Factors influencing horizontal gene transfer in the intestine

New challenge: Mitigation and control of antibiotic resistant genes in aquatic environments by biochar

With an increase of diverse contaminants in the environment, particularly antibiotics, the maintenance and propagation of antibiotic resistance genes (ARGs) are promoted by co-selection mechanisms. ARGs are difficult to degrade, cause long-lasting pollution, and are widely transmitted in aquatic environments. Biochar is frequently used to remove various pollutants during environmental remediation. Thus, this review provides a thorough analysis of the current state of ARGs in the aquatic environment as well as their removal by using biochar. This article summarizes the research and application of biochar and modified biochar to remove ARGs in aquatic environments, in order to refine the following contents: 1) fill gaps in the research on the various ARG behaviors mediated by biochar and some influence factors, 2) further investigate the mechanisms involved in effects of biochar on extracellular ARGs (eARGs) and intracellular ARGs (iARGs) in aquatic environments, including direct and the indirect effects, 3) describe the propagation process and resistance mechanisms of ARGs, 4) propose the challenges and prospects of feasibility of application and subsequent treatment in actual aquatic environment. Here we highlight the most recent research on the use of biochar to remove ARGs from aquatic environments and suggest future directions for optimization, as well as current perspectives to guide future studies on the removal of ARGs from aquatic environments.

Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance

The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.

Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity

BACKGROUND

Horizontal gene transfer (HGT) describes the transmission of DNA outside of direct ancestral lineages. The process is best characterised within the bacterial kingdom and can enable the acquisition of genetic traits that support bacterial adaptation to novel niches. The adaptation of bacteria to novel niches has particular relevance for faecal microbiota transplantation (FMT), a therapeutic procedure which aims to resolve gut-related health conditions of individuals, through transplanted gut microbiota from healthy donors.

RESULTS

Three hundred eighty-one stool metagenomic samples from a placebo-controlled FMT trial for obese adolescents (the Gut Bugs Trial) were analysed for HGT, using two complementary methodologies. First, all putative HGT events, including historical HGT signatures, were quantified using the bioinformatics application WAAFLE. Second, metagenomic assembly and gene clustering were used to assess and quantify donor-specific genes transferred to recipients following the intervention. Both methodologies found no difference between the level of putative HGT events in the gut microbiomes of FMT and placebo recipients, post-intervention. HGT events facilitated by engrafted donor species in the FMT recipient gut at 6 weeks post-intervention were identified and characterised. Bacterial strains contributing to this subset of HGT events predominantly belonged to the phylum Bacteroidetes. Engraftment-dependent horizontally transferred genes were retained within recipient microbiomes at 12 and 26 weeks post-intervention.

CONCLUSION

Our study suggests that novel microorganisms introduced into the recipient gut following FMT have no impact on the basal rate of HGT within the human gut microbiome. Analyses of further FMT studies are required to assess the generalisability of this conclusion across different FMT study designs and for the treatment of different gut-related conditions. Video Abstract.

The honeybee gut resistome and its role in antibiotic resistance dissemination

There is now general concern about widespread antibiotic resistance, and growing evidence indicates that gut microbiota is critical in providing antibiotic resistance. Honeybee is an important pollinator; the incidence of antibiotic resistance genes in honeybee gut causes potential risks to not only its own health but also to public and animal health, for its potential disseminator role, thus receiving more attention from the public. Recent analysis results reveal that the gut of honeybee serves as a reservoir of antibiotic resistance genes, probably due to antibiotics application history in beekeeping and horizontal gene transfer from the highly polluted environment. These antibiotic resistance genes accumulate in the honeybee gut and could be transferred to the pathogen, even having the potential to spread during pollination, tending, social interactions, etc. Newly acquired resistance traits may cause fitness reduction in bacteria whereas facilitating adaptive evolution as well. This review outlines the current knowledge about the resistome in honeybee gut and emphasizes its role in antibiotic resistance dissemination.

