Colonizing opportunistic pathogens (COPs): The beasts in all of us

Antibacterial activity of Shallots (Allium xwakegi Araki.) cultivars in Palu Valley against Salmonella Typhi ATCC 27870 through in vitro and in silico evaluation

Background and Objectives

Shallots, recognized for their minimal toxicity, cost-effectiveness, and widespread availability, are increasingly considered a viable source of biological activity. This study evaluates the antibacterial efficacy of a specific shallot cultivar from Palu Valley, Indonesia, against Salmonella typhi, the pathogen responsible for typhoid fever.

Materials and Methods

Utilizing thin-layer chromatography (TLC-bioautography) and gas chromatography-mass spectroscopy (GC-MS), the study identifies active compounds in shallot ethanol extract and employs molecular docking to assess interactions between receptors and ligands.

Results

Findings indicate significant antibacterial activity, with a notable inhibition zone diameter of 31.5 mm at spot Rf 0.28 in TLC bioautography and an optimum concentration of 2% yielding an average clear zone diameter of 28.27 mm in the agar diffusion test. GC-MS analysis reveals 41 compounds, predominantly dodecanoic acid and 1,2,3-propanetriyl ester. Additionally, molecular docking reveals the lowest binding affinity (-7.3 kcal/mol) for Ergost-8-En-3-Ol, 14-Methyl-, (3.Beta,5. Alpha.) against DNA gyrase.

Conclusion

This study confirms Palu Valley shallot extract's potent antibacterial effect against Salmonella typhi, highlighting its therapeutic potential.

The faecal microbiome of the Australian silver gull contains phylogenetically diverse ExPEC, aEPEC and Escherichia coli carrying the transmissible locus of stress tolerance

Wildlife are implicated in the dissemination of antimicrobial resistance, but their roles as hosts for Escherichia coli that pose a threat to human and animal health is limited. Gulls (family Laridae) in particular, are known to carry diverse lineages of multiple-antibiotic resistant E. coli, including extra-intestinal pathogenic E. coli (ExPEC). Whole genome sequencing of 431 E. coli isolates from 69 healthy Australian silver gulls (Chroicocephalus novaehollandiae) sampled during the 2019 breeding season, and without antibiotic selection, was undertaken to assess carriage in an urban wildlife population. Phylogenetic analysis and genotyping resolved 123 sequence types (STs) representing most phylogroups, and identified diverse ExPEC, including an expansive phylogroup B2 cluster comprising 103 isolates (24 %; 31 STs). Analysis of the mobilome identified: i) widespread carriage of the Yersinia High Pathogenicity Island (HPI), a key ExPEC virulence determinant; ii) broad distribution of two novel phage elements, each carrying sitABCD and iii) carriage of the transmissible locus of stress tolerance (tLST), an element linked to sanitation resistance. Of the 169 HPI carrying isolates, 49 (48 %) represented diverse B2 isolates hosting FII-64 ColV-like plasmids that lacked iutABC and sitABC operons typical of ColV plasmids, but carried the serine protease autotransporter gene, sha. Diverse E. coli also carried archetypal ColV plasmids (52 isolates; 12 %). Clusters of closely related E. coli (<50 SNVs) from ST58, ST457 and ST746, sourced from healthy gulls, humans, and companion animals, were frequently identified. In summary, anthropogenically impacted gulls host an expansive E. coli population, including: i) putative ExPEC that carry ColV virulence gene cargo (101 isolates; 23.4 %) and HPI (169 isolates; 39 %); ii) atypical enteropathogenic E. coli (EPEC) (17 isolates; 3.9 %), and iii) E. coli that carry the tLST (20 isolates; 4.6 %). Gulls play an important role in the evolution and transmission of E. coli that impact human health.

Genomic surveillance for antimicrobial resistance - a One Health perspective

Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.

Persistent enrichment of multidrug resistant Klebsiella in oral and nasal communities during long-term starvation

The human oral and nasal cavities can act as reservoirs for opportunistic pathogens capable of causing acute infection. These microbes asymptomatically colonize the human oral and nasal cavities which facilitates transmission within human populations via the environment, and they routinely possess a clinically-significant antibiotic-resistance genes. Among these opportunistic pathogens, the Klebsiella genus stands out as a notable example, with its members frequently linked to nosocomial infections and multidrug resistance. As with many colonizing opportunistic pathogens, how Klebsiella transitions from an asymptomatic colonizer to a pathogen remains unclear. Here, we explored a possible explanation by investigating the ability of oral and nasal Klebsiella to outcompete their native microbial community members under in vitro starvation conditions, which could be analogous to external hospital environments. When Klebsiella was present within a healthy human oral or nasal sample, the bacterial community composition shifted dramatically under starvation conditions and typically became dominated by Klebsiella. Furthermore, introducing K. pneumoniae exogenously into a native microbial community lacking K. pneumoniae, even at low inoculum, led to repeated dominance under starvation. K.pneumoniae strains isolated from healthy individuals' oral and nasal cavities also exhibited resistance to multiple classes of antibiotics and were genetically similar to clinical and gut isolates. In addition, we found that in the absence of Klebsiella, other understudied opportunistic pathogens, such as Peptostreptococcus, dominate under starvation conditions. Our findings establish an environmental circumstance that allows for the outgrowth of Klebsiella and other opportunistic pathogens. The ability to outcompete other commensal bacteria and to persist under harsh environmental conditions may contribute to the colonization-to-infection transition of these opportunistic pathogens.

