The human microbiome as a reservoir of antimicrobial resistance

Impact of Phage Therapy on Multidrug-Resistant Escherichia coli Intestinal Carriage in a Murine Model

INTRODUCTION

The growing resistance of bacteria to antibiotics is a major global public health concern. An important reservoir of this resistance is the gut microbiota. However, limited data are available on the ability of phage therapy to reduce the digestive carriage of multidrug-resistant bacteria.

MATERIALS AND METHODS

Four novel lytic phages were isolated in vitro for efficacy against an extended-spectrum beta-lactamase-producing (ESBL) Escherichia coli strain also resistant to carbapenems through a carbapenemase OXA-48. The first step was to develop models of ESBL E. coli digestive carriage in mice. The second step was to test the efficacy of an oral and rectal phage therapy (a cocktail of four phages or microencapsulated phage) to reduce this carriage.

RESULTS

The two most intense models of digestive carriage were obtained by administering amoxicillin (0.5 g·L^-1) continuously in the drinking water (Model 1) or pantoprazole (0.1 g·L^-1) continuously in the drinking water, combined with amoxicillin (0.5 g·L^-1), for the first 8 days (Model 2). Oral administration of the phage cocktail to Model 1 resulted in a transient reduction in the concentration of ESBL E. coli in the faeces 9 days after the bacterial challenge (median = 5.33 × 10⁸ versus 2.76 × 10⁹ CFU·g^-1, p = 0.02). In contrast, in Model 2, oral or oral + rectal administration of this cocktail did not alter the bacterial titre compared to the control (area under the curve, AUC, 3.49 × 10⁹; 3.41 × 10⁹ and 3.82 × 10⁹ for the control, oral and oral + rectal groups, respectively; p-value > 0.8 for each two-by-two group comparison), as well as the administration of an oral microencapsulated phage in Model 1 (AUC = 8.93 × 10⁹ versus 9.04 × 10⁹, p = 0.81).

CONCLUSIONS

Oral treatment with amoxicillin promoted digestive carriage in mice, which was also the case for the addition of pantoprazole. However, our study confirms the difficulty of achieving efficacy with phage therapy to reduce multidrug-resistant bacterial digestive carriage in vivo.

Optimizing antimicrobial use: challenges, advances and opportunities

An optimal antimicrobial dose provides enough drug to achieve a clinical response while minimizing toxicity and development of drug resistance. There can be considerable variability in pharmacokinetics, for example, owing to comorbidities or other medications, which affects antimicrobial pharmacodynamics and, thus, treatment success. Although current approaches to antimicrobial dose optimization address fixed variability, better methods to monitor and rapidly adjust antimicrobial dosing are required to understand and react to residual variability that occurs within and between individuals. We review current challenges to the wider implementation of antimicrobial dose optimization and highlight novel solutions, including biosensor-based, real-time therapeutic drug monitoring and computer-controlled, closed-loop control systems. Precision antimicrobial dosing promises to improve patient outcome and is important for antimicrobial stewardship and the prevention of antimicrobial resistance.

Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada

To better understand the contribution of wildlife to the dissemination of Salmonella and antimicrobial resistance in Salmonella and Escherichia coli, we examined whole-genome sequence data from Salmonella and E. coli isolates collected from raccoons (Procyon lotor) and environmental sources on farms in southern Ontario. All Salmonella and phenotypically resistant E. coli collected from raccoons, soil, and manure pits on five swine farms as part of a previous study were included. We assessed for evidence of potential transmission of these organisms between different sources and farms utilizing a combination of population structure assessments (using core-genome multi-locus sequence typing), direct comparisons of multi-drug resistant isolates, and epidemiological modeling of antimicrobial resistance (AMR) genes and plasmid incompatibility (Inc) types. Univariable logistic regression models were fit to assess the impact of source type, farm location, and sampling year on the occurrence of select resistance genes and Inc types. A total of 159 Salmonella and 96 resistant E. coli isolates were included. A diversity of Salmonella serovars and sequence types were identified, and, in some cases, we found similar or identical Salmonella isolates and resistance genes between raccoons, soil, and swine manure pits. Certain Inc types and resistance genes associated with source type were consistently more likely to be identified in isolates from raccoons than swine manure pits, suggesting that manure pits are not likely a primary source of those particular resistance determinants for raccoons. Overall, our data suggest that transmission of Salmonella and AMR determinants between raccoons and swine manure pits is uncommon, but soil-raccoon transmission appears to be occurring frequently. More comprehensive sampling of farms, and assessment of farms with other livestock species, as well as additional environmental sources (e.g., rivers) may help to further elucidate the movement of resistance genes between these various sources.

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.

Impact of interprofessional service-learning on the effectiveness of knowledge transfer of antimicrobial resistance to Hong Kong elders: a quasi-experiment

Background

Community perception on antimicrobials plays a role in driving the development of antimicrobial resistance (AMR). The aim of the study was to evaluate the impact of interprofessional service-learning on the effectiveness of AMR knowledge transfer in Hong Kong elders aged 65 or above and students from university and secondary schools.

Methods

A quasi-experimental pretest–posttest controlled study was carried out from July 2018 to March 2019 for elderly subjects and a pre- and post-test were conducted in students from May to August 2018. Elderly subjects were recruited from the university-based community outreach program. The community outreach team consisted of both university and secondary school students. Students were provided with training of geriatric care and AMR before they reached out to the community. The one-to-one intervention with the aid of video and verbal explanation to educate the elderly about the definition, causes, and consequences of AMR, and preventive measures against AMR was provided. Questionnaires on knowledge of antibiotics and AMR were used as tools to reflect on the effectiveness for both students and elderly subjects. The questionnaire was completed twice, before and 1 week after the intervention. Chi-square test, t tests and regression analysis were used to analyze the data.

Results

A total of 93 Chinese elders, 61 of them in the intervention group and 32 in the control group participated in the study. The score obtained by the intervention group increased from 40.1 to 83.3% (p < 0.001) following intervention, while that of control group increased from 33.0 to 44.0% (p < 0.001). The increase attained in the intervention group was significantly greater than that of the control group (p < 0.001). A total of 95 secondary students and 88 university students have completed the pre-post questionnaires with 42.21% and 13% increment in AMR knowledge after the training (p < 0.001).

Conclusion

The significant change in knowledge level showed effective AMR knowledge transfer to both elders and students. The study could be used as a reference when allocating resources to implement effective interprofessional service-learning for better community health education in elderly populations.

Trial registration: This study was approved by the Chinese University of Hong Kong Survey and Behavioural Research Ethics Committee in December 2018 (Ref no. SBRE-18-214).

Characterisation of the rumen resistome in Spanish dairy cattle

BACKGROUND

Rumen microorganisms carry antimicrobial resistance genes which pose a threaten to animals and humans in a One Health context. In order to tackle the emergence of antimicrobial resistance it is vital to understand how they appear, their relationship with the host, how they behave as a whole in the ruminal ecosystem or how they spread to the environment or humans. We sequenced ruminal samples from 416 Holstein dairy cows in 14 Spanish farms using nanopore technology, to uncover the presence of resistance genes and their potential effect on human, animal and environmental health.

RESULTS

We found 998 antimicrobial resistance genes (ARGs) in the cow rumen and studied the 25 most prevalent genes in the 14 dairy cattle farms. The most abundant ARGs were related to the use of antibiotics to treat mastitis, metritis and lameness, the most common diseases in dairy cattle. The relative abundance (RA) of bacteriophages was positively correlated to the ARGs RA. The heritability of the RA of the more abundant ARGs ranged between 0.10 (mupA) and 0.49 (tetW), similar to the heritability of the RA of microbes that carried those ARGs. Even though these genes are carried by the microorganisms, the host is partially controlling their RA by having a more suitable rumen pH, folds, or other physiological traits that promote the growth of those microorganisms.

CONCLUSIONS

We were able to determine the most prevalent ARGs (macB, msbA, parY, rpoB2, tetQ and TaeA) in the ruminal bacteria ecosystem. The rumen is a reservoir of ARGs, and strategies to reduce the ARG load from livestock must be pursued.