Horizontal transfer and driving factors of extended-spectrum β-lactamase-producing resistance genes in mice intestine after the ingestion of contaminated water

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) has been identified in various water environments, posing a serious risk to public health. However, whether and how ESBL-producing genes in water-derived E. coli can spread among mammalian gut microbiota via drinking water is largely unclear. To address this problem, horizontal transfer characterization of ESBL-producing genes in mice gut microbiota was determined after the oral ingestion of contaminated water by ESBL-producing E. coli, and then the driving factors were comprehensively examined from multiple different perspectives. The results showed that water-borne ESBL-producing E. coli can colonize in the mice intestine, the ESBL-producing genes can horizontally spread among gut microbiota, and the recipient bacteria include opportunistic pathogens Klebsiella pneumoniae and Salmonella enterica. This horizontal spread may be attributed to the intestinal micro-environment changes caused by the ingestion of contaminated water by ESBL-producing E. coli. These changes, including gut microbiota diversity, increased levels of inflammatory response and reactive oxygen species, cell membrane permeability, and expression levels of conjugative transfer-related genes, are all major driving factors for horizontal transfer of ESBL-producing genes in mice gut microbiota. Our findings highlight the potential for ESBL-producing E. coli to spread resistance genes to mammalian gut microbiota during ingestion of contaminated water.

Transfer of the Integrative and Conjugative Element ICESt3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem

Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, including (i) the TNO gastro-Intestinal tract Model 1 (TIM-1) system (for the upper part of the intestine), (ii) the ARtificial COLon (ARCOL) system (to mimic the colon), and (iii) a mouse model. To increase the likelihood of transfer by conjugation of the integrative and conjugative element studied in the artificial digestive systems, bacteria were entrapped in alginate, agar, and chitosan beads before being placed in the different gut compartments. The number of transconjugants detected decreased, while the complexity of the ecosystem increased (many clones in TIM-1 but only one clone in ARCOL). No clone was obtained in a natural digestive environment (germfree mouse model). In the human gut, the richness and diversity of the bacterial community would offer more opportunities for HGT events to occur. In addition, several factors (SOS-inducing agents, microbiota-derived factors) that potentially increase in vivo HGT efficiency were not tested here. Even if HGT events are rare, expansion of the transconjugant clones can happen if ecological success is fostered by selecting conditions or by events that destabilize the microbial community. IMPORTANCE The human gut microbiota plays a key role in maintaining normal host physiology and health, but its homeostasis is fragile. During their transit in the gastrointestinal tract, bacteria conveyed by food can exchange genes with resident bacteria. New traits acquired by HGT (e.g., new catabolic properties, bacteriocins, antibiotic resistance) can impact the gut microbial composition and metabolic potential. We showed here that TIM-1, a system mimicking the upper digestive tract, is a useful tool to evaluate HGT events in conditions closer to the physiological ones. Another important fact pointed out in this work is that Enterococcus faecalis is a good candidate for foreign gene acquisition. Due to its high ability to colonize the gut and acquire mobile genetic elements, this commensal bacterium could serve as an intermediate for HGT in the human gut.

Phthalates Promote Dissemination of Antibiotic Resistance Genes: An Overlooked Environmental Risk

Plastics-microorganism interactions have aroused growing environmental and ecological concerns. However, previous studies concentrated mainly on the direct interactions and paid little attention to the ecotoxicology effects of phthalates (PAEs), a common plastic additive that is continuously released and accumulates in the environment. Here, we provide insights into the impacts of PAEs on the dissemination of antibiotic resistance genes (ARGs) among environmental microorganisms. Dimethyl phthalate (DMP, a model PAE) at environmentally relevant concentrations (2-50 μg/L) significantly boosted the plasmid-mediated conjugation transfer of ARGs among intrageneric, intergeneric, and wastewater microbiota by up to 3.82, 4.96, and 4.77 times, respectively. The experimental and molecular dynamics simulation results unveil a strong interaction between the DMP molecules and phosphatidylcholine bilayer of the cell membrane, which lowers the membrane lipid fluidity and increases the membrane permeability to favor transfer of ARGs. In addition, the increased reactive oxygen species generation and conjugation-associated gene overexpression under DMP stress also contribute to the increased gene transfer. This study provides fundamental knowledge of the PAE-bacteria interactions to broaden our understanding of the environmental and ecological risks of plastics, especially in niches with colonized microbes, and to guide the control of ARG environmental spreading.

