Genomic characterisation of a multidrug-resistant TEM-52b extended-spectrum β-lactamase-positive Escherichia coli ST219 isolated from a cat in France

Recent development and fighting strategies for lincosamide antibiotic resistance

SUMMARYLincosamides constitute an important class of antibiotics used against a wide range of pathogens, including methicillin-resistant Staphylococcus aureus. However, due to the misuse of lincosamide and co-selection pressure, the resistance to lincosamide has become a serious concern. It is urgently needed to carefully understand the phenomenon and mechanism of lincosamide resistance to effectively prevent and control lincosamide resistance. To date, six mobile lincosamide resistance classes, including lnu, cfr, erm, vga, lsa, and sal, have been identified. These lincosamide resistance genes are frequently found on mobile genetic elements (MGEs), such as plasmids, transposons, integrative and conjugative elements, genomic islands, and prophages. Additionally, MGEs harbor the genes that confer resistance not only to antimicrobial agents of other classes but also to metals and biocides. The ultimate purpose of discovering and summarizing bacterial resistance is to prevent, control, and combat resistance effectively. This review highlights four promising strategies, including chemical modification of antibiotics, the development of antimicrobial peptides, the initiation of bacterial self-destruct program, and antimicrobial stewardship, to fight against resistance and safeguard global health.

CTX-M-producing Escherichia coli ST602 carrying a wide resistome in South American wild birds: Another pandemic clone of One Health concern

Wild birds have emerged as novel reservoirs and potential spreaders of antibiotic-resistant priority pathogens, being proposed as sentinels of anthropogenic activities related to the use of antimicrobial compounds. The aim of this study was to investigate the occurrence and genomic features of extended-spectrum β-lactamase (ESBL)-producing bacteria in wild birds in South America. In this regard, we have identified two ESBL (CTX-M-55 and CTX-M-65)-positive Escherichia coli (UNB7 and GP188 strains) colonizing Creamy-bellied Thrush (Turdus amaurochalinus) and Variable Hawk (Geranoaetus polyosoma) inhabiting synanthropic and wildlife environments from Brazil and Chile, respectively. Whole-genome sequence (WGS) analysis revealed that E. coli UNB7 and GP188 belonged to the globally disseminated clone ST602, carrying a wide resistome against antibiotics (β-lactams), heavy metals (arsenic, copper, mercury), disinfectants (quaternary ammonium compounds), and pesticides (glyphosate). Additionally, E. coli UNB7 and GP188 strains harbored virulence genes encoding hemolysin E, type II and III secretion systems, increased serum survival, adhesins and siderophores. SNP-based phylogenomic analysis, using an international genome database, revealed genomic relatedness (19-363 SNP differences) of GP188 with livestock and poultry strains, and genomic relatedness (61-318 differences) of UNB7 with environmental, human and livestock strains (Table S1), whereas phylogeographical analysis confirmed successful expansion of ST602 as a global clone of One Health concern. In summary, our results support that ESBL-producing E. coli ST602 harboring a wide resistome and virulome have begun colonizing wild birds in South America, highlighting a potential new reservoir of critical priority pathogens.

A Cross-Sectional Study of Companion Animal-Derived Multidrug-Resistant Escherichia coli in Hangzhou, China

Antimicrobial resistance poses a challenge to global public health, and companion animals could serve as the reservoir for antimicrobial-resistant bacteria. However, the prevalence of antimicrobial-resistant bacteria, especially multidrug-resistant (MDR) bacteria, and the associated risk factors from companion animals are partially understood. Here, we aim to investigate the prevalence of MDR Escherichia coli, as an indicator bacterium, in pet cats and dogs in Hangzhou, China, and evaluate the factors affecting the prevalence of MDR E. coli. The proportion of pets carrying MDR E. coli was 35.77% (49/137), i.e., 40.96% (34/83) for dogs and 27.28% (15/54) for cats. Isolates resistant to trimethoprim-sulfamethoxazole (49.40% and 44.44%), amoxicillin-clavulanic acid (42.17% and 38.89%), and nalidixic acid (40.96% and 35.19%) were the most prevalent in dogs and cats. Interestingly, comparable prevalence of MDR E. coli was observed in pet dogs and cats regardless of the health condition and the history of antibiotic use. Genetic diversity analysis indicates a total of 86 sequencing types (23 clonal complexes), with ST12 being the most dominant. Further genomic investigation of a carbapenem-resistant E. coli ST410 isolate reveals abundant antimicrobial-resistance genes and a plasmid-borne carbapenemase gene (NDM-5) flanked by insertion sequences of IS91 and IS31, suggesting the plasmid and insertion sequences may be involved in carbapenem-resistance dissemination. These data show that companion animal-derived MDR bacteria could threaten public health, and further regulation and supervision of antimicrobial use in pet clinics should be established in China. IMPORTANCE MDR Escherichia coli are considered a global threat because of the decreasing options for antimicrobial therapy. Companion animals could be a reservoir of MDR E. coli, and the numbers of pets and households owning pets in China are booming. However, the prevalence and risk factors of MDR E. coli carriage in Chinese pets were rarely studied. Here, we investigated the prevalence of MDR E. coli in pets in Hangzhou, one of the leading cities with the most established pet market in China, and explored the factors that affected the prevalence. Our findings showed high prevalences of MDR E. coli in pet dogs and cats regardless of their health condition and the history of antibiotic use, suggesting their potential role of public health risk. A call-to-action for improved regulation of antimicrobial use in companion animal is needed in China.