Single-cell RNA-Seq reveals intracellular microbial diversity within immune cells during SARS-CoV-2 infection and recovery

Intracellular microorganisms, like viruses, bacteria, and fungi, pose challenges in detection due to their non-culturable forms. Transcriptomic analysis at cellular level enables exploration of distributions and the impact of these microorganisms on host cells, a domain that remains underexplored because of methodological limitations. Single-cell technology shows promise in addressing this by capturing polyadenine-tailed transcripts, because recent studies confirmed polyadenylation in microbial transcriptomes. We utilized single-cell RNA-seq from PBMCs to probe intracellular microbes in healthy, SARS-CoV-2-positive, and recovered individuals. Among 76 bacterial species detected, 16 showed significant abundance differences. Buchnera aphidicola, Streptomyces clavuligerus, and Ehrlichia canis emerged significantly in memory-B, Naïve-T, and Treg cells. Staphylococcus aureus, Mycoplasma mycoides, Leptospira interrogans, and others displayed elevated levels in SARS-CoV-2-positive patients, suggesting possible disease association. This highlights the strength of single-cell technology in revealing potential microorganism's cell-specific functions. Further research is essential for functional understanding of their cell-specific abundance across physiological states.

Treatment of antibiotic-resistant bacteria colonizing diabetic foot ulcers by OLED induced antimicrobial photodynamic therapy

We evaluate the efficacy of antimicrobial Photodynamic Therapy (APDT) for inactivating a variety of antibiotic-resistant clinical strains from diabetic foot ulcers. Here we are focused on APDT based on organic light-emitting diodes (OLED). The wound swabs from ten patients diagnosed with diabetic foot ulcers were collected and 32 clinical strains comprising 22 bacterial species were obtained. The isolated strains were identified with the use of mass spectrometry coupled with a protein profile database and tested for antibiotic susceptibility. 74% of isolated bacterial strains exhibited adaptive antibiotic resistance to at least one antibiotic. All strains were subjected to the APDT procedure using an OLED as a light source and 16 µM methylene blue as a photosensitizer. APDT using the OLED led to a large reduction in all cases. For pathogenic bacteria, the reduction ranged from 1.1-log to > 8 log (Klebsiella aerogenes, Enterobacter cloaca, Staphylococcus hominis) even for high antibiotic resistance (MRSA 5-log reduction). Opportunistic bacteria showed a range from 0.4-log reduction for Citrobacter koseri to > 8 log reduction for Kocuria rhizophila. These results show that OLED-driven APDT is effective against pathogens and opportunistic bacteria regardless of drug resistance.

Developing home cleaning intervention through community engagement to reduce infections and antimicrobial resistance in Ghanaian homes

Globally Antimicrobial Resistance (AMR) constitutes a health crisis, particularly in developing countries, where infectious disease are commonly fatal. There is clear evidence for microbial exposure and infection transmission within the home. Personal and environmental hygiene are the best ways of reducing household infections thus decreasing the need for antibiotics and consequently diminishing AMR. Despite this being an obvious step, research efforts to understand the home environment and its impact on AMR, cleaning and possible interventions on household cleaning are limited. We combined design and microbiology methods in an innovative mixed-method approach. A traditional survey design (n = 240), a design ethnography (n = 12), a co-design workshop and a pre-intervention microbiological dust sample analysis was undertaken to provide insights for codesign workshops in which new cleaning practices might be developed to minimise any AMR bacteria present in the household environments located in the Greater Accra Region of Ghana. Microbiological analysis of household dust showed that 36.6% of bacterial isolates detected were found to carry at least one resistance to the panel of antibiotics tested. Four scenarios were generated from an economic segmentation of the survey data. 50 ethnographic insights were 'presented' and descriptions of 12 bacteria species that showed resistance to one or more antibiotics (representing 176 bacterial isolates that showed resistance to one or more antibiotics found in the dust samples) were presented to the participants in a codesign workshop. An intervention, a new regime of cleaning practices agreed through the co-design workshop and practiced for thirty days, was made in (n = 7) households. The high prevalence of multidrug resistance observed in this study indicate the need for antibiotics surveillance program, not only in hospital settings but also in the household environment. There is, thus, an urgent need for targeting of interventions at the household level. Activating knowledge through community engagement in the research helps in increasing public perception and breaking down the scientist-public barrier.