Hypoxia triggers the proliferation of antibiotic resistance genes in a marine aquaculture system

The transmission of antibiotic resistance genes (ARGs) affects the safety of aquaculture animals. Dissolved oxygen (DO) can affect the transmission of ARGs, but its mechanism of action in this process is unclear. We conducted laboratory breeding experiment with low and control DO groups. Combined quantitative PCR and 16S rRNA sequencing to study the effect of DO on the spread of ARGs. Hypoxia treatment significantly increased the accumulation of ammonium and nitrite in aquaculture water, and it increased the relative abundances of ARGs and mobile genetic elements (MGEs), especially the ARGs resistant to drugs in the categories of sulfonamide, (flor)/(chlor)/(am)phenicol, and MLSB (macrolide, lincosamide and streptogramin B) and the MGE intI-1(clinic), by 2.39-95.69 % in 28 days relative to the control DO treatment. Though the abundance of ARG carries, especially the Rhodocyclaceae, Caldilineaceae, Cyclobacteriaceae, Saprospiraceae, Enterobacteriaceae, Sphingomonadaceae families, showed higher abundance in low DO groups, relating to the vertical transmission of ARGs. Hypoxia treatment is more likely to promote the horizontal gene transfer (HGT)-related pathways, including ABC transporters, two component system, and quorum sensing, thus to induce the HGT of ARGs. The changed bacterial proliferation also altered the abundance of MGEs, especially intI-1(clinic), which induced HGT of ARGs as well. Additionally, pearson correlation results revealed that the succession of bacterial community function played the strongest role in ARG proliferation, followed by bacterial community structure and MGEs. Our results highlight the importance of suitable DO concentration in controlling the spread of ARGs especially the HGT of ARGs. In the context of global attention to food safety, our results provide important information for ensuring the safety of aquatic products and the sustainable development of aquaculture.

Systematic In Silico Assessment of Antimicrobial Resistance Dissemination across the Global Plasmidome

The emergence of pathogenic strains resistant to multiple antimicrobials is a pressing problem in modern healthcare. Antimicrobial resistance is mediated primarily by dissemination of resistance determinants via horizontal gene transfer. The dissemination of some resistance genes has been well documented, but few studies have analyzed the patterns underpinning the dissemination of antimicrobial resistance genes. Analyzing the %GC content of plasmid-borne antimicrobial resistance genes relative to their host genome %GC content provides a means to efficiently detect and quantify dissemination of antimicrobial resistance genes. In this work we automate %GC content analysis to perform a comprehensive analysis of known antimicrobial resistance genes in publicly available plasmid sequences. We find that the degree to which antimicrobial resistance genes are disseminated depends primarily on the resistance mechanism. Our analysis identifies conjugative plasmids as primary dissemination vectors and indicates that most broadly disseminated genes have spread from single genomic backgrounds. We show that resistance dissemination profiles vary greatly among antimicrobials, oftentimes reflecting stewardship measures. Our findings establish %GC content analysis as a powerful, intuitive and scalable method to monitor the dissemination of resistance determinants using publicly available sequence data.

The Impact of Non-Pathogenic Bacteria on the Spread of Virulence and Resistance Genes

This review discusses the fate of antimicrobial resistance and virulence genes frequently present among microbiomes. A central concept in epidemiology is the mean number of hosts colonized by one infected host in a population of susceptible hosts: R₀. It characterizes the disease's epidemic potential because the pathogen continues its propagation through susceptible hosts if it is above one. R₀ is proportional to the average duration of infections, but non-pathogenic microorganisms do not cause host death, and hosts do not need to be rid of them. Therefore, commensal bacteria may colonize hosts for prolonged periods, including those harboring drug resistance or even a few virulence genes. Thus, their R₀ is likely to be (much) greater than one, with peculiar consequences for the spread of virulence and resistance genes. For example, computer models that simulate the spread of these genes have shown that their diversities should correlate positively throughout microbiomes. Bioinformatics analysis with real data corroborates this expectation. Those simulations also anticipate that, contrary to the common wisdom, human's microbiomes with a higher diversity of both gene types are the ones that took antibiotics longer ago rather than recently. Here, we discuss the mechanisms and robustness behind these predictions and other public health consequences.

In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome

Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence, and manipulability of horizontal gene transfer in the gut microbiome.

