to evaluate the contamination of chilled and frozen carcasses sold in the Northeast of Brazil, by Campylobacter species, identify virulence genes, evaluate bacterial resistance to antibiotics and verify the antimicrobial action of the Crude Extract Containing Enterocins (CECE) produced by a probiotic strain of Enterococcus faecium. In this study, 12 chilled carcasses and 12 frozen carcasses were collected, sold retail in supermarkets. The following regions of the carcass were sampled: breast skin, wing skin, belly skin, neck skin, gizzard and liver. Samples of chicken carcasses were analyzed following ISO 10272-2 guidelines for the isolation of Campylobacter spp. The isolates were tested by PCR to identify genus, species C. jejuni, C. coli and C. lari and genes cdtA, cdtB, cdtC, sodB, dnaJ, cmeA, cmeB, cmeC. The assessment of susceptibility to antibiotics was carried out using the standard disk diffusion method and the antimicrobial activity of CECE was determined using the Minimum Inhibitory Concentration (MIC), the methodologies followed the recommendations and cutoff points according to EUCAST and CLSI. A total of 376 isolates of Campylobacter spp. were obtained, among these, 26 (7.0%) were positive for C. jejuni and no isolates were detected for C. coli and C. lari. The highest frequency of C. jejuni was obtained in chilled carcasses with 23 isolates (88.5%, p < 0.0001), in frozen carcasses three isolates were obtained (11.5%). The most frequency site of C. jejuni was the chest skin (7/27.0%), followed by skin of the wing (6/23.0%), skin of the cloaca (5/19.0%), gizzard (4/15.0%), skin of the neck (2/8.0%) and liver (2/8.0%), no significant differences were found between the sites sampled. The gene frequency was determined in: cdtA (3/11.5%), cdtB (3/11.5%), cdtC (5/19.0%), sodB (9/34.5%), dnaJ (3/11.5%), cmeA (4/15.0%), cmeB (4/15.0%) and cmeC (4/15.0%). The three efflux pump genes were amplified in four isolates (15.3%) and all tested genes were amplified in three isolates (11.5%). All C. jejuni isolates (26/100.0%) were found to be multiresistant to three or more classes of antimicrobials. The index of multiple resistance to antimicrobial drugs (IRMA) ranged from 0.4 to 1.0 among isolates of C. jejuni. The antimicrobial activity of CECE was able to inhibit at least 98.5% of the growth of all C. jejuni isolates. Therefore, chilled chicken carcasses present a greater risk of contamination than frozen carcasses, for this reason it is necessary to adopt practices that avoid cross-contamination during the preparation of chicken meat, in order to prevent campylobacteriosis. Furthermore, the presence of multiresistant and potentially virulent isolates highlights the need for further investigations to better understand the use of enterocins as alternative methods in the control of Campylobacter.

Recovery of clinically relevant multidrug-resistant Klebsiella pneumoniae lineages from wastewater in Kumasi Metropolis, Ghana

Antimicrobial resistance (AMR) is under-monitored in Africa, with few reports characterizing resistant bacteria from the environment. This study examined physicochemical parameters, chemical contaminants and antibiotic-resistant bacteria in waste stabilization pond effluents, hospital wastewater and domestic wastewater from four sewerage sites in Kumasi. The bacteria isolates were sequenced. Three sites exceeded national guidelines for total suspended solids, biochemical oxygen demand, chemical oxygen demand and electrical conductivity. Although sulfamethoxazole levels were low, the antibiotic was detected at all sites. Multi-drug-resistant Klebsiella pneumoniae and Pseudomonas aeruginosa were isolated with multi-locus sequence typing identifying K. pneumoniae strains as ST18 and ST147, and P. aeruginosa as ST235, all of clinical relevance. A comparison of ST147 genomes with isolates from human infections in Africa showed remarkable similarity and shared AMR profiles. Thirteen of the twenty-one plasmids from ST147 harbored at least one AMR gene, including blaCTX-M-15 linked to copper-resistance genes. Our study demonstrated high bacterial counts and organic matter in the analysed wastewater. The recovery of clinically significant isolates with multiple antibiotic and heavy metal resistance genes from the wastewater samples raises public health concerns.

Metagenomic insights into resistome, mobilome and virulome in different fecal waste

Fecal waste is a significant source of antimicrobial resistance (AMR) pollution and provides valuable insights into the AMR development in animal and human populations within the "One health" framework. Various genetic elements, including antibiotic resistance genes (ARGs), biocide and metal resistance genes (BMGs), mobile genetic elements (MGEs), and virulence factor genes (VFGs), are crucial AMR risk determinants (ARDs). However, few studies focused on compositional characteristics of ARDs in different feces. Here, we analyzed 753 public metagenomes from human, pig, chicken, and cattle feces, revealing significant differences in ARD richness and abundance across fecal types, notably lowest in cattle samples. Tetracycline, multi-metal, and -biocide resistance genes were dominant resistome. A few core genes contributed to 25.6%-91.1% of gene abundance, and their correlations were stronger in cattle samples. Procrustes analysis showed that microbial composition had higher correlations with ARGs (M2 = 0.579) and BMGs (M2 = 0.519). Gammaproteobacteria was identified as major ARD-hosts especially in human and pig feces, and they mainly carried multi-resistance genes. MGEs exhibited direct positive effects on ARGs and BMGs, indirectly impacting VFGs. Utilizing random forest methods, we identified 42 indicator genes for tracking AMR pollution originating from fecal sources in the environments. This study offers new insights into understanding and controlling the AMR pollution of fecal waste from human and food animals.

