Plasmid Distribution among Escherichia coli from Livestock and Associated Wastewater: Unraveling Factors That Shape the Presence of Genes Conferring Third-Generation Cephalosporin Resistance

Non-negligible roles of upstream rivers in determining the antibiotic resistance genes community in an interconnected river-lake system (Dongting lake, China)

Emergence and spread of antibiotic resistance genes (ARGs) in lakes have been considered as a global health threat. However, a thorough understanding of the distribution patterns and ecological processes that shape the ARGs profile in interconnected river-lake systems remains largely unexplored. In this study, we collected paired water and sediment samples from a typical interconnected river-lake system, Dongting Lake in China, during both wet and dry seasons. Using high-throughput quantitative PCR, we investigated the spatial and temporal distribution of ARGs and the factors that influence them. A total of 8 major antibiotic classes and 10 mobile genetic elements were detected across the Dongting Lake basin. The unique hydrological characteristics of this interconnected river-lake system result in a relatively stable abundance of ARGs across different seasons and interfaces. During the wet season, deterministic processes dominated the assembly of ARGs, allowing environmental factors, such as heavy metals, to serve as main driving forces of ARGs distribution. When the dry season arrived, variations in hydrological conditions and changes in ARGs sources caused stochastic processes to dominate the assembly of ARGs. Our findings provide valuable insights for understanding the ecological processes of ARGs in interconnected river-lake systems, emphasizing the necessity of upstream restoration and clarifying river-lake relationships to mitigate ARGs dissemination.

Insights into the circular: The cryptic plasmidome and its derived antibiotic resistome in the urban water systems

Plasmids have been a concern in the dissemination and evolution of antibiotic resistance in the environment. In this study, we investigated the total pool of plasmids (plasmidome) and its derived antibiotic resistance genes (ARGs) in different compartments of urban water systems (UWSs) in three European countries representing different antibiotic usage regimes. We applied a direct plasmidome approach using wet-lab methods to enrich circular DNA in the samples, followed by shotgun sequencing and in silico contig circularisation. We identified 9538 novel sequences in a total of 10,942 recovered circular plasmids. Of these, 66 were identified as conjugative, 1896 mobilisable and 8970 non-mobilisable plasmids. The UWSs' plasmidome was dominated by small plasmids (≤10 Kbp) representing a broad diversity of mobility (MOB) types and incompatibility (Inc) groups. A shared collection of plasmids from different countries was detected in all treatment compartments, and plasmids could be source-tracked in the UWSs. More than half of the ARGs-encoding plasmids carried mobility genes for mobilisation/conjugation. The richness and abundance of ARGs-encoding plasmids generally decreased with the flow, while we observed that non-mobilisable ARGs-harbouring plasmids maintained their abundance in the Spanish wastewater treatment plant. Overall, our work unravels that the UWS plasmidome is dominated by cryptic (i.e., non-mobilisable, non-typeable and previously unknown) plasmids. Considering that some of these plasmids carried ARGs, were prevalent across three countries and could persist throughout the UWSs compartments, these results should alarm and call for attention.

Bird's-eye MApping of plasmids (BeMAp) for visualization and comparison of genomic structures of different plasmids by mapping antimicrobial resistance genes on spreadsheets

Effective classification and visualization of multiple antimicrobial resistance plasmids can be challenging, and few tools to analyze similarities among plasmids depending on the location of genes are available. We created a new plasmid mapping program called Bird's-eye MApping of plasmids (BeMAp) to map antimicrobial resistance genes across multiple plasmids onto a spreadsheet and visualize their similarities based on gene types, locations, alignments, and organization. We analyzed plasmids containing various antimicrobial resistance genes, together with genes coding for IMP-type metallo-β-lactamases. Moreover, the mapping of plasmids with antimicrobial resistance genes and Incompatibility (Inc) groups showed that clustered plasmids with a similar organization of antimicrobial resistance genes were not always classified into the same Inc groups, indicating that the program displays multiple plasmids regardless of the Inc group classification. Our results showed that this calculation protocol and mapping strategy could provide a valuable tool for the practical and convenient visualization and comparison of the genomic structure of multiple plasmids in parallel.

Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America

Extended-spectrum cephalosporins (ESCs) are critically important antimicrobial agents for human and veterinary medicine. ESC resistance (ESC-R) genes have spread worldwide through plasmids and clonal expansion, yet the distribution and dynamics of ESC-R genes in different ecological compartments are poorly understood. Here we use whole genome sequence data of Enterobacterales isolates of human and animal origin from Europe and North America and identify contrasting temporal dynamics. AmpC β-lactamases were initially more dominant in North America in humans and farm animals, only later emerging in Europe. In contrast, specific extended-spectrum β-lactamases (ESBLs) were initially common in animals from Europe and later emerged in North America. This study identifies differences in the relative importance of plasmids and clonal expansion across different compartments for the spread of different ESC-R genes. Understanding the mechanisms of transmission will be critical in the design of interventions to reduce the spread of antimicrobial resistance.