Transmission of antimicrobial resistance (AMR) during animal transport

The transmission of antimicrobial resistance (AMR) between food-producing animals (poultry, cattle and pigs) during short journeys (< 8 h) and long journeys (> 8 h) directed to other farms or to the slaughterhouse lairage (directly or with intermediate stops at assembly centres or control posts, mainly transported by road) was assessed. Among the identified risk factors contributing to the probability of transmission of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs), the ones considered more important are the resistance status (presence of ARB/ARGs) of the animals pre-transport, increased faecal shedding, hygiene of the areas and vehicles, exposure to other animals carrying and/or shedding ARB/ARGs (especially between animals of different AMR loads and/or ARB/ARG types), exposure to contaminated lairage areas and duration of transport. There are nevertheless no data whereby differences between journeys shorter or longer than 8 h can be assessed. Strategies that would reduce the probability of AMR transmission, for all animal categories include minimising the duration of transport, proper cleaning and disinfection, appropriate transport planning, organising the transport in relation to AMR criteria (transport logistics), improving animal health and welfare and/or biosecurity immediately prior to and during transport, ensuring the thermal comfort of the animals and animal segregation. Most of the aforementioned measures have similar validity if applied at lairage, assembly centres and control posts. Data gaps relating to the risk factors and the effectiveness of mitigation measures have been identified, with consequent research needs in both the short and longer term listed. Quantification of the impact of animal transportation compared to the contribution of other stages of the food-production chain, and the interplay of duration with all risk factors on the transmission of ARB/ARGs during transport and journey breaks, were identified as urgent research needs.

Metagenomics Analysis of Microbial Species and Antibiotic Resistance Genes (ARGs) in Untreated Wastewater from Different Types of Hospitals in Hangzhou

Antibiotic resistance genes (ARGs) are contaminants that can propagate through a variety of environmental media. They contribute to an increase in the number of antibiotic-resistant microbes and thereby pose a danger to human health. Discharge from hospitals is the most significant contributor of ARGs and antibiotic-resistant bacteria to the natural environment. A comprehensive understanding of the microbiological structure and the distribution of ARGs in hospital wastewater can facilitate appropriate treatment of such wastewater and can improve our understanding of the pathophysiology of several epidemic illnesses. In this work, metagenomics techniques were used to compare the microbial species and ARGs in a control group with those in untreated wastewater from three types of hospitals (a general hospital, a hospital of traditional Chinese medicine, and an oral specialty hospital). The microbiota found in the hospital wastewater represented 6,415 species and 244 phyla. The composition of the bacterial community in the wastewater from the three hospitals was significantly different from that in the control group. The ARGs in the samples were also analyzed using the Antibiotic Resistance Genes Database (ARDB) and Comprehensive Antibiotic Resistance Database (CARD). Finally, the link between abundant species and ARGs in the samples was examined. The findings of this study indicate that a connection exists between the microbial species and the ARG composition found in the wastewater samples. A variety of distinct genera of ARGs, each having their own unique correlations, have been found in wastewater from various hospitals. Consequently, the ARGs and microbial species found in the untreated wastewater from various hospitals have unique characteristics. Therefore, more detailed protocols need to be established to treat wastewater from various types of hospitals. Further studies should examine whether a connection exists between the various microbial species found in the wastewater of various types of hospitals and certain illnesses.

Models for Gut-Mediated Horizontal Gene Transfer by Bacterial Plasmid Conjugation

The emergence of new antimicrobial resistant and virulent bacterial strains may pose a threat to human and animal health. Bacterial plasmid conjugation is a significant contributor to rapid microbial evolutions that results in the emergence and spread of antimicrobial resistance (AR). The gut of animals is believed to be a potent reservoir for the spread of AR and virulence genes through the horizontal exchange of mobile genetic elements such as plasmids. The study of the plasmid transfer process in the complex gut environment is limited due to the confounding factors that affect colonization, persistence, and plasmid conjugation. Furthermore, study of plasmid transfer in the gut of humans is limited to observational studies, leading to the need to identify alternate models that provide insight into the factors regulating conjugation in the gut. This review discusses key studies on the current models for in silico, in vitro, and in vivo modeling of bacterial conjugation, and their ability to reflect the gut of animals. We particularly emphasize the use of computational and in vitro models that may approximate aspects of the gut, as well as animal models that represent in vivo conditions to a greater extent. Directions on future research studies in the field are provided.