Using source-associated mobile genetic elements to identify zoonotic extraintestinal E. coli infections

A one-health perspective may provide new and actionable information about Escherichia coli transmission. E. coli colonizes a broad range of vertebrates, including humans and food-production animals, and is a leading cause of bladder, kidney, and bloodstream infections in humans. Substantial evidence supports foodborne transmission of pathogenic E. coli strains from food animals to humans. However, the relative contribution of foodborne zoonotic E. coli (FZEC) to the human extraintestinal disease burden and the distinguishing characteristics of such strains remain undefined. Using a comparative genomic analysis of a large collection of contemporaneous, geographically-matched clinical and meat-source E. coli isolates (n = 3111), we identified 17 source-associated mobile genetic elements - predominantly plasmids and bacteriophages - and integrated them into a novel Bayesian latent class model to predict the origins of clinical E. coli isolates. We estimated that approximately 8 % of human extraintestinal E. coli infections (mostly urinary tract infections) in our study population were caused by FZEC. FZEC strains were equally likely to cause symptomatic disease as non-FZEC strains. Two FZEC lineages, ST131-H22 and ST58, appeared to have particularly high virulence potential. Our findings imply that FZEC strains collectively cause more urinary tract infections than does any single non-E. coli uropathogenic species (e.g., Klebsiella pneumoniae). Our novel approach can be applied in other settings to identify the highest-risk FZEC strains, determine their sources, and inform new one-health strategies to decrease the heavy public health burden imposed by extraintestinal E. coli infections.

Evaluation of the BioFire® FilmArray® Pneumonia Panel with Conventional Bacterial Culture in Conjunction with Leukocyte Esterase Test

We evaluated the performance of the BioFire^® FilmArray^® Pneumonia panel (PN-panel) in detecting bacterial pathogens by comparing it to cultures and to the usefulness of the leukocyte esterase (LE) urine strip test. Between January and June 2022, a total of 67 sputum specimens were obtained from community-acquired pneumonia patients. The PN-panel and LE test were performed simultaneously with conventional cultures. The pathogen detection rates of the PN-panel and culture were 40/67 (59.7%) and 25/67 (37.3%), respectively. The concordance rate between the PN-panel and culture was high (76.9%) when the bacterial burden was high (10⁷ copies/mL), but it was low (8.6%) when it was 10^4-6 copies/mL, irrespective of the sputum quality. According to the LE positivity, the overall culture positive rate and PN-panel positive rate were significantly higher among the LE-positive specimens (23/45, 31/45) than among the LE-negative specimens (2/21, 8/21). Moreover, the difference in concordance rate between the PN-panel test and culture was significant according to the LE positivity, but not the Gram stain grading. In conclusion, the PN-panel showed high concordance when the bacterial burden was high (10⁷ copies/mL) and ancillary use of LE test will be helpful in interpreting the PN-panel results, especially when the copy number of bacterial pathogens is low.

Genetic Identification of Methicillin-Resistant Staphylococcus aureus Nasal Carriage and Its Antibiogram among Kidney Dialysis Patients at a Tertiary Care Hospital in AL-Karak, Jordan

Background. Methicillin-resistant Staphylococcus aureus (MRSA) is a major bacterial pathogen. Aim. The present study aimed to determine the incidence of MRSA infections among kidney dialysis patients and the antibiotic susceptibility patterns and investigate the prevalence of mecA gene among MRSA isolates. Materials and Methods. A total of 83 nasal sterile cotton swabs samples were obtained from hemodialysis patients from Al-Karak Governmental Hospital, Al-Karak, Jordan. Collected and cultured on nutrient agar and mannitol salt agar and incubating at 37°C for 24–48 hours, Staphylococcus aureus (S. aureus) strains were identified by gram stain, coagulase test, and catalase tests. The MRSA isolates were tested for the presence of MecA and SCCmec genes using the Xpert SA Nasal Complete assay real-time PCR. Factors such as age and gender were included in the study. The antibiotic profile tested by using the disc diffusion method tested all MRSA isolates. Results. This study showed that 10.8% of the cultures’ growth was S. aureus and 9.6% of all the patients were infected with MRSA, with no relationship between the number and frequency of MRSA according to the patient’s gender or age. All MRSA (100%) isolates have both genes (MecA genes and SCCmec genes), and all samples were resistant to oxacillin, ceftazidime, cefoxitin, aztreonam, and ampicillin. Conclusion. The MRSA prevalence was determined among kidney dialysis patients in the hospital. All positive samples were resistant to oxacillin, ceftazidime, cefoxitin, aztreonam, and ampicillin, which is a very rare finding, and this will give the scientists and doctors a dangerous indication about health-care centers in the Al-Karak city of Jordan.