Reference-based read clustering improves the de novo genome assembly of microbial strains

Constructing accurate microbial genome assemblies is necessary to understand genetic diversity in microbial genomes and its functional consequences. However, it still remains as a challenging task especially when only short-read sequencing technologies are used. Here, we present a new read-clustering algorithm, called RBRC, for improving de novo microbial genome assembly, by accurately estimating read proximity using multiple reference genomes. The performance of RBRC was confirmed by simulation-based evaluation in terms of assembly contiguity and the number of misassemblies, and was successfully applied to existing fungal and bacterial genomes by improving the quality of the assemblies without using additional sequencing data. RBRC is a very useful read-clustering algorithm that can be used (i) for generating high-quality genome assemblies of microbial strains when genome assemblies of related strains are available, and (ii) for upgrading existing microbial genome assemblies when the generation of additional sequencing data, such as long reads, is difficult.

Genomic features of a multidrug-resistant and mercury-tolerant environmental Escherichia coli recovered after a mining dam disaster in South America

Mining dam disasters contribute to the contamination of aquatic environments, impacting associated ecosystems and wildlife. A multidrug-resistant Escherichia coli strain (B2C) was isolated from a river water sample in Brazil after the Mariana mining dam disaster. The genome was sequenced using the Illumina MiSeq platform, and de novo assembled using Unicycler. Resistome, virulome, and plasmidome were predicted using bioinformatics tools. Data analysis revealed that E. coli B2C belonged to sequence type ST219 and phylogroup E. Strikingly, a broad resistome (antibiotics, hazardous heavy metals, and biocides) was predicted, including the presence of the clinically relevant bla_CTX-M-2 extended-spectrum β-lactamase (ESBL) gene, qacE∆1 efflux pump gene, and the mer (mercury resistance) operon. SNP-based analysis revealed that environmental E. coli B2C was clustered along to ESBL-negative E. coli strains of ST219 isolated between 1980 and 2021 from livestock in the United States of America. Acquisition of clinically relevant genes by ST219 seems to be a recent genetic event related to anthropogenic activities, where polluted water environments may contribute to its dissemination at the human-animal-environment interface. In addition, the presence of genes conferring resistance to heavy metals could be related to environmental pollution from mining activities. Antimicrobial resistance genes could be essential biomarkers of environmental exposure to human and mining pollution.

Global prevalence and molecular characterization of extended-spectrum β-lactamase producing-Escherichia coli in dogs and cats - A scoping review and meta-analysis

Antimicrobial resistance (AMR) represents a major threat to human and animal health. Part of the AMR dimension is the circulation of extended-spectrum β-lactamases producing-Escherichia coli (ESBL-E. coli), which is now commonly reported among companion animals. However, the global perspective of the prevalence and population structure of ESBL-E. coli circulating in dogs and cats has not been estimated limiting our understanding of their role in the dissemination of ESBL-E. coli. The aim of this study was to compare the prevalence of ESBL-E. coli between dogs and cats and across countries through meta-analysis. We also performed a scoping review to summarize the current knowledge on ESBL genes and E. coli clones circulating among companion animals. A total of 128 studies published in PubMed, Web of Science, and Scopus up to April 2020 were selected and contained information on prevalence and/or molecular characterization of ESBL genes and ESBL-E. coli clones. Our review shows an increase in the number of publications between 2000 and 2019, concentrated mainly in Europe. Prevalence varied across continents, ranging from 0.63% (Oceania) to 16.56% (Africa) in dogs and from 0% (Oceania) to 16.82% (Asia) in cats. Although there were twice as many studies reporting prevalence on dogs (n = 61) than on cats (n = 32), and only 9 studies focused exclusively on cats, our meta-analysis showed no difference in the global prevalence of ESBL-E. coli between dogs (6.87% [95% CI: 4.46-10.45%]) and cats (5.04% [95% CI: 2.42-10.22%]). A considerable diversity of ESBL genes (n = 60) and sequence types (ST) (n = 171) were recovered from companion animals. ESBL-E. coli encoded by CTX-M-15 (67.5%, 77/114) and SHV-12 (21.9%, 25/114), along with resistant strains of ST38 (22.7%, 15/66) and ST131 (50%, 33/66) were widespread and detected in all continents. While presence of ESBL-E. coli is widespread, the drivers influencing the observed ESBL-E. coli prevalence and the clinical relevance in veterinary medicine and public health along with economic impact of ESBL-E. coli infections among companion animals need to be further investigated.