mcr-1-Mediated In Vitro Inhibition of Plasmid Transfer Is Reversed by the Intestinal Environment

Colistin is regarded as an antibiotic of last resort against multidrug-resistant Gram-negative bacteria, including Klebsiella pneumoniae and Escherichia coli. Colistin resistance is acquired by microorganisms via chromosome-mediated mutations or plasmid-mediated mobile colistin resistance (mcr) gene, in which the transfer of mcr is the predominant factor underlying the spread of colistin resistance. However, the factors that are responsible for the spread of the mcr gene are still unclear. In this study, we observed that mcr-1 inhibited the transfer of the pHNSHP45 backbone in liquid mating. Similar inhibitory effect of mcr-1.6 and chromosomal mutant ΔmgrB suggested that colistin resistance, acquired from either plasmid or chromosomal mutation, hindered the transfer of colistin resistance-related plasmid in vitro. Dual plasmid system further proved that co-existing plasmid transfer was reduced too. However, this inhibitory effect was reversed in vivo. Some factors in the gut, including bile salt and anaerobic conditions, could increase the transfer frequency of the mcr-1-containing plasmid. Our results demonstrated the potential risk for the spread of colistin resistance in the intestine, provide a scientific basis against the transmission of colistin resistance threat.

Drosophila Model for Gut-Mediated Horizontal Transfer of Narrow- and Broad-Host-Range Plasmids

Horizontal gene transfer (HGT) is a driving force of microbial evolution. The gut of animals acts as a potent reservoir for the lateral transfer of virulence, fitness, and antimicrobial resistance genes through plasmids. Reduced-complexity models for the examination of host-microbe interactions involved in plasmid transfer are greatly desired. Thus, this study identifies the use of Drosophila melanogaster as a model organism for the conjugation of plasmids of various incompatibility groups in the gut. Enterobacteriaceae conjugation pairs were identified in vitro and used for oral inoculation of the Drosophila gut. Flies were enumerated for the donor, recipient, and transconjugant populations. Each donor-recipient pair was observed to persist in fly guts for the duration of the experiment. Gut concentrations of the donors and recipients were significantly different between male and female flies, with females generally demonstrating increased concentrations. Furthermore, host genetics significantly altered the concentrations of donors and recipients. However, transconjugant concentrations were not affected by host sex or genetics and were detected only in the IncPε and IncI1 plasmid groups. This study demonstrates Drosophila melanogaster as a model for gut-mediated plasmid transfer.

IMPORTANCE Microbial evolution in the gut of animals due to horizontal gene transfer (HGT) is of significant interest for microbial evolution as well as within the context of human and animal health. Microbial populations evolve within the host, and factors from the bacteria and host interact to regulate this evolution. However, little is currently known about how host and bacterial factors regulate plasmid-mediated HGT in the gut. This study demonstrates the use of Drosophila and the roles of sexual dimorphism as well as plasmid incompatibility groups in HGT in the gut.

Detection of ESBL/AmpC-Producing and Fosfomycin-Resistant Escherichia coli From Different Sources in Poultry Production in Southern Brazil

This study discussed the use of antimicrobials in the commercial chicken production system and the possible factors influencing the presence of Extended-spectrum β-lactamase (ESBL)/AmpC producers strains in the broiler production chain. The aim of this study was to perform longitudinal monitoring of ESBL-producing and fosfomycin-resistant Escherichia coli from poultry farms in southern Brazil (Paraná and Rio Grande do Sul states) and determine the possible critical points that may be reservoirs for these strains. Samples of poultry litter, cloacal swabs, poultry feed, water, and beetles (Alphitobius sp.) were collected during three distinct samplings. Phenotypic and genotypic tests were performed for characterization of antimicrobial resistant strains. A total of 117 strains were isolated and 78 (66%) were positive for ESBL production. The poultry litter presented ESBL positive strains in all three sampled periods, whereas the cloacal swab presented positive strains only from the second period. The poultry litter represents a significant risk factor mainly at the beginning poultry production (odds ratio 6.43, 95% confidence interval 1-41.21, p < 0.05). All beetles presented ESBL positive strains. The predominant gene was bla CTX-M group 2, which occurred in approximately 55% of the ESBL-producing E. coli. The cit gene was found in approximately 13% of the ESBL-producing E. coli as AmpC type determinants. A total of 19 out of 26 fosfomycin-resistant strains showed the fosA3 gene, all of which produced ESBL. The correlation between fosA3 and bla CTX-M group 1 (bla CTX-M55 ) genes was significant among ESBL-producing E. coli isolated from Paraná (OR 3.66, 95% CI 1.9-9.68) and these genetic determinants can be transmitted by conjugation to broiler chicken microbiota strains. Our data revealed that poultry litter and beetles were critical points during poultry production and the presence of fosfomycin-resistant strains indicate the possibility of risks associated with the use of this antimicrobial during production. Furthermore, the genetic determinants encoding CTX-M and fosA3 enzymes can be transferred to E. coli strains from broiler chicken microbiota, thereby creating a risk to public health.

Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota

In the past decade, the initial studies of the gut microbiota started focusing on the correlation of the composition of the gut microbiota and the health or diseases of the host, and there are extensive literature reviews pertaining to this theme. However, little is known about the association between the microbiota, the host, and pathogenic bacteria, such as Salmonella enterica, which is among the most important foodborne pathogens and identified as the source of multiple outbreaks linked to contaminated foods causing salmonellosis. Secretion systems, flagella, fimbriae, endotoxins, and exotoxins are factors that play the most important roles in the successful infection of the host cell by Salmonella. Infections with S. enterica, which is a threat to human health, can alter the genomic, taxonomic, and functional traits of the gut microbiota. The purpose of this review is to outline the state of knowledge on the impacts of S. enterica on the intestinal microbiota and highlight the need to identify the gut bacteria that could contribute to salmonellosis.

Letter to the Editor: Escherichia fergusonii Harboring IncHI2 Plasmid Containing mcr-1 Gene-A Novel Reservoir for Colistin Resistance in Brazil

Emergence of colistin-resistant bacteria harboring mobile colistin resistance genes (mcr genes) pose a threat for food-producing animals and humans. In this article, we aim to highlight the emergence of Escherichia fergusonii as an important new reservoir to mcr-1-harboring plasmid in poultry production. Three strains closely related were isolated from cloacal swabs. Their genome contains four plasmids, including a 182,869 bp IncHI2 plasmid harboring the colistin resistance gene mcr-1. These results will contribute to our understanding of plasmid-mediated mcr-1 gene presence and transmission in E. fergusonii.

In Vitro Characterization of Indigenous Probiotic Strains Isolated from Colombian Creole Pigs

Three lactic acid strains were isolated from feces of the native Zungo Pelado breed of pigs (n = 5) and presumably identified as belonging to the Lactobacillaceae family by morphological techniques showing that they were Gram-positive/rod-shaped and catalase- and oxidase-negative. They were then identified by biochemical tests using API 50CHL as Lactobacillus plantarum (CAM6), Lactobacillus brevis (CAM7), and Lactobacillus acidophilus (CL4). However, 16S rRNA identification showed that all three strains were Lactobacillus plantarum. Additionally, all three isolates were able to grow in pH 3 and 4. Interestingly, the growth of the CAM7 strain decreased at pH 5.6 compared to that of the CAM6 strain (p < 0.05), and the growth of the CL4 strain was reduced at pH 7(p < 0.05). All three candidates showed good growth on bile salts (≥0.15%), and CAM6 and CAM7 showed better tolerance at higher concentrations (0.30%). Similarly, all strains tolerated sodium chloride (NaCl) concentrations from 2 to 10%. These strains also grew well at all temperatures tested (30, 37, and 42 °C). The CAM6 strain showed in vitro antibacterial activity against selected enteropathogenic bacteria (Escherichia coli strain NBRC 102203 and Salmonella enterica serovar Typhimurium 4.5.12) and commensal bacteria (Klebsiella pneumoniae ATCC BAA-1705D-5 and Pseudomonas aeruginosa ATCC 15442) and resistance to all antibiotics except amoxicillin. Further studies to evaluate the effects of these probiotic candidate strains in commercial pigs are currently underway.