Integrating sample similarities into latent class analysis: a tree-structured shrinkage approach

This paper is concerned with using multivariate binary observations to estimate the probabilities of unobserved classes with scientific meanings. We focus on the setting where additional information about sample similarities is available and represented by a rooted weighted tree. Every leaf in the given tree contains multiple samples. Shorter distances over the tree between the leaves indicate a priori higher similarity in class probability vectors. We propose a novel data integrative extension to classical latent class models with tree-structured shrinkage. The proposed approach enables (1) borrowing of information across leaves, (2) estimating data-driven leaf groups with distinct vectors of class probabilities, and (3) individual-level probabilistic class assignment given the observed multivariate binary measurements. We derive and implement a scalable posterior inference algorithm in a variational Bayes framework. Extensive simulations show more accurate estimation of class probabilities than alternatives that suboptimally use the additional sample similarity information. A zoonotic infectious disease application is used to illustrate the proposed approach. The paper concludes by a brief discussion on model limitations and extensions.

Current Limitations of Staph Infection Diagnostics, and the Role for VOCs in Achieving Culture-Independent Detection

Staphylococci are broadly adaptable and their ability to grow in unique environments has been widely established, but the most common and clinically relevant staphylococcal niche is the skin and mucous membranes of mammals and birds. S. aureus causes severe infections in mammalian tissues and organs, with high morbidities, mortalities, and treatment costs. S. epidermidis is an important human commensal but is also capable of deadly infections. Gold-standard diagnostic methods for staph infections currently rely upon retrieval and characterization of the infectious agent through various culture-based methods. Yet, obtaining a viable bacterial sample for in vitro identification of infection etiology remains a significant barrier in clinical diagnostics. The development of volatile organic compound (VOC) profiles for the detection and identification of pathogens is an area of intensive research, with significant efforts toward establishing breath tests for infections. This review describes the limitations of existing infection diagnostics, reviews the principles and advantages of VOC-based diagnostics, summarizes the analytical tools for VOC discovery and clinical detection, and highlights examples of how VOC biomarkers have been applied to diagnosing human and animal staph infections.

Hypoxia-Driven Changes in a Human Intestinal Organoid Model and the Protective Effects of Hydrolyzed Whey

Many whey proteins, peptides and protein-derived amino acids have been suggested to improve gut health through their anti-oxidant, anti-microbial, barrier-protective and immune-modulating effects. Interestingly, although the degree of hydrolysis influences peptide composition and, thereby, biological function, this important aspect is often overlooked. In the current study, we aimed to investigate the effects of whey protein fractions with different degrees of enzymatic hydrolysis on the intestinal epithelium in health and disease with a novel 2D human intestinal organoid (HIO) monolayer model. In addition, we aimed to assess the anti-microbial activity and immune effects of the whey protein fractions. Human intestinal organoids were cultured from adult small intestines, and a model enabling apical administration of nutritional components during hypoxia-induced intestinal inflammation and normoxia (control) in crypt-like and villus-like HIO was established. Subsequently, the potential beneficial effects of whey protein isolate (WPI) and two whey protein hydrolysates with a 27.7% degree of hydrolysis (DH28) and a 50.9% degree of hydrolysis (DH51) were assessed. In addition, possible immune modulatory effects on human peripheral immune cells and anti-microbial activity on four microbial strains of the whey protein fractions were investigated. Exposure to DH28 prevented paracellular barrier loss of crypt-like HIO following hypoxia-induced intestinal inflammation with a concomitant decrease in hypoxia inducible factor 1 alpha (HIF1α) mRNA expression. WPI increased Treg numbers and Treg expression of cluster of differentiation 25 (CD25) and CD69 and reduced CD4+ T cell proliferation, whereas no anti-microbial effects were observed. The observed biological effects were differentially mediated by diverse whey protein fractions, indicating that (degree of) hydrolysis influences their biological effects. Moreover, these new insights may provide opportunities to improve immune tolerance and promote intestinal health.