A global perspective on the abundance, diversity and mobility of antibiotic resistance genes in Escherichia coli

Introduction

Escherichia coli (E. coli), a ubiquitous opportunistic pathogen, poses a growing threat to human health due to the increasing prevalence of antibiotic resistance. However, a comprehensive understanding of the global distribution, diversity, and transmission of antibiotic resistance genes (ARGs) in E. coli remains lacking, hindering effective strategies to combat resistance.

Methods

In this study, we analyzed 94,762 E. coli genome sequences obtained from the NCBI database using advanced bioinformatics tools. ARGs were identified by comparing sequences against a custom ARG database using BLAST. Mobile genetic element (MGE)-associated ARGs were identified by matching with ISfinder databases. Global distribution of ARGs was analyzed by clustering mobile ARG sequences with 99% genetic similarity.

Results

Our analysis revealed that 50.51% of the E. coli genome sequences contained ARGs, totaling 301,317 identified ARG sequences. These ARGs were categorized into 12 major classes and 229 subtypes. Notably, ARGs associated with multi-drug resistance (MDR), β-lactams, macrolide-lincosamide-streptogramins (MLS), tetracyclines, and aminoglycosides were particularly abundant, with the subtypes mdtK, macB, and ampC being especially prevalent. Additionally, significant differences in ARG abundance and diversity were observed across countries, with higher diversity found in high-income nations. Furthermore, 9.28% of the ARG sequences were linked to MGEs, accounting for 98.25% of all ARG subtypes. Notably, 4.20% of mobile ARGs were identified in over 20 countries, with β-lactam and aminoglycoside ARGs being the most widespread.

Discussion

This study provides a comprehensive overview of the global distribution and transmission of ARGs in E. coli. The high abundance of MDR and β-lactam-related ARGs, along with their widespread transmission across countries, highlights the urgent need for global surveillance and control measures. Furthermore, the strong association between ARGs and MGEs underscores the role of horizontal gene transfer in the spread of resistance. The observed variations in ARG diversity between countries suggest that socioeconomic factors, such as healthcare infrastructure and antibiotic usage patterns, significantly influence ARG prevalence. These findings are crucial for informing global strategies to mitigate the spread of antibiotic resistance and improve public health outcomes.

Public awareness, risk perceptions and behaviour towards antibiotic use in food-producing animals and antimicrobial resistance in Malaysia: A cross-sectional study

Antimicrobial resistance (AMR) is a growing global public health problem, particularly in low- and middle-income countries, including Malaysia. Understanding risk perceptions on antimicrobial use (AMU) in food-producing animals from the general public perspective is an essential component in addressing AMR. However, little is known about public risk perceptions of AMU and AMR in food-producing animals in Malaysia. The objectives of this study were to assess the level of awareness, risk perceptions, and behaviour regarding antibiotic use in food-producing animals and antimicrobial resistance and to examine the factors associated with risk perceptions and the relationship between knowledge, awareness, risk perceptions and behaviour among the general public in Malaysia. A cross-sectional survey was used. Both descriptive and analytical statistics were used to analyse data and present results. Correlation and regression analyses were conducted to examine the factors associated with risk perceptions and the relationship between risk perceptions and behaviour. A total of 416 individuals participated in the study. The majority of the participants (69.2 %) had low knowledge of antibiotics and antibiotic use in food-producing animals. The levels of awareness of antibiotic use and the perceived route of antibiotic resistance transfer were moderate. Participants had a high level of general risk perception (GRP) of antibiotic use, a moderate level of personal-level risk perception (PRP) of antibiotic resistance transmission, and a high level of societal-level risk perception (SRP) of antibiotic resistance transmission. Awareness of antibiotic use was a significant predictor of GRP (β = 0.27, 95 %CI: 0.12-0.31, P < 0.001). Awareness of route of resistance transfer was a significant predictor of PRP (β = 0.54, 95 %CI: 0.32-0.44, P < 0.001) and SRP (β = 0.47, 95 %CI: 0.32-0.46, P < 0.001). PRP is the only significant predictor of behavioural changes towards antibiotic use and antibiotic resistance (OR = 1.45 [1.02-2.07], P = 0.041). Overall, there is a general lack of knowledge and little awareness of antibiotic use and antibiotic resistance in food-producing animals in Malaysia. Risk perceptions were moderate to high and were significantly predicted by awareness of antibiotic use and route of resistance transfer. Personal-level risk perception was a significant predictor of behavioural changes aimed at reducing the risk of AMU and AMR. It is imperative to raise public awareness and understanding of the risks associated with AMU in food-producing animals. Risk communication should be emphasised to ensure the translation of public risk perceptions into behavioural changes.

Biological properties of active compounds from Ageratina adenophora

Ageratina adenophora is an invasive weed with widespread distribution. During the last several decades, many biologically active secondary metabolites have been isolated and characterized from A. adenophora, some of them having inspired the research and development of new therapeutic agents. This review mainly focuses on biological properties of A. adenophora, including the toxicity, antibacterial, antifungal, insecticidal, antiviral activities and others. In addition, the current limits and potentials of A. adenophora and its extracts are also discussed.