Sub-chronic exposure to antibiotics doxycycline, oxytetracycline or florfenicol impacts gut barrier and induces gut microbiota dysbiosis in adult zebrafish (Daino rerio)

Antibiotics are widely used in the treatment of bacterial infections and as food additives in the livestock industry. The wide usage of antibiotics causes residues in animal products, like milk, eggs and meat. A number of studies have reported that antibiotic residues exist at high concentrations in watercourses around the world. Doxycycline (DH), oxytetracycline (OTCC) and florfenicol (FF) are the three most commonly used veterinary antibiotics in China. However, studies of the toxic effects of DH, OTCC and FF are limited. In this study, six-moth-old healthy male adult zebrafish were exposed to 0, 10, 30, 100 μg/L DH, OTCC or FF for 21 days. After exposure, some biochemical parameters changed significantly, including total cholesterol (TC), triglyceride (TG), pyruvate and acid phosphatase (ACP). In addition, mucus secretion in the gut decreased and the transcription of related genes also decreased significantly. Moreover, the composition of microbiota in the gut changed significantly. DH, OTCC and FF exposure caused the decrease of diversity of gut microbiota. The relative abundance of Proteobacteria increased significantly after OTCC and FF exposure and Fusobacteria decreased in all antibiotic-treated groups. Further functional prediction analysis also suggested changes in gut microbiota in the OTCC and FF-treated groups, especially those linked to metabolism. To support this idea, we confirmed that some glycolipid related genes also increased significantly in the liver of adult zebrafish after antibiotic exposure. According to these results, DH, OTCC or FF exposure could cause the gut microbiota dysbiosis and dysfunction, and hepatic metabolic disorder in adult male zebrafish.

Simulated Microgravity Promotes Horizontal Gene Transfer of Antimicrobial Resistance Genes between Bacterial Genera in the Absence of Antibiotic Selective Pressure

Bacteria are able to adapt and survive in harsh and changing environments through many mechanisms, with one of them being horizontal gene transfer (HGT). This process is one of the leading culprits in the spread of antimicrobial resistance (AMR) within bacterial communities and could pose a significant health threat to astronauts if they fell ill, especially on long-duration space missions. In order to better understand the degree of HGT activity that could occur in space, biosafety level-2, donor and recipient bacteria were co-cultured under simulated microgravity (SMG) on Earth with concomitant 1G controls. Two AMR genes, bla_OXA-500 and ISAba1, from the donor Acinetobacter pittii, were tracked in four recipient strains of Staphylococcus aureus (which did not harbor those genes) using polymerase chain reaction. All four S. aureus strains that were co-cultured with A. pittii under SMG had a significantly higher number of isolates that were now bla_OXA-500- and ISAba1-positive compared to growth at 1G. The acquisition of these genes by the recipient induced a phenotypic change, as these isolates were now resistant to oxacillin, which they were previously susceptible to. This is a novel study, presenting, for the first time, increased HGT activity under SMG and the potential impact of the space environment in promoting increased gene dissemination within bacterial communities.

Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms

Antimicrobial resistance (AMR) is becoming one of the largest threats to public health worldwide, with the opportunistic pathogen Escherichia coli playing a major role in the AMR global health crisis. Unravelling the complex interplay between drug resistance and metabolic rewiring is key to understand the ability of bacteria to adapt to new treatments and to the development of new effective solutions to combat resistant infections. We developed a computational pipeline that combines machine learning with genome-scale metabolic models (GSMs) to elucidate the systemic relationships between genetic determinants of resistance and metabolism beyond annotated drug resistance genes. Our approach was used to identify genetic determinants of 12 AMR profiles for the opportunistic pathogenic bacterium E. coli. Then, to interpret the large number of identified genetic determinants, we applied a constraint-based approach using the GSM to predict the effects of genetic changes on growth, metabolite yields, and reaction fluxes. Our computational platform leads to multiple results. First, our approach corroborates 225 known AMR-conferring genes, 35 of which are known for the specific antibiotic. Second, integration with the GSM predicted 20 top-ranked genetic determinants (including accA, metK, fabD, fabG, murG, lptG, mraY, folP, and glmM) essential for growth, while a further 17 top-ranked genetic determinants linked AMR to auxotrophic behavior. Third, clusters of AMR-conferring genes affecting similar metabolic processes are revealed, which strongly suggested that metabolic adaptations in cell wall, energy, iron and nucleotide metabolism are associated with AMR. The computational solution can be used to study other human and animal pathogens.

IMPORTANCEEscherichia coli is a major public health concern given its increasing level of antibiotic resistance worldwide and extraordinary capacity to acquire and spread resistance via horizontal gene transfer with surrounding species and via mutations in its existing genome. E. coli also exhibits a large amount of metabolic pathway redundancy, which promotes resistance via metabolic adaptability. In this study, we developed a computational approach that integrates machine learning with metabolic modeling to understand the correlation between AMR and metabolic adaptation mechanisms in this model bacterium. Using our approach, we identified AMR genetic determinants associated with cell wall modifications for increased permeability, virulence factor manipulation of host immunity, reduction of oxidative stress toxicity, and changes to energy metabolism. Unravelling the complex interplay between antibiotic resistance and metabolic rewiring may open new opportunities to understand the ability of E. coli, and potentially of other human and animal pathogens, to adapt to new treatments.

Impact of Antibiotic Resistance Genes in Gut Microbiome of Patients With Cirrhosis

BACKGROUND AND AIMS

Cirrhosis is associated with changes in intestinal microbiota that can lead to hepatic encephalopathy (HE) and infections, especially with antibiotic-resistant organisms. However, the impact of gut microbial antibiotic resistance gene (ARG) burden on clinical outcomes is unclear. The aims of the study were to determine the impact of ARGs in cirrhosis-related gut metagenome on outcomes and disease progression, study the effect of rifaximin on ARG burden, and compare ARGs in cirrhosis with chronic kidney disease (CKD) and diabetes.

METHODS

In outpatients with cirrhosis who underwent metagenomics, we evaluated change in ARG abundances with progression and their multivariable impact on 90-day hospitalizations and deaths over 1 year. We also studied ARGs pre- and 8 weeks post-rifaximin in patients with compensated cirrhosis in an open-label trial. Finally, ARGs from CKD and diabetes studies were compared with cirrhosis on machine learning.

RESULTS

A total of 163 patients with cirrhosis (43 compensated, 20 ascites-only, 30 HE-only, 70 both) and 40 controls were included. ARG abundances were higher in cirrhosis versus controls and worsened with advancing cirrhosis severity; 44 patients were hospitalized and 14 died. ARG abundances were associated with hospitalizations and mortality while controlling for cirrhosis complications, medications, and demographics. Rifaximin trial: ARG abundance patterns were minimally affected in 19 patients post-rifaximin. CKD/diabetes comparison: ARG abundance patterns in cirrhosis are distinguishable on machine learning and include more gram-positive ARGs.

CONCLUSIONS

Cirrhosis is associated with high gut microbial ARG gene burden compared with controls, which worsens with disease progression and may be different from CKD and diabetes. ARGs are not affected by rifaximin and are associated with hospitalizations and death.

The Intestinal Microbiota: Impacts of Antibiotics Therapy, Colonization Resistance, and Diseases

Trillions of microbes exist in the human body, particularly the gastrointestinal tract, coevolved with the host in a mutually beneficial relationship. The main role of the intestinal microbiome is the fermentation of non-digestible substrates and increased growth of beneficial microbes that produce key antimicrobial metabolites such as short-chain fatty acids, etc., to inhibit the growth of pathogenic microbes besides other functions. Intestinal microbiota can prevent pathogen colonization through the mechanism of colonization resistance. A wide range of resistomes are present in both beneficial and pathogenic microbes. Giving antibiotic exposure to the intestinal microbiome (both beneficial and hostile) can trigger a resistome response, affecting colonization resistance. The following review provides a mechanistic overview of the intestinal microbiome and the impacts of antibiotic therapy on pathogen colonization and diseases. Further, we also discuss the epidemiology of immunocompromised patients who are at high risk for nosocomial infections, colonization and decolonization of multi-drug resistant organisms in the intestine, and the direct and indirect mechanisms that govern colonization resistance to the pathogens.

Prevalence of and risk factors for extended-spectrum beta-lactamase genes carriership in a population-based cohort of middle-aged and elderly

INTRODUCTION

Increasing resistance to beta-lactam antibiotics is an alarming development worldwide. Fecal carriership of TEM, SHV, CTX-M and CMY was studied in a community-dwelling population of middle-aged and elderly individuals.

PATIENTS AND METHODS

Feces was obtained from individuals of the Rotterdam Study. Carriership of the TEM, SHV, CTX-M and CMY genes was determined using real-time polymerase chain reaction (qPCR). Possible associations were investigated between carriership of these genes and several risk factors, such as the use of antimicrobial drugs, diabetes mellitus, protein pump inhibitor (PPI) use, travelling, the composition of the gut microbiota, and intake of certain foods.