Laboratory diagnosed microbial infection in English UK Biobank participants in comparison to the general population

Understanding the genetic and environmental risk factors for serious bacterial infections in ageing populations remains incomplete. Utilising the UK Biobank (UKB), a prospective cohort study of 500,000 adults aged 40-69 years at recruitment (2006-2010), can help address this. Partial implementation of such a system helped groups around the world make rapid progress understanding risk factors for SARS-CoV-2 infection and COVID-19, with insights appearing as early as May 2020. In principle, such approaches could also to be used for bacterial isolations. Here we report feasibility testing of linking an England-wide dataset of microbial reporting to UKB participants, to enable characterisation of microbial infections within the UKB Cohort. These records pertain mainly to bacterial isolations; SARS-CoV-2 isolations were not included. Microbiological infections occurring in patients in England, as recorded in the Public Health England second generation surveillance system (SGSS), were linked to UKB participants using pseudonymised identifiers. By January 2015, ascertainment of laboratory reports from UKB participants by SGSS was estimated at 98%. 4.5% of English UKB participants had a positive microbiological isolate in 2015. Half of UKB isolates came from 12 laboratories, and 70% from 21 laboratories. Incidence rate ratios for microbial isolation, which is indicative of serious infection, from the UKB cohort relative to the comparably aged general population ranged from 0.6 to 1, compatible with the previously described healthy participant bias in UKB. Data on microbial isolations can be linked to UKB participants from January 2015 onwards. This linked data would offer new opportunities for research into the role of bacterial agents on health and disease in middle to-old age.

More than Meets the Eye: Untargeted Metabolomics and Lipidomics Reveal Complex Pathways Spurred by Activation of Acid Resistance Mechanisms in Escherichia coli

Escherichia coli is a ubiquitous group of bacteria that can be either commensal gut microbes or enterohemorrhagic food-borne pathogens. Regardless, both forms must survive acidic environments in the stomach and intestines to reach and colonize the gut, a process that partially relies on amino acid-dependent acid resistance (AR) mechanisms and modifications to membrane phospholipids. However, only the basic tenets of these mechanisms have been elucidated. In this paper, we aim to conduct a full-scale metabolic and lipidomic characterization of E. coli's adaptations to acid stress. We hypothesized that the use of untargeted metabolomics and lipidomics would reveal mechanisms downstream of AR processes that provide novel contributions to acid stress survival. We detected significant differences in the extracellular metabolome and the lipidome induced by amino acid supplementation (glutamine, arginine, or lysine) and contextualized these results using real-time quantitative polymerase chain reaction (RT-qPCR). We additionally identified several metabolic pathways as well as a significant alteration in phospholipid synthetic pathways induced by differential amino acid supplementation. These results demonstrate that AR may extend beyond canonical mechanisms to a coordinated metabolic phenotype. Future studies may benefit from our analysis to further elucidate distinct targets for prebiotic supplements to cultivate commensal strains or therapies to combat pathogenic ones.

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.

Nasal Microbiome and Its Interaction with the Host in Childhood Asthma

Childhood asthma is a major chronic non-communicable disease in infants and children, often triggered by respiratory tract infections. The nasal cavity is a reservoir for a broad variety of commensal microbes and potential pathogens associated with respiratory illnesses including asthma. A healthy nasal microenvironment has protective effects against respiratory tract infections. The first microbial colonisation in the nasal region is initiated immediately after birth. Subsequently, colonisation by nasal microbiota during infancy plays important roles in rapidly establishing immune homeostasis and the development and maturation of the immune system. Dysbiosis of microbiota residing in the mucosal surfaces, such as the nasopharynx and guts, triggers immune modulation, severe infection, and exacerbation events. Nasal microbiome dysbiosis is related to the onset of symptomatic infections. Dynamic interactions between viral infections and the nasal microbiota in early life affect the later development of respiratory infections. In this review, we summarise the existing findings related to nasal microbiota colonisation, dynamic variations, and host–microbiome interactions in childhood health and respiratory illness with a particular examination of asthma. We also discuss our current understanding of biases produced by environmental factors and technical concerns, the importance of standardised research methods, and microbiome modification for the prevention or treatment of childhood asthma. This review lays the groundwork for paying attention to an essential but less emphasized topic and improves the understanding of the overall composition, dynamic changes, and influence of the nasal microbiome associated with childhood asthma.

The effect of nickel ions on the susceptibility of bacteria to ciprofloxacin and ampicillin

To explore the interaction effects of ciprofloxacin and ampicillin with nickel on the growth of bacteria, Staphylococcus aureus strain ATCC 29213, Enterococcus faecalis ATCC 29212 and Escherichia coli ATCC 25922 were used. Minimum inhibitory concentrations (MICs) were determined for nickel, ciprofloxacin and ampicillin, and the checkerboard method was used to assess their cumulative effects on bacterial growth. The interactions between the metal and antibiotics were assessed by the fractional inhibitory concentration (FIC). The MICs for ciprofloxacin and ampicillin were 0.31 and 1 mg/L for E. faecalis, 0.62 and 1 mg/L for S. aureus and 0.005 and 2.5 for E. coli, respectively. The MIC for nickel was 1000 mg/L for all bacteria. The FIC results for ciprofloxacin and nickel demonstrated an antagonistic effect of the two agents on the growth of E. coli and E. faecalis and an additive effect on S. aureus. The FICs for ampicillin and nickel demonstrated a synergistic effect on the growth of E. faecalis and E. coli. Different interactions of metals and antibiotics were observed depending on the bacteria and the type of antibiotic.