Multidrug Resistance (MDR) and Collateral Sensitivity in Bacteria, with Special Attention to Genetic and Evolutionary Aspects and to the Perspectives of Antimicrobial Peptides-A Review

Antibiotic poly-resistance (multidrug-, extreme-, and pan-drug resistance) is controlled by adaptive evolution. Darwinian and Lamarckian interpretations of resistance evolution are discussed. Arguments for, and against, pessimistic forecasts on a fatal “post-antibiotic era” are evaluated. In commensal niches, the appearance of a new antibiotic resistance often reduces fitness, but compensatory mutations may counteract this tendency. The appearance of new antibiotic resistance is frequently accompanied by a collateral sensitivity to other resistances. Organisms with an expanding open pan-genome, such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, can withstand an increased number of resistances by exploiting their evolutionary plasticity and disseminating clonally or poly-clonally. Multidrug-resistant pathogen clones can become predominant under antibiotic stress conditions but, under the influence of negative frequency-dependent selection, are prevented from rising to dominance in a population in a commensal niche. Antimicrobial peptides have a great potential to combat multidrug resistance, since antibiotic-resistant bacteria have shown a high frequency of collateral sensitivity to antimicrobial peptides. In addition, the mobility patterns of antibiotic resistance, and antimicrobial peptide resistance, genes are completely different. The integron trade in commensal niches is fortunately limited by the species-specificity of resistance genes. Hence, we theorize that the suggested post-antibiotic era has not yet come, and indeed might never come.

Antimicrobial resistance genes in bacteria from animal-based foods

Antimicrobial resistance is a worldwide public health threat. Farm animals are important sources of bacteria containing antimicrobial resistance genes (ARGs). Although the use of antimicrobials in aquaculture and livestock has been reduced in several countries, these compounds are still routinely applied in animal production, and contribute to ARGs emergence and spread among bacteria. ARGs are transmitted to humans mainly through the consumption of products of animal origin (PAO). Bacteria can present intrinsic resistance, and once antimicrobials are administered, this resistance may be selected and multiply. The exchange of genetic material is another mechanism used by bacteria to acquire resistance. Some of the main ARGs found in bacteria present in PAO are the bla, mcr-1, cfr and tet genes, which are directly associated to antibiotic resistance in the human clinic.

Protection against avian pathogenic Escherichia coli and Salmonella Kentucky exhibited in chickens given both probiotics and live Salmonella vaccine

Commercial poultry farms are increasingly threatened by bacterial infections from avian pathogenic Escherichia coli (APEC) and broad-host Salmonella serovars. Recombinant attenuated Salmonella vaccines (RASV) elicit cross-reactive immune responses against APEC in chickens; however, assessment of broad protection is lacking. Probiotics boost chicken immunity and improve vaccination responses. The objective of this study was to determine whether the RASV, the probiotics, or their combination had protection against APEC and Salmonella. White Leghorn chicks were randomly placed into 4 groups: no treatment (CON), probiotics (PRO), RASV (VAX), or both prophylactics (P + V). Chicks in the PRO and P + V groups were fed probiotics daily, beginning at the age of 1-day-old. Chicks in the P + V and VAX groups were orally inoculated with RASV at the age of 4 D and boosted 2 wks later. Total and antigen-specific IgY responses to Salmonella (lipolysaccharide [LPS]) and E. coli (IroN and IutA) were measured in serum samples via ELISA. Bactericidal potential of both serum and blood against 42 APEC isolates comprising 25 serotypes was assessed in vitro. In vivo protection against APEC was evaluated by air sac challenge with APEC χ7122 (O78:K80), gross pathological lesions were scored, and bacterial loads were enumerated. In a second similar study, birds were orally challenged with S. Kentucky (CVM29188), and feces were enumerated for Salmonella at multiple time points. Vaccination elicited significant LPS-specific antibodies regardless of probiotics (P < 0.0001). Chicks in the P + V group demonstrated increased blood and serum bactericidal abilities against multiple APEC strains in vitro compared with the CON group. Following χ7122 challenge, P+V birds had less APEC in their blood (P < 0.001) and lower signs of airsacculitis (P < 0.01) and pericarditis/perihepatitis (P < 0.05) than CON birds. Finally, only P + V birds were negative for fecal Salmonella at all time points. This study shows this combination treatment may be a feasible method to reduce infection by APEC and Salmonella in chickens.

Within-host heterogeneity and flexibility of mcr-1 transmission in chicken gut

OBJECTIVES

To characterize the colistin-resistant bacterial population in the gut and assess diversity of mcr-1 transmission within a single individual.