RESULTS

The most prevalent gene was TEM (53.0%), followed by SHV (18.4%), CTX-M (5.4%) and CMY (3.6%). Use of penicillins with extended spectrum was associated with TEM carriership, whereas use of macrolides and lincosamides was associated with TEM and SHV carriership. Interestingly, use of PPIs was associated with a higher prevalence of carriership of TEM, SHV and CMY (TEM: odds ratio [OR] 1.34; 95% confidence interval [CI] 1.05-1.77; SHV: OR 2.17; 95%CI 1.55-2.87; CMY: OR 2.26; 95%CI 1.23-4.11). Furthermore, associations were found between the richness and composition of the gut microbiota and TEM and SHV carriership.

CONCLUSIONS

The prevalence of carriership of TEM was substantial, but the prevalence of carriership of the extended-spectrum β-lactamase gene, CTX-M and the AmpC β-lactamase gene, CMY was relatively low in this community-dwelling, population-based cohort. The composition of the microbiota might play a role in the retention of resistance genes, but future studies are necessary to further elucidate this relationship.

Molecular Mechanisms Influencing Bacterial Conjugation in the Intestinal Microbiota

Bacterial conjugation is a widespread and particularly efficient strategy to horizontally disseminate genes in microbial populations. With a rich and dense population of microorganisms, the intestinal microbiota is often considered a fertile environment for conjugative transfer and a major reservoir of antibiotic resistance genes. In this mini-review, we summarize recent findings suggesting that few conjugative plasmid families present in Enterobacteriaceae transfer at high rates in the gut microbiota. We discuss the importance of mating pair stabilization as well as additional factors influencing DNA transfer efficiency and conjugative host range in this environment. Finally, we examine the potential repurposing of bacterial conjugation for microbiome editing.

Dietary Factors of blaNDM Carriage in Health Community Population: A Cross-Sectional Study

AIM

There is an ongoing debate as to what extent antimicrobial resistance (AMR) can be transmitted from dietary to humans via the consumption of food products. We investigated this association between dietary and global spreading carbapenem-resistant gene bla_NDM Methods: We did a cross-sectional study to assess the risk factors for carrier of bla_NDM in health community. Healthy adults were recruited from the residents attending Community Healthcare Service in Shenzhen City (Guangdong Province, China), through 1February 2018 to 31December 2019, and 718 pre-participants were included in this study. Questionnaire were obtained and the qualitative food frequency questionnaire (Q-FFQ) were used to assess dietary intake. qPCR was applied to confirm the carrier of bla_NDM in participants'fecal samples. Multivariable logistic regression was used to estimate the odds ratio (OR) and 95% confidence interval (95% CI) of each outcome according to each dietary factor before and after prosperity score matching (PSM).

RESULTS

we showed that a high intake of coarse grain (OR 1.003; 95% CI 1.001-1.005, p < 0.01) and root and tuber crops (OR 1.003; 95% CI 1.001-1.004, p < 0.05) were independent risk factor for bla_NDM carrier in health communities, suggesting a possible transfer of AMRbetweendietary andhumans. Surprisingly, we also showed an association between a higher intake of poultry as a protective, which may be explained by the beneficial effects on the gut microbiota.

CONCLUSION

Dietary factors such as intake of coarse grain, root and tuber crops and poultry were associated with bla_NDM carrier in health communities. The influence of dietary factorson bla_NDM carrier in the present study provides insights for the tangible dietary advice with guidelines to the routine of people with the risk of bla_NDM carrier. This demonstrates the role of dietary intake in the prevention of bla_NDM carrier, since prevention is the best way to control modifiable risk factors. A lower carrier rate of bla_NDM is helpful to reduce the possibility of transmission and pathogenicity. Further studies on food, microbiota and antimicrobial resistance are necessary to confirm this possible association and unravel underlying mechanisms.

Knowledge and attitudes of adolescents towards the human microbiome and antibiotic resistance: a qualitative study

Background

Antibiotic and dietary behaviour affect the human microbiome and influence antibiotic resistance development. Adolescents are a key demographic for influencing knowledge and behaviour change.

Objectives

To explore adolescents' knowledge and attitudes towards the microbiome and antibiotic resistance, and the capability, motivation and opportunity for educators to integrate microbiome teaching in schools.

Methods

Qualitative study informed by the Theoretical Domains Framework (TDF) and COM-B model. Six educational establishments were purposively selected by rural/city and socioeconomic status, within Gloucestershire, South West England in 2019. Forty 14-18-year olds participated in focus groups, and eight science or health educators participated in interviews. Data were analysed thematically, double-coded and mapped to the TDF/COM-B.

Results

Adolescents were aware of 'good microbes' in the body but lacked deeper knowledge. Adolescents' knowledge of, and intentions to use, antibiotics appropriately differed by their levels of scientific study. Adolescents lacked knowledge on the consequences of diet on the microbiome, and therefore lacked capability and motivation to change behaviour. Educators felt capable and motivated to teach microbiome topics but lacked opportunity though absence of topics in the national curriculum and lack of time to teach additional topics.

Conclusions

A disparity in knowledge of adolescents needs to be addressed through increasing antibiotic and microbiome topics in the national curriculum. Public antibiotic campaigns could include communication about the microbiome to increase awareness. Educational resources could motivate adolescents and improve their knowledge, skills and opportunity to improve diet and antibiotic use; so, supporting the UK antimicrobial resistance (AMR) national action plan.

Viewing Emerging Human Infectious Epidemics through the Lens of Invasion Biology

Invasion biology examines species originated elsewhere and moved with the help of humans, and those species’ impacts on biodiversity, ecosystem services, and human well-being. In a globalized world, the emergence and spread of many human infectious pathogens are quintessential biological invasion events. Some macroscopic invasive species themselves contribute to the emergence and transmission of human infectious agents. We review conceptual parallels and differences between human epidemics and biological invasions by animals and plants. Fundamental concepts in invasion biology regarding the interplay of propagule pressure, species traits, biotic interactions, eco-evolutionary experience, and ecosystem disturbances can help to explain transitions between stages of epidemic spread. As a result, many forecasting and management tools used to address epidemics could be applied to biological invasions and vice versa. Therefore, we advocate for increasing cross-fertilization between the two disciplines to improve prediction, prevention, treatment, and mitigation of invasive species and infectious disease outbreaks, including pandemics.

Vaccines for multidrug resistant Gram negative bacteria: lessons from the past for guiding future success

Antimicrobial resistance is a major threat to global public health. Vaccination is an effective approach for preventing bacterial infections, however it has not been successfully applied to infections caused by some of the most problematic multidrug resistant pathogens. In this review, the potential for vaccines to contribute to reducing the burden of disease of infections caused by multidrug resistant Gram negative bacteria is presented. Technical, logistical and societal hurdles that have limited successful vaccine development for these infections in the past are identified, and recent advances that can contribute to overcoming these challenges are assessed. A synthesis of vaccine technologies that have been employed in the development of vaccines for key multidrug resistant Gram negative bacteria is included, and emerging technologies that may contribute to future successes are discussed. Finally, a comprehensive review of vaccine development efforts over the last 40 years for three of the most worrisome multidrug resistant Gram negative pathogens, Acinetobacter baumannii, Klebsiella pneumoniae and Pseudomonas aeruginosa is presented, with a focus on recent and ongoing studies. Finally, future directions for the vaccine development field are highlighted.

Market Chickens as a Source of Antibiotic-Resistant Escherichia coli in a Peri-Urban Community in Lima, Peru

The widespread and poorly regulated use of antibiotics in animal production in low- and middle-income countries (LMICs) is increasingly associated with the emergence and dissemination of antibiotic resistance genes (ARGs) in retail animal products. Here, we compared Escherichia coli from chickens and humans with varying levels of exposure to chicken meat in a low-income community in the southern outskirts of Lima, Peru. We hypothesize that current practices in local poultry production result in highly resistant commensal bacteria in chickens that can potentially colonize the human gut. E. coli was isolated from cloacal swabs of non-organic (n = 41) and organic chickens (n = 20), as well as from stools of market chicken vendors (n = 23), non-vendors (n = 48), and babies (n = 60). 315 E. coli isolates from humans (n = 150) and chickens (n = 165) were identified, with chickens showing higher rates of multidrug-resistant and extended-spectrum beta-lactamase phenotypes. Non-organic chicken isolates were more resistant to most antibiotics tested than human isolates, while organic chicken isolates were susceptible to most antibiotics. Whole-genome sequencing of 118 isolates identified shared phylogroups between human and animal populations and 604 ARG hits across genomes. Resistance to florfenicol (an antibiotic commonly used as a growth promoter in poultry but not approved for human use) was higher in chicken vendors compared to other human groups. Isolates from non-organic chickens contained genes conferring resistance to clinically relevant antibiotics, including mcr-1 for colistin resistance, blaCTX-M ESBLs, and blaKPC-3 carbapenemase. Our findings suggest that E. coli strains from market chickens are a potential source of ARGs that can be transmitted to human commensals.