Metagenomic Assessment of the Pathogenic Risk of Microorganisms in Sputum of Postoperative Patients With Pulmonary Infection

Respiratory infections are complicated biological processes associated with an unbalanced microbial community and a wide range of pathogens. To date, robust approaches are still required for distinguishing the pathogenic microorganisms from the colonizing ones in the clinical specimens with complex infection. In this study, we retrospectively analyzed the data of conventional culture testing and metagenomic next-generation sequencing (mNGS) of the sputum samples collected from 50 pulmonary infected patients after cardiac surgery from December 2020 and June 2021 in Ruijin Hospital. Taxonomic classification of the sputum metagenomes showed that the numbers of species belonging to bacteria, fungi, and viruses were 682, 58, and 21, respectively. The full spectrum of microorganisms present in the sputum microbiome covered all the species identified by culture, including 12 bacterial species and two fungal species. Based on species-level microbiome profiling, a reference catalog of microbial abundance detection limits was constructed to assess the pathogenic risks of individual microorganisms in the specimens. The proposed screening procedure detected 64 bacterial pathogens, 10 fungal pathogens, and three viruses. In particular, certain opportunistic pathogenic strains can be distinguished from the colonizing ones in the individual specimens. Strain-level identification and phylogenetic analysis were further performed to decipher molecular epidemiological characteristics of four opportunistic etiologic agents, including Klebsiella pneumoniae, Corynebacterium striatum, Staphylococcus aureus, and Candida albicans. Our findings provide a novel metagenomic insight into precision diagnosis for clinically relevant microbes, especially for opportunistic pathogens in the clinical setting.

Clinical Reasoning Behind Antibiotic Use in PICUs: A Qualitative Study

OBJECTIVES

To describe the reasoning processes used by pediatric intensivists to make antibiotic-related decisions.

DESIGN

Grounded theory qualitative study.

SETTING

Three Canadian university-affiliated tertiary medical, surgical, and cardiac PICUs.

PATIENTS

Twenty-one PICU physicians.

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

We conducted field observation during morning rounds followed by semistructured interviews with participants to examine the clinical reasoning behind antibiotic-related decisions (starting/stopping antibiotics, or treatment duration) made for patients with a suspected/proven bacterial infection. We used a grounded theory approach for data collection and analysis. Thematic saturation was reached after 21 interviews. Of the 21 participants, 10 (48%) were female, 15 (71%) were PICU attending staff, and 10 (48%) had greater than 10 years in clinical practice. Initial clinical reasoning involves using an analytical approach to determine the likelihood of bacterial infection. In case of uncertainty, an assessment of patient safety is performed, which partly overlaps with the use of intuitive clinical reasoning. Finally, if uncertainty remains, physicians tend to consult infectious diseases experts. Factors that override this clinical reasoning process include disease severity, pressure from consultants, and the tendency to continue antibiotic treatment initiated by colleagues.

CONCLUSIONS

Antibiotic-related decisions for critically ill children are complex, and pediatric intensivists use several clinical reasoning strategies to decrease the uncertainty around the bacterial etiology of infections. However, disease severity and patient safety concerns may overrule decisions based on clinical evidence and lead to antibiotic use. Several cognitive biases were identified in the clinical reasoning processes.

Meta-Analysis of Drug Delivery Approaches for Treating Intracellular Infections

This meta-analysis aims to evaluate the trend, methodological quality and completeness of studies on intracellular delivery of antimicrobial agents. PubMed, Embase, and reference lists of related reviews were searched to identify original articles that evaluated carrier-mediated intracellular delivery and pharmacodynamics (PD) of antimicrobial therapeutics against intracellular pathogens in vitro and/or in vivo. A total of 99 studies were included in the analysis. The most commonly targeted intracellular pathogens were bacteria (62.6%), followed by viruses (16.2%) and parasites (15.2%). Twenty-one out of 99 (21.2%) studies performed neither microscopic imaging nor flow cytometric analysis to verify that the carrier particles are present in the infected cells. Only 31.3% of studies provided comparative inhibitory concentrations against a free drug control. Approximately 8% of studies, albeit claimed for intracellular delivery of antimicrobial therapeutics, did not provide any experimental data such as microscopic imaging, flow cytometry, and in vitro PD. Future research on intracellular delivery of antimicrobial agents needs to improve the methodological quality and completeness of supporting data in order to facilitate clinical translation of intracellular delivery platforms for antimicrobial therapeutics.