Origin, fluxes, and reservoirs of Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa in aquatic ecosystems of a French floodplain

The release and spread of opportunistic pathogens - some of which are resistant to antibiotics - in the environment is a major public health challenge worldwide. In this study, we found evidence of the origin of such microorganisms and characterized their dispersal and survival in floodplain ecosystems to understand their fate in the environment. We determined the concentrations of Escherichia coli, extended-spectrum β-lactamases (ESBL)-producing E. coli, Klebsiella pneumoniae, ESBL-producing K. pneumoniae, and Pseudomonas aeruginosa in a floodplain of Eastern France using a culture-based method. Furthermore, we assessed the population structure of E. coli isolates by quadruplex PCR, their plasmid replicon content by PCR-based replicon typing, and the nature of their bla_ESBL genes by PCR and sequencing. The main aquatic ecosystems of the floodplain (river, tributaries, riverine wetlands, and groundwater) were sampled monthly over a one-year cycle. The majority of E. coli isolates retrieved in the studied floodplain were likely of human origin. Moreover, contamination of floodplain aquatic ecosystems by opportunistic pathogens mainly resulted from hydrological fluxes during high-flow periods, suggesting that dispersal and dilution predominated. During low-flow periods, E. coli may be able to survive for several months in isolated ecosystems in which it may find favourable conditions to thrive. The most nutrient-rich and isolated wetlands are consequently potential pathogen reservoirs. The production of ESBL was not a disadvantage for E. coli in low-anthropized floodplain ecosystems.

Antibiotic tolerance and degradation capacity of the organic pollutant-degrading bacterium Rhodococcus biphenylivorans TG9T

Antibiotics are ubiquitous in soil due to natural ecological competition, as well as emerging contaminants due to anthropogenic inputs. Under environmental factors like antibiotic stress, some bacteria, including those that degrade environmental pollutants, can enter a dormant state as a survival strategy, thereby limiting their metabolic activity and function. Dormancy has a critical influence on the degradative activity of bacteria, dramatically decreasing the rate at which they transform organic pollutants. To better understand this phenomenon in environmental pollutant-degrading bacteria, we investigated dormancy transitions induced with norfloxacin in Rhodococcus biphenylivorans TG9^T using next-generation proteomics, proteogenomics, and additional experiments. Our results suggest that exposure to norfloxacin inhibited DNA replication, which led to damage to the cell. Dormant cells then likely triggered DNA repair, particularly homologous recombination, for continued survival. The results also indicated that substrate transport (ATP-binding cassette transporter), ATP production, and the tricarboxylic acid (TCA) cycle were repressed during dormancy, and degradation of organic pollutants was down-regulated. Given the widespread phenomenon of dormancy among bacteria involved in pollutant removal systems, this study improves our understanding of possible implications of antibiotic survival strategies on biotransformation of mixtures containing antibiotics as well as other organics.

Pyroligneous acid mitigated dissemination of antibiotic resistance genes in soil

Strategies to mitigate the spread of antibiotic resistance genes (ARGs) in soils are urgently needed. Therefore, a pristine pyroligneous acid (PA) from pyrolyzing blended woody waste at 450 °C and its three fractions distilled at 98, 130, and 220 °C (F1, F2, and F3) were used to evaluate their feasibility of reducing ARGs in soil. Application of PA, F2, and F3 effectively decreased the relative ARG abundance by 22.4-75.4% and 39.7-66.7% in the rhizosphere and bulk soil relative to control, respectively, and the removal efficiency followed an order of F3 > PA > F2. Contrarily, F1 increased the abundance of ARGs. The decreased abundance of two mobile genetic elements and impaired conjugative transfer of RP4 plasmid in the presence of PA, F2 and F3 demonstrated that the weakened horizontal gene transfer (HGT) contributed to the reduced ARG level. Variation partitioning analysis and structural equation models confirmed that ARG reduction was primarily driven by the weakened HGT, followed by the decreased co-selection of heavy metals and shifted bacterial community (e.g., reduced potential host bacteria of ARGs). Our findings provide practical and technical support for developing PA-based technology in remediating ARG-contaminated soil to ensure food safety and protect human health.