Colonization Dynamics of Multidrug-Resistant Klebsiella pneumoniae Are Dictated by Microbiota-Cluster Group Behavior over Individual Antibiotic Susceptibility: A Metataxonomic Analysis

Gastrointestinal carriage of multidrug-resistant (MDR) bacteria is one of the main risk factors for developing serious, difficult-to-treat infections. Given that there is currently no all-round solution to eliminate colonization with MDR bacteria, it is particularly important to understand the dynamic process of colonization to aid the development of novel decolonization strategies. The aim of our present study was to perform metataxonomic analyses of gut microbiota dynamics during colonization with an extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Klebsiella pneumoniae (ECKP) strain in mice; additionally, to ascertain the effects of antibiotic administration (ampicillin, ceftazidime, and ciprofloxacin) on the establishment and elimination of ECKP intestinal colonization. We have found that the phyla Bacteroidetes and Firmicutes were most dominant in all of the treatment groups; however, Bacteroidetes was more common in the groups treated with antibiotics compared to the control group. Significant differences were observed among the different antibiotic-treated groups in beta but not alpha diversity, implying that the difference is the relative abundance of some bacterial community members. Bacteria from the Lachnospiraceae family (including Agathobacter, Anaerostipes, Lachnoclostridium 11308, Lachnospiraceae UCG-004, Lachnospiraceae NK3A20 group 11318, Lachnospiraceae NK4A136 group 11319, Roseburia, and Tyzzerella) showed an inverse relationship with the carriage rate of the ECKP strain, whereas members of Enterobacteriaceae and the ECKP strain have shown a correlational relationship. Our results suggest that the composition of the microbial community plays a primary role in the MDR-colonization rate, whereas the antibiotic susceptibility of individual MDR strains affects this process to a lesser extent. Distinct bacterial families have associated into microbial clusters, collecting taxonomically close species to produce survival benefits in the gut. These associations do not develop at random, as they may be attributed to the presence of specific metabolomic networks. A new concept should be introduced in designing future endeavors for MDR decolonization, supplemented by knowledge of the composition of the host bacterial community and the identification of bacterial clusters capable of suppressing or enhancing the invader species.

Ancient Antibiotics, Ancient Resistance

As the spread of antibiotic resistance threatens our ability to treat infections, avoiding the return of a preantibiotic era requires the discovery of new drugs. While therapeutic use of antibiotics followed by the inevitable selection of resistance is a modern phenomenon, these molecules and the genetic determinants of resistance were in use by environmental microbes long before humans discovered them. In this review, we discuss evidence that antibiotics and resistance were present in the environment before anthropogenic use, describing techniques including direct sampling of ancient DNA and phylogenetic analyses that are used to reconstruct the past. We also pay special attention to the ecological and evolutionary forces that have shaped the natural history of antibiotic biosynthesis, including a discussion of competitive versus signaling roles for antibiotics, proto-resistance, and substrate promiscuity of biosynthetic and resistance enzymes. Finally, by applying an evolutionary lens, we describe concepts governing the origins and evolution of biosynthetic gene clusters and cluster-associated resistance determinants. These insights into microbes' use of antibiotics in nature, a game they have been playing for millennia, can provide inspiration for discovery technologies and management strategies to combat the growing resistance crisis.

Fecal Microbiota Transplant in Cirrhosis Reduces Gut Microbial Antibiotic Resistance Genes: Analysis of Two Trials

Antibiotic resistance leads to poor outcomes in cirrhosis. Fecal microbiota transplant (FMT) is associated with reduction in antibiotic resistance gene (ARG) burden in patients without cirrhosis; however, the impact in cirrhosis is unclear. We aimed to study the effect of capsule and enema FMT on ARG abundance in fecal samples, which were collected during two published FMT trials in patients with cirrhosis on rifaximin, lactulose, and proton pump inhibitors. ARGs were identified using metagenomics and mapped against the Comprehensive Antibiotic Resistance Database. Changes in ARG abundance were studied within/between groups. The capsule FMT trial involved a one-time FMT or placebo capsule administration with stool collection at baseline and week 4 postintervention. Antibiotics+enema FMT included preprocedure antibiotics followed by FMT enema versus standard-of-care (SOC). Stool was collected at baseline, postantibiotics, and day 7/15 postintervention. Both trials included 20 patients each. There was no safety/infection signal linked to FMT. In the capsule trial, beta-lactamase (OXY/LEN) expression decreased post-FMT versus baseline. Compared to placebo, patients who were post-FMT had lower abundance of vancomycin (VanH), beta-lactamase (ACT), and rifamycin ARGs; the latter was associated with cognitive improvement. No changes were seen within patients treated with placebo. In the antibiotics+enema trial for postantibiotics at day 7 versus baseline, there was an increase in vancomycin and beta-lactamase ARGs, which decreased at day 15. However, quinolone resistance increased at day 15 versus baseline. Between SOC and FMT, day 7 had largely lower ARG (CfxA beta-lactamase, VanW, and VanX) that continued at day 15 (cepA beta-lactamase, VanW). No changes were seen within the SOC group. Conclusion: Despite differences in routes of administration and preintervention antibiotics, we found that ARG abundance is largely reduced after FMT compared to pre-FMT baseline and non-FMT groups in decompensated cirrhosis.

Quantity of Antibiotic Use and Resistance Pattern of Gut Normal Flora Escherichia coli at Intensive Care Unit and Tropic Infection Ward, Dr Soetomo Hospital, Surabaya, Indonesia

Resistance to antibiotics is increasing worldwide, including in Indonesia. The use of antibiotics is the most common cause of microorganism resistance. Individuals who received antibiotic therapy impacton changes of normal micro-flora resistance through selective pressure. This study aims to analyze the relationship of the quantity of antibiotic use with the pattern of resistance of gut normal flora Escherichia coliamong patients in Intensive Care Unit (ICU) and Tropic Infection Ward, Dr. Soetomo Hospital, Surabaya. This study was cross-sectional design with 64 samples (32 the ICU and 32 in Tropic Infection Ward). The total sample were collected for three Months. Identification of intestinal microflora was done with McConkey differential selective medium, followed by IMViC biochemical test, and sensitivity test by antibiotic disc diffusion method. Data were analyzed with Chi square test and Fisher'sExact test. There was no significant difference (p=0.441) in the quantity of antibiotic use between ICU and Tropic Infection Ward. There was no significant difference (p>0.05) in normal intestinal flora Escherichia coli resistance pattern between Tropic Infection Ward and ICU against12 types of antibiotics. Ceftriaxone was the most widely used antibiotic in the Tropic Infection Ward of 54 DDD and ICU of 100 DDD. The highest percentage of intestinal flora Escherichia coli  resistance at the ICU was ceftriaxone as manyas 18 (56.3%) and at Tropic Infection Ward on ciprofloxacin and levofloxacin 20 (62.5%). The other study in Primary Health center, showed that theresistance rates of both wards were significantly different as compared to intestinal flora of patients in primary health center (p <0.001), in whichthe use of antibiotics in primary health center was also lower (1.6 DDD). There was no significant difference (p>0.05) The pattern of bacterial resistance between patient with and without antibiotic use at Tropic Infection Ward and ICU Conclusion: the quantity of antibiotic use was not significantly different against resistnt gut flora between patients in ICU and Tropic Infection ward. The pattern of bacterial resistance between patient with and without antibiotic use was also not significantly different.

Oxygen and Metabolism: Digesting Determinants of Antibiotic Susceptibility in the Gut

Microbial metabolism is a major determinant of antibiotic susceptibility. Environmental conditions that modify metabolism, notably oxygen availability and redox potential, can directly fine-tune susceptibility to antibiotics. Despite this, relatively few studies have discussed these modifications within the gastrointestinal tract and their implication on in vivo drug activity and the off-target effects of antibiotics in the gut. In this review, we discuss the environmental and biogeographical complexity of the gastrointestinal tract in regard to oxygen availability and redox potential, addressing how the heterogeneity of gut microhabitats may modify antibiotic activity in vivo. We contextualize the current literature surrounding oxygen availability and antibiotic efficacy and discuss empirical treatments. We end by discussing predicted patterns of antibiotic activity in prominent microbiome taxa, given gut heterogeneity, oxygen availability, and polymicrobial interactions. We also propose additional work required to fully elucidate the role of oxygen metabolism on antibiotic susceptibility in the context of the gut.