Rapid differentiation of antibiotic-susceptible and -resistant bacteria through mediated extracellular electron transfer

Conventional methods for testing antibiotic susceptibility rely on bacterial growth on agar plates (diffusion assays) or in liquid culture (microdilution assays). These time-consuming assays use population growth as a proxy for cellular respiration. Herein we propose to use mediated extracellular electron transfer as a rapid and direct method to classify antibiotic-susceptible and -resistant bacteria. We tested antibiotics with diverse mechanisms of action (ciprofloxacin, imipenem, oxacillin, or tobramycin) with four important nosocomial pathogens (Acinetobacter baumannii, Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae) by adding the bacterial culture to a custom-designed electrochemical cell with a glassy-carbon electrode and growth media supplemented with a soluble electron transfer mediator, phenazine methosulfate (PMS). During cell respiration, liberated electrons reduce PMS, which is then oxidized on the electrode surface, and current is recorded. Using this novel approach, we were able to consistently classify strains as antibiotic-resistant or -susceptible in <90 min for methodology development and <150 min for blinded tests.

Transmission of COVID-19 and other infectious diseases in public washrooms: A systematic review

BACKGROUND

The risk of infectious disease transmission in public washrooms causes concern particularly in the context of the COVID-19 pandemic. This systematic review aims to assess the risk of transmission of viral or bacterial infections through inhalation, surface contact, and faecal-oral routes in public washrooms in healthcare and non-healthcare environments.

METHODS

We systematically reviewed environmental sampling, laboratory, and epidemiological studies on viral and bacterial infection transmission in washrooms using PubMed and Scopus. The review focused on indoor, publicly accessible washrooms.

RESULTS

Thirty-eight studies from 13 countries were identified, including 14 studies carried out in healthcare settings, 10 in laboratories or experimental chambers, and 14 studies in restaurants, workplaces, commercial and academic environments. Thirty-three studies involved surface sampling, 15 air sampling, 8 water sampling, and 5 studies were risk assessments or outbreak investigations. Infectious disease transmission was studied in relation with: (a) toilets with flushing mechanisms; (b) hand drying systems; and (c) water taps, sinks and drains. A wide range of enteric, skin and soil bacteria and enteric and respiratory viruses were identified in public washrooms, potentially posing a risk of infection transmission. Studies on COVID-19 transmission only examined washroom contamination in healthcare settings.

CONCLUSION

Open-lid toilet flushing, ineffective handwashing or hand drying, substandard or infrequent surface cleaning, blocked drains, and uncovered rubbish bins can result in widespread bacterial and/or viral contamination in washrooms. However, only a few cases of infectious diseases mostly related to faecal-oral transmission originating from washrooms in restaurants were reported. Although there is a risk of microbial aerosolisation from toilet flushing and the use of hand drying systems, we found no evidence of airborne transmission of enteric or respiratory pathogens, including COVID-19, in public washrooms. Appropriate hand hygiene, surface cleaning and disinfection, and washroom maintenance and ventilation are likely to minimise the risk of infectious disease transmission.

The Darkest Place Is under the Candlestick-Healthy Urogenital Tract as a Source of Worldwide Disseminated Extraintestinal Pathogenic Escherichia coli Lineages

Since the discovery of the urinary microbiome, including the identification of Escherichia coli in healthy hosts, its involvement in UTI development has been a subject of high interest. We explored the population diversity and antimicrobial resistance of E. coli (n = 22) in the urogenital microbiome of ten asymptomatic women (representing 50% of the sample tested). We evaluated their genomic relationship with extraintestinal pathogenic E. coli (ExPEC) strains from healthy and diseased hosts, including the ST131 lineage. E. coli prevalence was higher in vaginal samples than in urine samples, and occasionally different lineages were observed in the same individual. Furthermore, B2 was the most frequent phylogenetic group, with the most strains classified as ExPEC. Resistance to antibiotics of therapeutic relevance (e.g., amoxicillin-clavulanate conferred by blaTEM-30) was observed in ExPEC widespread lineages sequence types (ST) 127, ST131, and ST73 and ST95 clonal complexes. Phylogenomics of ST131 and other ExPEC lineages revealed close relatedness with strains from gastrointestinal tract and diseased host. These findings demonstrate that healthy urogenital microbiome is a source of potentially pathogenic and antibiotic resistant E. coli strains, including those causing UTI, e.g., ST131. Importantly, diverse E. coli lineages can be observed per individual and urogenital sample type which is relevant for future studies screening for this uropathogen.