A One Health Comparative Assessment of Antimicrobial Resistance in Generic and Extended-Spectrum Cephalosporin-Resistant Escherichia coli from Beef Production, Sewage and Clinical Settings

This study aimed to compare antimicrobial resistance (AMR) in extended-spectrum cephalosporin-resistant and generic Escherichia coli from a One Health continuum of the beef production system in Alberta, Canada. A total of 705 extended-spectrum cephalosporin-resistant E. coli (ESC^r) were obtained from: cattle feces (CFeces, n = 382), catch basins (CBasins, n = 137), surrounding streams (SStreams, n = 59), beef processing plants (BProcessing, n = 4), municipal sewage (MSewage; n = 98) and human clinical specimens (CHumans, n = 25). Generic isolates (663) included: CFeces (n = 142), CBasins (n = 185), SStreams (n = 81), BProcessing (n = 159) and MSewage (n = 96). All isolates were screened for antimicrobial susceptibility to 9 antimicrobials and two clavulanic acid combinations. In ESC^r, oxytetracycline (87.7%), ampicillin (84.4%) and streptomycin (73.8%) resistance phenotypes were the most common, with source influencing AMR prevalence (p < 0.001). In generic E. coli, oxytetracycline (51.1%), streptomycin (22.6%), ampicillin (22.5%) and sulfisoxazole (14.3%) resistance were most common. Overall, 88.8% of ESC^r, and 26.7% of generic isolates exhibited multi-drug resistance (MDR). MDR in ESC^r was high from all sources: CFeces (97.1%), MSewage (96.9%), CHumans (96%), BProcessing (100%), CBasins (70.5%) and SStreams (61.4%). MDR in generic E. coli was lower with CFeces (45.1%), CBasins (34.6%), SStreams (23.5%), MSewage (13.6%) and BProcessing (10.7%). ESBL phenotypes were confirmed in 24.7% (n = 174) ESC^r and 0.6% of generic E. coli. Prevalence of bla genes in ESC^r were bla_CTXM (30.1%), bla_CTXM-1 (21.6%), bla_TEM (20%), bla_CTXM-9 (7.9%), bla_OXA (3.0%), bla_CTXM-2 (6.4%), bla_SHV (1.4%) and AmpC β-lactamase bla_CMY (81.3%). The lower AMR in ESC^r from SStreams and BProcessing and higher AMR in CHumans and CFeces likely reflects antimicrobial use in these environments. Although MDR levels were higher in ESC^r as compared to generic E. coli, AMR to the same antimicrobials ranked high in both ESC^r and generic E. coli sub-populations. This suggests that both sub-populations reflect similar AMR trends and are equally useful for AMR surveillance. Considering that MDR ESC^r MSewage isolates were obtained without enrichment, while those from CFeces were obtained with enrichment, MSewage may serve as a hot spot for MDR emergence and dissemination.

Whole Genome Sequencing Differentiates Presumptive Extended Spectrum Beta-Lactamase Producing Escherichia coli along Segments of the One Health Continuum

Antimicrobial resistance (AMR) has important implications for the continued use of antibiotics to control infectious diseases in both beef cattle and humans. AMR along the One Health continuum of the beef production system is largely unknown. Here, whole genomes of presumptive extended-spectrum β-lactamase E. coli (ESBL-EC) from cattle feces (n = 40), feedlot catch basins (n = 42), surrounding streams (n = 21), a beef processing plant (n = 4), municipal sewage (n = 30), and clinical patients (n = 25) are described. ESBL-EC were isolated from ceftriaxone selective plates and subcultured on ampicillin selective plates. Agreement of genotype-phenotype prediction of AMR ranged from 93.2% for ampicillin to 100% for neomycin, trimethoprim/sulfamethoxazole, and enrofloxacin resistance. Overall, β-lactam (100%; bla_EC, bla_TEM-1, bla_SHV, bla_OXA, bla_CTX-M-), tetracycline (90.1%; tet(A), tet(B)) and folate synthesis (sul2) antimicrobial resistance genes (ARGs) were most prevalent. The ARGs tet(C), tet(M), tet(32),bla_CTX-M-1, bla_CTX-M-14, bla_OXA-1, dfrA18, dfrA19, catB3, and catB4 were exclusive to human sources, while bla_TEM-150, bla_SHV-11–12,dfrA12, cmlA1, and cmlA5 were exclusive to beef cattle sources. Frequently encountered virulence factors across all sources included adhesion and type II and III secretion systems, while IncFIB(AP001918) and IncFII plasmids were also common. Specificity and prevalence of ARGs between cattle-sourced and human-sourced presumptive ESBL-EC likely reflect differences in antimicrobial use in cattle and humans. Comparative genomics revealed phylogenetically distinct clusters for isolates from human vs. cattle sources, implying that human infections caused by ESBL-EC in this region might not originate from beef production sources.