A cosmic virosphere

The concept of a cosmic virosphere that serves as the repository of information for all life on Earth and throughout the Universe is discussed. Recent studies in geology, astronomy and biology point to an intimate connection between the evolution of life and a cosmic virosphere/biosphere.

Highly efficient gene transfer in the mouse gut microbiota is enabled by the Incl2 conjugative plasmid TP114

The gut microbiota is a suspected hotspot for bacterial conjugation due to its high density and diversity of microorganisms. However, the contribution of different conjugative plasmid families to horizontal gene transfer in this environment remains poorly characterized. Here, we systematically quantified the transfer rates in the mouse intestinal tract for 13 conjugative plasmids encompassing 10 major incompatibility groups. The vast majority of these plasmids were unable to perform conjugation in situ or only reached relatively low transfer rates. Surprisingly, IncI₂ conjugative plasmid TP114 was identified as a proficient DNA delivery system in this environment, with the ability to transfer to virtually 100% of the probed recipient bacteria. We also show that a type IV pilus present in I-complex conjugative plasmids plays a crucial role for the transfer of TP114 in the mouse intestinal microbiota, most likely by contributing to mating pair stabilization. These results provide new insights on the mobility of genes in the gut microbiota and highlights TP114 as a very efficient DNA delivery system of interest for microbiome editing tools.

The Toothbrush Microbiome: Impact of User Age, Period of Use and Bristle Material on the Microbial Communities of Toothbrushes

Toothbrushes play a central role in oral hygiene and must be considered one of the most common articles of daily use. We analysed the bacterial colonization of used toothbrushes by next generation sequencing (NGS) and by cultivation on different media. Furthermore, we determined the occurrence of antibiotic resistance genes (ARGs) and the impact of different bristle materials on microbial growth and survival. NGS data revealed that Enterobacteriaceae, Micrococcaceae, Actinomycetaceae, and Streptococcaceae comprise major parts of the toothbrush microbiome. The composition of the microbiome differed depending on the period of use or user age. While higher fractions of Actinomycetales, Lactobacillales, and Enterobacterales were found after shorter periods, Micrococcales dominated on both toothbrushes used for more than four weeks and on toothbrushes of older users, while in-vitro tests revealed increasing counts of Micrococcus on all bristle materials as well. Compared to other environments, we found a rather low frequency of ARGs. We determined bacterial counts between 1.42 × 10⁶ and 1.19 × 10⁷ cfu/toothbrush on used toothbrushes and no significant effect of different bristles materials on bacterial survival or growth. Our study illustrates that toothbrushes harbor various microorganisms and that both period of use and user age might affect the microbial composition.

Bacterial Vaginosis: Current Diagnostic Avenues and Future Opportunities

A healthy female genital tract harbors a microbiome dominated by lactic acid and hydrogen peroxide producing bacteria, which provide protection against infections by maintaining a low pH. Changes in the bacterial compositions of the vaginal microbiome can lead to bacterial vaginosis (BV), which is often associated with vaginal inflammation. Bacterial vaginosis increases the risk of acquiring sexually transmitted infections (STIs) like human immunodeficiency virus (HIV) and affects women's reproductive health negatively. In pregnant women, BV can lead to chorioamnionitis and adverse pregnancy outcomes, including preterm premature rupture of the membranes and preterm birth. In order to manage BV effectively, good diagnostic procedures are required. Traditionally clinical and microscopic methods have been used to diagnose BV; however, these methods require skilled staff and time and suffer from reduced sensitivity and specificity. New diagnostics, including highly sensitive and specific point-of-care (POC) tests, treatment modalities and vaccines can be developed based on the identification of biomarkers from the growing pool of vaginal microbiome and vaginal metabolome data. In this review the current and future diagnostic avenues will be discussed.

Resistencia a antibióticos β-lactámicos y eritromicina en bacterias de la cavidad oral

Introducción. La microbiota humana como fuente de bacterias y genes de resistencia constituyen un problema de salud pública. En este estudio se investigó la prevalencia de bacilos entéricos Gram negativos resistentes a β-lactámicos y de los Streptococcus del grupo viridans (EGV) con resistencia a eritromicina en la cavidad oral. Métodos. Se realizó un estudio descriptivo de corte transversal con 193 aislamientos de la cavidad oral sana de 178 adultos que asistieron a una Clínica Odontológica de la ciudad de Cali durante el 2018. La evaluación de la sensibilidad antimicrobiana se realizó en 59 bacilos entéricos y 134 EGV y se identificó por PCR los genes que confieren resistencia a β-lactámicos y eritromicina. El análisis estadístico se realizó mediante el empleo del paquete SPSS vs 23. Resultados. El 84,7% de los bacilos entéricos fueron multirresistentes y presentaron genes bla, siendo blaTEM-1 (49,2%) y blaVIM-2 (30,5%,) los más prevalentes. Los EGV fueron resistentes a eritromicina (38,8%) y clindamicina (28,4%). El 18,7% presentaron el fenotipo cMLSβ, 4,5% el iMLSβ y el 14,9% fueron M.  El gen ermB se detectó en los cMLSβ, (13,4%) y el gen mef  en los M (9,7%). Conclusión. En este estudio se demostró la presencia de EGV y bacilos entéricos resistentes a los antibióticos y portadores de genes de resistencia a eritromicina y genes bla en la cavidad oral sana. La presencia de estas bacterias representa un riesgo para la salud de los individuos portadores y contribuyen a la creciente epidemia de resistencia bacteriana.

Insights Into the Resistome of Bovine Clinical Mastitis Microbiome, a Key Factor in Disease Complication

Bovine clinical mastitis (CM) is one of the most prevalent diseases caused by a wide range of resident microbes. The emergence of antimicrobial resistance in CM bacteria is well-known, however, the genomic resistance composition (the resistome) at the microbiome-level is not well characterized. In this study, we applied whole metagenome sequencing (WMS) to characterize the resistome of the CM microbiome, focusing on antibiotics and metals resistance, biofilm formation (BF), and quorum sensing (QS) along with in vitro resistance assays of six selected pathogens isolated from the same CM samples. The WMS generated an average of 21.13 million reads (post-processing) from 25 CM samples that mapped to 519 bacterial strains, of which 30.06% were previously unreported. We found a significant (P = 0.001) association between the resistomes and microbiome composition with no association with cattle breed, despite significant differences in microbiome diversity among breeds. The in vitro investigation determined that 76.2% of six selected pathogens considered "biofilm formers" actually formed biofilms and were also highly resistant to tetracycline, doxycycline, nalidixic acid, ampicillin, and chloramphenicol and remained sensitive to metals (Cr, Co, Ni, Cu, Zn) at varying concentrations. We also found bacterial flagellar movement and chemotaxis, regulation and cell signaling, and oxidative stress to be significantly associated with the pathophysiology of CM. Thus, identifying CM microbiomes, and analyzing their resistomes and genomic potentials will help improve the optimization of therapeutic schemes involving antibiotics and/or metals usage in the prevention and control of bovine CM.

Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors

Klebsiella spp. are frequently enriched in the gut microbiota of preterm neonates, and overgrowth is associated with necrotizing enterocolitis (NEC), nosocomial infections and late-onset sepsis. Little is known about the genomic and phenotypic characteristics of preterm-associated Klebsiella, as previous studies have focused on the recovery of antimicrobial-resistant isolates or culture-independent molecular analyses. The aim of this study was to better characterize preterm-associated Klebsiella populations using phenotypic and genotypic approaches. Faecal samples from a UK cohort of healthy and sick preterm neonates (n=109) were screened on MacConkey agar to isolate lactose-positive Enterobacteriaceae. Whole-genome sequences were generated for Klebsiella spp., and virulence and antimicrobial resistance genes identified. Antibiotic susceptibility profiling and in vitro macrophage and iron assays were undertaken for the Klebsiella strains. Metapangenome analyses with a manually curated genome dataset were undertaken to examine the diversity of Klebsiella oxytoca and related bacteria in a publicly available shotgun metagenome dataset. Approximately one-tenth of faecal samples harboured Klebsiella spp. (Klebsiella pneumoniae, 7.3 %; Klebsiella quasipneumoniae, 0.9 %; Klebsiella grimontii, 2.8 %; Klebsiella michiganensis, 1.8 %). Isolates recovered from NEC- and sepsis-affected infants and those showing no signs of clinical infection (i.e. 'healthy') encoded multiple β-lactamases. No difference was observed between isolates recovered from healthy and sick infants with respect to in vitro siderophore production (all encoded enterobactin in their genomes). All K. pneumoniae, K. quasipneumoniae, K. grimontii and K. michiganensis faecal isolates tested were able to reside and persist in macrophages, indicating their immune evasion abilities. Metapangenome analyses of published metagenomic data confirmed our findings regarding the presence of K. michiganensis in the preterm gut. There is little difference in the phenotypic and genomic characteristics of Klebsiella isolates recovered from healthy and sick infants. Identification of β-lactamases in all isolates may prove problematic when defining treatment regimens for NEC or sepsis, and suggests that healthy preterm infants contribute to the resistome. Refined analyses with curated sequence databases are required when studying closely related species present in metagenomic data.

Toward Antibiotic Stewardship: Route of Antibiotic Administration Impacts the Microbiota and Resistance Gene Diversity in Swine Feces

Oral antibiotics are a critical tool for fighting bacterial infections, yet their use can have negative consequences, such as the disturbance of healthy gut bacterial communities and the dissemination of antibiotic residues in feces. Altering antibiotic administration route may limit negative impacts on intestinal microbiota and reduce selective pressure for antimicrobial resistance genes (ARG) persistence and mobility. Thus, a study was performed in pigs to evaluate route of therapeutic oxytetracycline (oxytet) administration, an antibiotic commonly used in the U.S. swine industry, on intestinal microbial diversity and ARG abundance. Given that oral antibiotics would be in direct contact with intestinal bacteria, we hypothesized that oral administration would cause a major shift in intestinal bacterial community structure when compared to injected antibiotic. We further postulated that the impact would extend to the diversity and abundance of ARG in swine feces. At approximately 3 weeks-of-age, piglets were separated into three groups (n = 21–22 per group) with two groups receiving oxytet (one via injection and the second via feed) and a third non-medicated group. Oxytet levels in the plasma indicated injected antibiotic resulted in a spike 1 day after administration, which decreased over time, though oxytet was still detected in plasma 14 days after injection. Conversely, in-feed oxytet delivery resulted in lower but less variable oxytet levels in circulation and high concentrations in feces. Similar trends were observed in microbial community changes regardless of route of oxytet administration; however, the impact on the microbial community was more pronounced at all time points and in all samples with in-feed administration. Fecal ARG abundance was increased with in-feed administration over injected, with genes for tetracycline and aminoglycoside resistance enriched specifically in the feces of the in-feed group. Sequencing of plasmid-enriched samples revealed multiple genetic contexts for the resistance genes detected and highlighted the potential role of small plasmids in the movement of antibiotic resistance genes. The findings are informative for disease management in food animals, but also manure management and antibiotic therapy in human medicine for improved antibiotic stewardship.

Probing the Mobilome: Discoveries in the Dynamic Microbiome

There has been an explosion of metagenomic data representing human, animal, and environmental microbiomes. This provides an unprecedented opportunity for comparative and longitudinal studies of many functional aspects of the microbiome that go beyond taxonomic classification, such as profiling genetic determinants of antimicrobial resistance, interactions with the host, potentially clinically relevant functions, and the role of mobile genetic elements (MGEs). One of the most important but least studied of these aspects are the MGEs, collectively referred to as the 'mobilome'. Here we elaborate on the benefits and limitations of using different metagenomic protocols, discuss the relative merits of various sequencing technologies, and highlight relevant bioinformatics tools and pipelines to predict the presence of MGEs and their microbial hosts.

Faecal microbiota transplantation for eradication of co-infection with Clostridioides difficile and extensively drug-resistant KPC-producing Klebsiella pneumoniae

Clostridioides difficile infection may be complicated by co-infection with other pathogens. We here describe the successful use of faecal microbiota transplantation to eradicate concomitant C. difficile and extensively drug-resistant (XDR) KPC-producing Klebsiella pneumoniae. Donor microbiota efficiently engrafted in the patient, and a donor-like microbial assemblage persisted in the patient during six months follow-up. The report explores the potential for the donor microbiota to eradicate and replace multi-resistant microorganisms.

Antimicrobial Resistance Gene Prevalence in a Population of Patients with Advanced Dementia Is Related to Specific Pathobionts

Long-term care facilities are significant reservoirs of antimicrobial-resistant organisms, and patients with advanced dementia are particularly vulnerable to multidrug-resistant organism (MDRO) acquisition and antimicrobial overuse. In this study, we longitudinally examined a group of patients with advanced dementia using metagenomic sequencing. We found significant inter- and intra-subject heterogeneity in microbiota composition, suggesting temporal instability. We also observed a link between the antimicrobial resistance gene density in a sample and the relative abundances of several pathobionts, particularly Escherichia coli, Proteus mirabilis, and Enterococcus faecalis, and used this relationship to predict resistance gene density in samples from additional subjects. Furthermore, we used metagenomic assembly to demonstrate that these pathobionts had higher resistance gene content than many gut commensals. Given the frequency and abundances at which these pathobionts were found in this population and the underlying vulnerability to MDRO of patients with advanced dementia, attention to microbial blooms of these species may be warranted.

Probiotic Supplements: Hope or Hype?

Probiotic bacteria have been associated with various health benefits and included in overwhelming number of foods. Today, probiotic supplements are consumed with increasing regularity and record a rapidly growing economic value. With billions of heterogeneous populations of probiotics per serving, probiotic supplements contain the largest quantity of probiotics across all functional foods. They often carry antibiotic-resistant determinants that can be transferred to and accumulate in resident bacteria of the gastrointestinal tract and risk their acquisitions by opportunistic pathogens. While the health benefits of probiotics have been widely publicized, this health risk, however, is underrepresented in both scientific studies and public awareness. On the other hand, the human gut presents conditions that are unfavorable for bacteria, including probiotics. It remains uncertain if probiotics from supplements can tolerate acids and bile salts that may undermine their effectiveness in conferring health benefits. Here, we put into perspective the perceived health benefits and the long-term safety of consuming probiotic supplements, specifically bringing intolerance to acids and bile salts, and the long-standing issue of antibiotic-resistant gene transfer into sharp focus. We report that probiotics from supplements examined in this study have poor tolerance to acids and bile salts while also displaying resistance to multiple antibiotics. They could also adapt and gain resistance to streptomycin in vitro. In an environment where consuming supplements is considered a norm, our results and that of others will put in perspective the persisting concerns surrounding probiotic supplements so that the current hype does not overpower the hope.

Heterogeneity of Moraxella isolates found in the nasal cavities of piglets

BACKGROUND

Previous studies have shown that the genus Moraxella is commonly present in the nasal microbiota of swine.

RESULTS

In this study, 51 isolates of Moraxella were obtained from nasal swabs from 3 to 4 week old piglets, which represented 26 different fingerprintings by enterobacterial repetitive intergenic consensus (ERIC)-PCR. Whole 16S rRNA gene sequencing allowed the identification at species level of the Moraxella spp. isolates. The majority of the field strains were identified as Moraxella pluranimalium, but Moraxella porci was also detected. In addition, a cluster of 7 strains did not group with any described Moraxella species, probably representing a new species. Subsequent phenotypic characterization indicated that strains of Moraxella pluranimalium were mainly sensitive to serum complement, while the cluster representing the putative new species was highly resistant. Biofilm formation capacity was very variable among the Moraxella spp. isolates, while adherence to epithelial cell lines was similar among selected strains. Additionally, variability was also observed in the association of selected strains to porcine alveolar macrophages. Antimicrobial tests evidenced the existence of multidrug-resistance in the strains.

CONCLUSIONS

In summary, phenotypic characterization revealed heterogeneity among Moraxella strains from the nasal cavity of piglets. Strains with pathogenic potential were detected as well as those that may be commensal members of the nasal microbiota. However, the role of Moraxella in porcine diseases and health should be further evaluated.