METHODS

Large numbers of isolates (>100 colonies/chicken cecum sample) were collected from nine randomly selected mcr-1-positive chickens in China and used for comprehensive microbiological, molecular and comparative genomics analyses.

RESULTS

Of 1273 colonies, 968 were mcr-1 positive (962 Escherichia coli, two Escherichia fergusonii, two Klebsiella pneumoniae and two Klebsiella quasipneumoniae). One to six colistin-resistant species and three to 10 E. coli pulsed-field gel electrophoresis (PFGE) clusters could be identified from each sample. Whole-genome sequencing (WGS) analysis of the representative E. coli strains revealed three to nine sequence types observed in a single chicken host. The mcr-1 genes are located in either chromosomes or plasmids of different types, including IncI2 (n=30), IncHI2 (n=14), IncX4 (n=4), p0111(n=2) and IncHI1(n=1). Strikingly, in single cecum samples, one to five Inc type plasmids harbouring mcr-1 could be identified. Great diversity was also observed for the same IncI2 plasmid within a single chicken host. In addition, up to eight genetic contexts of the mcr-1 gene occurred within a single chicken.

CONCLUSIONS

There is extensive heterogeneity and flexibility of mcr-1 transmission in chicken gut due to bacterial species differences, distant clonal relatedness of isolates, many types and variations of mcr-positive plasmids, and the flexible genetic context of the mcr-1 gene. These compelling findings indicate that the gut is a 'melting pot' for active horizontal transfer of the mcr-1 gene.

Distribution of ExPEC Virulence Factors, bla CTX-M, fosA3, and mcr-1 in Escherichia coli Isolated From Commercialized Chicken Carcasses

Pathogenic Escherichia coli found in humans and poultry carcasses harbor similar virulence and resistance genes. The present study aimed to analyze the distribution of extraintestinal pathogenic E. coli (ExPEC) virulence factors (VF), bla_CTX−M groups, fosA3, and mcr-1 genes in E. coli isolated from commercialized chicken carcasses in southern Brazil and to evaluate their pathogenic risk. A total of 409 E. coli strains were isolated and characterized for genes encoding virulence factors described in ExPEC. Results of antimicrobial susceptibility testing confirmed that the strains were resistant to β-lactams, fosfomycin, colistin, and others resistance groups. The highest prevalence of VFs was observed in isolates belonging to the CTX-M groups, especially the CTX-M-2 group, when compared to those in other susceptible strains or strains with different mechanisms of resistance. Furthermore, ESBL strains were found to be 1.40 times more likely to contain three to five ExPEC virulence genes than non-ESBL strains. Our findings revealed the successful conjugation between ESBL-producing E. coli isolated from chicken carcass and the E. coli recipient strain J53, which suggested that genetic determinants encoding CTX-M enzymes may have originated from animals and could be transmitted to humans via food chain. In summary, chicken meat is a potential reservoir of MDR E. coli strains harboring resistance and virulence genes that could pose serious risks to human public health.

Prevalence of Antibiotic Residues and Antibiotic Resistance in Isolates of Chicken Meat in Korea

The aim of study was to investigate the correlation between the level of 17 antibiotic residues and 6 antibiotic resistances of Escherichia coli isolates in chicken meats. A total of 58 chicken meats were collected from retail grocery stores in five provinces in Korea. The total detection rate of antibiotic residues was 45% (26 out of 58). Ten out of 17 antibiotics were detected in chicken meats. None of the antibiotics exceeded the maximum residue level (MRLs) in chicken established by the Ministry of Food and Drug Safety (MFDS). The most detected antibiotics were amoxicillin (15.5%), followed by enrofloxacin (12.1%) and sulfamethoxazole (10.3%). In a total of 58 chicken meats, 51 E. coli strains were isolated. E. coli isolates showed the highest resistance to ampicillin (75%), followed by tetracycline (69%), ciprofloxacin (65%), trimethoprim/ sulfamethoxazole (41%), ceftiofur (22%), and amoxicillin/clavulanic acid (12%). The results of study showed basic information on relationship between antibiotic residue and resistance for 6 compounds in 13 chicken samples. Further investigation on the antibiotic resistance patterns of various bacteria species is needed to improve food safety.