Mouse Genetic Background Affects Transfer of an Antibiotic Resistance Plasmid in the Gastrointestinal Tract

Dissemination of antibiotic resistance (AR) genes, often on plasmids, leads to antibiotic-resistant bacterial infections, which is a major problem for animal and public health. Bacterial conjugation is the primary route of AR gene transfer in the mammalian gastrointestinal tract. Significant gaps in knowledge about which gastrointestinal communities and host factors promote plasmid transfer remain. Here, we used Salmonella enterica serovar Kentucky strain CVM29188 carrying plasmid pCVM29188_146 (harboring streptomycin and tetracycline resistance genes) to assess plasmid transfer to Escherichia coli under in vitro conditions and in various mouse strains with a conventional or defined microbiota. As an initial test, the transfer of pCVM29188_146 to the E. coli strains was confirmed in vitro Colonization resistance and, therefore, a lack of plasmid transfer were found in wild-type mice harboring a conventional microbiota. Thus, mice harboring the altered Schaedler flora (ASF), or ASF mice, were used to probe for host factors in the context of a defined microbiota. To assess the influence of inflammation on plasmid transfer, we compared interleukin-10 gene-deficient 129S6/SvEv ASF mice (proinflammatory environment) to wild-type 129S6/SvEv ASF mice and found no difference in transconjugant yields. In contrast, the mouse strain influenced plasmid transfer, as C3H/HeN ASF mice had significantly lower levels of transconjugants than 129S6/SvEv ASF mice. Although gastrointestinal members were identical between the ASF mouse strains, a few differences from C3H/HeN ASF mice were detected, with C3H/HeN ASF mice having significantly lower abundances of ASF members 356 (Clostridium sp.), 492 (Eubacterium plexicaudatum), and 502 (Clostridium sp.) than 129S6/SvEv ASF mice. Overall, we demonstrate that microbiota complexity and mouse genetic background influence in vivo plasmid transfer.IMPORTANCE Antibiotic resistance is a threat to public health. Many clinically relevant antibiotic resistance genes are carried on plasmids that can be transferred to other bacterial members in the gastrointestinal tract. The current study used a murine model to study the transfer of a large antibiotic resistance plasmid from a foodborne Salmonella strain to a gut commensal E. coli strain in the gastrointestinal tract. We found that different mouse genetic backgrounds and a different diversity of microbial communities influenced the level of Escherichia coli that acquired the plasmid in the gastrointestinal tract. This study suggests that the complexity of the microbial community and host genetics influence plasmid transfer from donor to recipient bacteria.

Prevalence of Antimicrobial Resistance Genes and Integrons in Commensal Gram-Negative Bacteria in a College Community

Although the human intestinal microbiome has been shown to harbor antimicrobial drug resistance genes (ARGs), the prevalence of such genes in a healthy population and their impact on extraintestinal infections that occur in that community are not well established. This study sought to identify ARG prevalence and their mobile elements in the intestines of a healthy community population at a California University, and compared these genes to those previously identified among uropathogenic Escherichia coli isolated from patients with urinary tract infection from the same community. We isolated Gram-negative bacteria (GNB) from fecal samples of healthy volunteers and screened them by polymerase chain reaction for class 1 integron cassette sequences and ARGs encoding resistance against ampicillin, trimethoprim-sulfamethoxazole, gentamicin, and colistin. We found antimicrobial-resistant GNB from 83 (81%) of 102 nonredundant rectal swab samples. Seventy-four (72%) of these samples contained β-lactamase genes (bla_TEM, bla_SHV, bla_CTX-M, bla_OXA, and bla_OXY), dihydrofolate reductase (DHFR) genes (dhfr-A17, dhfr-A12, dhfr-A7, dhfr-A5, dhfr-A21, dhfr-A1, dhfr-A13, and dhfr-7), and aminoglycoside resistance genes (aadA5, aadA2, aadA1, and aadB). Integron sequences were found in 37 (36%) fecal samples. These genes were found in 11 different GNB species. The high prevalence of clinically common ARGs and integrons harbored by GNB in the intestine of a healthy population suggest that human intestines may serve as a major reservoir of these mobile ARGs that appear in E. coli strains causing extraintestinal infections in the same community.

SYN-007, an Orally Administered Beta-Lactamase Enzyme, Protects the Gut Microbiome from Oral Amoxicillin/Clavulanate without Adversely Affecting Antibiotic Systemic Absorption in Dogs

Beta-lactamases, enzymes produced by bacteria to degrade beta-lactam antibiotics, have been harnessed as therapeutics to protect the gut microbiome from damage caused by antibiotics. Proof-of-concept of this approach using SYN-004 (ribaxamase), a beta-lactamase formulated for oral delivery with intravenous (IV) penicillins and cephalosporins, was demonstrated with animal models and in humans. Ribaxamase degraded ceftriaxone in the gastrointestinal tract, protected the gut microbiome, significantly reduced the incidence of Clostridioides difficile disease and attenuated emergence of antibiotic resistant organisms. SYN-007 is a delayed release formulation of ribaxamase intended for use with oral beta-lactams. In dogs treated with oral amoxicillin, SYN-007 diminished antibiotic-mediated microbiome disruption and reduced the emergence of antibiotic resistance without altering amoxicillin systemic absorption. Here, SYN-007 function in the presence of clavulanate, a beta-lactamase inhibitor, was investigated. Dogs received amoxicillin (40 mg/kg, orally (PO), three times a day (TID)) or the combined antibiotic/beta-lactamase inhibitor, amoxicillin/clavulanate (40 mg/kg amoxicillin, 5.7 mg/kg clavulanate, PO, TID) +/™ SYN-007 (10 mg, PO, TID) for five days. Serum amoxicillin levels were not significantly different +/™ SYN-007 compared to amoxicillin alone or amoxicillin/clavulanate alone as controls for both first and last doses, indicating SYN-007 did not interfere with systemic absorption of the antibiotic. Whole genome shotgun metagenomics analyses of the fecal microbiomes demonstrated both amoxicillin and amoxicillin/clavulanate significantly reduced diversity and increased the frequency of antibiotic resistance genes. Microbiome damage appeared more severe with amoxicillin/clavulanate. In contrast, with SYN-007, microbiome diversity was not significantly altered, and frequency of antibiotic resistance genes did not increase. Importantly, SYN-007 functioned in the presence of clavulanate to protect the gut microbiome indicating that SYN-007 activity was not inhibited by clavulanate in the dog gastrointestinal tract. SYN-007 has the potential to expand microbiome protection to beta-lactam/beta-lactamase inhibitor combinations delivered orally or systemically.

Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae

Metagenomic sequencing of fecal DNA can usefully characterise an individual's intestinal resistome but is limited by its inability to detect important pathogens that may be present at low abundance, such as carbapenemase or extended-spectrum beta-lactamase producing Enterobacteriaceae. Here we aimed to develop a hybrid protocol to improve detection of resistance genes in Enterobacteriaceae by using a short period of culture enrichment prior to sequencing of DNA extracted directly from the enriched sample. Volunteer feces were spiked with carbapenemase-producing Enterobacteriaceae and incubated in selective broth culture for 6 hours before sequencing. Different DNA extraction methods were compared, including a plasmid extraction protocol to increase the detection of plasmid-associated resistance genes. Although enrichment prior to sequencing increased the detection of carbapenemase genes, the differing growth characteristics of the spike organisms precluded accurate quantification of their concentration prior to culture. Plasmid extraction increased detection of resistance genes present on plasmids, but the effects were heterogeneous and dependent on plasmid size. Our results demonstrate methods of improving the limit of detection of selected resistance mechanisms in a fecal resistome assay, but they also highlight the difficulties in using these techniques for accurate quantification and should inform future efforts to achieve this goal.

Investigating Antibiotic Resistance Genes in Marketed Ready-to-Eat Small Crickets (Acheta domesticus)

The present investigation was aimed at evaluating the occurrence of transferable genes conferring resistance to tetracyclines, macrolide-lincosamide-streptogramin B (MLS_B ), vancomycin, beta-lactams, and aminoglycosides in 32 samples from eight batches of ready-to-eat crickets (Acheta domesticus) commercialized by four European Union producers (two batches per producer). Bacterial DNA extracted directly from the insects was subjected to optimized polymerase chain reaction (PCR) and nested-PCR assays for the qualitative detection of 12 selected antibiotic resistance (AR) genes. Microbial enumeration demonstrated high counts of spore-forming bacteria and total mesophilic aerobes. Statistical analyses revealed significant differences between different producers and insect batches. Regarding AR genes, a high prevalence of genes conferring resistance to tetracycline [tet(M), tet(O), tet(K), tet(S)] was observed, together with the presence of genes conferring resistance to erythromycin [erm(B), erm(C)], beta-lactams (blaZ and mecA), and aminoglycosides [aac(6')-Ie aph(2")-Ia]. We performed a principal component analysis based on the AR gene frequencies that differentiated samples of batch 1 from those of batch 2. This analysis provided evidence for a difference between the producer from France and all the other producers among the batch 1 samples. PRACTICAL APPLICATION: Overall, an intrabatch variation was seen in the transferable resistances among different producers. This evidence, coupled with the observed differences in the viable counts, suggests a low standardization of the production processes. Hence, a prudent use of antimicrobials during the rearing of insects destined for human consumption is strongly recommended, as well as a need for a full standardization of production technologies.

The microbiome and tuberculosis: state of the art, potential applications, and defining the clinical research agenda

The diverse microbial communities within our bodies produce metabolites that modulate host immune responses. Even the microbiome at distal sites has an important function in respiratory health. However, the clinical importance of the microbiome in tuberculosis, the biggest infectious cause of death worldwide, is only starting to be understood. Here, we critically review research on the microbiome's association with pulmonary tuberculosis. The research indicates five main points: (1) susceptibility to infection and progression to active tuberculosis is altered by gut Helicobacter co-infection, (2) aerosol Mycobacterium tuberculosis infection changes the gut microbiota, (3) oral anaerobes in the lung make metabolites that decrease pulmonary immunity and predict progression, (4) the increased susceptibility to reinfection of patients who have previously been treated for tuberculosis is likely due to the depletion of T-cell epitopes on commensal gut non-tuberculosis mycobacteria, and (5) the prolonged antibiotic treatment required for cure of tuberculosis has long-term detrimental effects on the microbiome. We highlight knowledge gaps, considerations for addressing these knowledge gaps, and describe potential targets for modifying the microbiome to control tuberculosis.

Fecal Microbiome Characteristics and the Resistome Associated With Acquisition of Multidrug-Resistant Organisms Among Elderly Subjects

Infections caused by multidrug-resistant organisms (MDRO) lead to considerable morbidity and mortality. The elderly population residing in nursing homes are a major reservoir of MDRO. Our objective was to characterize the fecal microbiome of 82 elderly subjects from 23 nursing homes and compare their resistome to that of healthy young persons. Comparisons of microbiome composition and the resistome between subjects who acquired MDRO or not were analyzed to characterize specific microbiome disruption indices (MDI) associated with MDRO acquisition. An approach based on both 16S rRNA amplicon and whole metagenome shotgun (WMS) sequencing data was used. The microbiome of the study cohort was substantially perturbed, with Bacteroides, Firmicutes, and Proteobacteria predominating. Compared to healthy persons, the cohort of elderly persons had an increased number, abundance, and diversity of antimicrobial resistance genes. High proportions of study subjects harbored genes for multidrug-efflux pumps (96%) and linezolid resistance (52%). Among the 302 antimicrobial resistance gene families identified in any subject, 60% were exclusively detected within the study cohort, including Class D beta-lactamase genes. Subjects who acquired MDRO or not had significant differences in bacterial taxa; Odoribacter laneus, and Akkermansia muciniphila were significantly greater among subjects who did not acquire MDRO whereas Blautia hydrogenotrophica predominated among subjects who acquired MDRO. These findings suggest that specific MDI may identify persons at high risk of acquiring MDRO.

Potential impacts of horizontal gene transfer on human health and physiology and how anthropogenic activity can affect it

Horizontal gene transfer (HGT) is widespread among prokaryotes driving their evolution. In this paper, we review the potential impact in humans of the HGT between prokaryotes living in close association with humans in two scenarios: horizontal transfer in human microbiomes and transfer between microbes living in human managed environments. Although our vision is focused on the possible impact of these transfers in the propagation of antibiotic resistance genes or pathogenicity determinants, we also discuss possible human physiological adaptations via gene transfer between resident and occasional bacteria in the human microbiome.

Human Milk Microbiota: Transferring the Antibiotic Resistome to Infants

Commensal bacterial population is believed to be a reservoir for antibiotic resistance genes (ARGs). The infant gut microbiota has relatively higher abundance of ARGs than the adults. These genes can get transferred from commensals to pathogens by horizontal gene transfer, which magnifies the spectrum of antibiotic resistance in the environment. The presence of ARGs in neo-nates and infants, with no prior antibiotic exposure, questions their origin in the naïve commensal population. Breast milk microbiota that is responsible for the initial seeding of infant gut microbiota has also been found to harbour a vast array of ARGs. This review discusses the recent findings that indicate the potential of breast milk microbiota to act as a vehicle for transmission of ARGs to infants.

Characterization of the Microbial Resistome in Conventional and "Raised Without Antibiotics" Beef and Dairy Production Systems

Metagenomic investigations have the potential to provide unprecedented insights into microbial ecologies, such as those relating to antimicrobial resistance (AMR). We characterized the microbial resistome in livestock operations raising cattle conventionally (CONV) or without antibiotic exposures (RWA) using shotgun metagenomics. Samples of feces, wastewater from catchment basins, and soil where wastewater was applied were collected from CONV and RWA feedlot and dairy farms. After DNA extraction and sequencing, shotgun metagenomic reads were aligned to reference databases for identification of bacteria (Kraken) and antibiotic resistance genes (ARGs) accessions (MEGARes). Differences in microbial resistomes were found across farms with different production practices (CONV vs. RWA), types of cattle (beef vs. dairy), and types of sample (feces vs. wastewater vs. soil). Feces had the greatest number of ARGs per sample (mean = 118 and 79 in CONV and RWA, respectively), with tetracycline efflux pumps, macrolide phosphotransferases, and aminoglycoside nucleotidyltransferases mechanisms of resistance more abundant in CONV than in RWA feces. Tetracycline and macrolide–lincosamide–streptogramin classes of resistance were more abundant in feedlot cattle than in dairy cow feces, whereas the β-lactam class was more abundant in dairy cow feces. Lack of congruence between ARGs and microbial communities (procrustes analysis) suggested that other factors (e.g., location of farms, cattle source, management practices, diet, horizontal ARGs transfer, and co-selection of resistance), in addition to antimicrobial use, could have impacted resistome profiles. For that reason, we could not establish a cause–effect relationship between antimicrobial use and AMR, although ARGs in feces and effluents were associated with drug classes used to treat animals according to farms’ records (tetracyclines and macrolides in feedlots, β-lactams in dairies), whereas ARGs in soil were dominated by multidrug resistance. Characterization of the “resistance potential” of animal-derived and environmental samples is the first step toward incorporating metagenomic approaches into AMR surveillance in agricultural systems. Further research is needed to assess the public-health risk associated with different microbial resistomes.

A Comprehensive Antimicrobial Activity Evaluation of the Recombinant Microcin J25 Against the Foodborne Pathogens Salmonella and E. coli O157:H7 by Using a Matrix of Conditions

Natural microcin J25 (MccJ25) represent promising alternatives to traditional antibiotics for the treatment of drug-resistant infections. However, little is known about the antibacterial activity of recombinant MccJ25 against foodborne pathogens. Here, the activity of recombinant MccJ25 was examined using a matrix of conditions in order to assess the efficacy of recombinant MccJ25 as a mitigation against foodborne pathogens, such as Salmonella species and Escherichia coli (E. coli) O157:H7. Results showed that recombinant MccJ25 displayed excellent antimicrobial activity against these foodborne pathogens, including clinical isolates of Salmonella and E. coli, as well as clinical antibiotic-resistant Salmonella and E. coli isolates with different minimal inhibitory concentrations. In addition, antimicrobial activity curves and Live/Dead assay evidenced that recombinant MccJ25 harbors strong bactericidal activity against Salmonella and E. coli O157:H7. Notably, recombinant MccJ25 also had great potency and induced fast mortality against different growth phase of Salmonella and E. coli. The stability analysis results showed that the activity of recombinant MccJ25 was not influenced by temperatures as high as 121°C. Varying the pH from 2.0 to 9.0 did not appear to affect the activity of recombinant MccJ25. Under the challenge of several proteases, simulated gastrointestinal fluids and serum, recombinant MccJ25 still maintained exceptionally strong antimicrobial activity. Significant reductions in Salmonella Pullorum levels were also achieved in food biological environments, such as milk, egg and meat. Moreover, we demonstrated that recombinant MccJ25 appeared to act by inducing membrane breaks, thinning, and disintegration in the Salmonella Pullorum cytoplasmic membrane. Taken together, these results indicated that recombinant MccJ25 could be an effective alternative for mitigating and prevention of Salmonella and E. coli infection in food, animal and agriculture applications.