A 21-Year Survey of Escherichia coli from Bloodstream Infections (BSI) in a Tertiary Hospital Reveals How Community-Hospital Dynamics of B2 Phylogroup Clones Influence Local BSI Rates

This is a longitudinal study comprising 649 Escherichia coli isolates representing all 7,165 E. coli bloodstream infection (BSI) episodes recorded in a hospital (1996 to 2016). Strain analysis included clonal identification (phylogenetic groups/subgroups, STc131 subclades, pulsed-field gel electrophoresis [PFGE], and whole-genome sequencing [WGS]), antibiotic susceptibility (13 antibiotics), and virulence-associated genes (VAGs; 29 genes). The incidence of E. coli BSI increased from 1996 to 2016 (5.5 to 10.8 BSI episodes/1,000 hospitalizations, average 7 to 8/1,000). B2 isolates predominate (53%), with subgroups B2-I (STc131), B2-II, B2-IX, and B2-VI representing 25%, 25%, 14%, and 9%, respectively. Intertwined waves of community-acquired (CA) plus health care-associated and community-onset health care-associated (HCA) and hospital-acquired (HA) episodes of both B2 and non-B2 phylogroups occurred. A remarkable increase was observed only for B2-I-STc131 (C1/C2 subclades), with oscillations for other B2 subgroups and phylogroups throughout the years. Epidemic and persistent clones (comprising isolates with highly similar/identical PFGE types and genomes differing in 6 to 173 single nucleotide polymorphisms [SNPs]) of B2-I (STc131), B2-II (STc73), B2-III (STc127), B2-IX (STc95), and B2-VI (STc12) were recovered from different patients, most at hospital admission, for long periods (2 to 17 years), and extended-spectrum beta-lactamase (ESBL) producers or resistance to ciprofloxacin in B2 isolates was almost restricted to B2-I (STc131) subclade C. STc131 contributed to increasing the B2 rates but only transiently altered the E. coli population structure. The increase of E. coli BSI was determined by waves of CA+HCA BSI episodes that predate the waves of HA BSI. Besides the risk of hospital transmission that led to temporal increases in BSI, this study suggests that E. coli populations/clones from community-based healthy individuals may occasionally have an epidemic structure and provide a source of transmissible strains influencing the HA BSI incidence.

IMPORTANCE Sepsis is the third leading cause of mortality in Western countries and one of the Global Health Threats recognized by the WHO since 2017. Despite Escherichia coli constituting the most common cause of bloodstream infections (BSI), its epidemiology is not fully understood, in part due to the scarcity of local and longitudinal studies. Our work analyzes the long-term dynamics of E. coli causing bacteremia in a single institution and reveals waves of different clonal lineages that emerge periodically and successfully spread afterward in both the community and hospitals. Because the origin of E. coli bloodstream infections is the gut, the microbiota of healthy individuals might occasionally have an epidemic structure, providing a source of E. coli strains to influence the incidence of hospital BSI. The study complements previous fractionated observations focusing on specific E. coli lineages or antibiotic-resistant isolates in the last decades and helps to understand the epidemiology of E. coli BSI and the dynamics of pandemic clones.

Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance

Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.

Examining the Effects of 4He Exposure on the Gut-Brain Axis

Beyond low-Earth orbit, space radiation poses significant risks to astronaut health. Previous studies have shown that the microbial composition of the gastrointestinal (GI) microbiome changes upon exposure to high-linear energy transfer radiation. Interestingly, radiation-induced shifts in GI microbiota composition are linked to various neuropsychological disorders. Herein, we aimed to study changes in GI microbiota and behaviors of rats exposed to whole-body radiation (0, 5 or 25 cGy 4He, 250 MeV/n) at approximately 6 months of age. Fecal samples were collected 24 h prior to 4He irradiation and 24 h and 7 days postirradiation for quantitative PCR analyses to assess fecal levels of spore-forming bacteria (SFB), Bifidobacterium, Lactobacillus and Akkermansia. Rats were also tested in the social odor recognition memory (SORM) test at day 7 after 4He exposure. A subset of rats was euthanized 90 min after completion of the SORM test, and GI tissue from small intestine to colon were prepared for examining overall histological changes and immunohistochemical staining for serotonin (5-HT). No notable pathological changes were observed in GI tissues. Akkermansia spp. and SFB were significantly decreased in the 25 cGy group at 24 h and 7 days postirradiation compared to pre-exposure, respectively. Bifidobacterium and Lactobacillus spp. showed no significant changes. 5-HT production was significantly higher in the proximal small intestine and the cecum in the 25 cGy group compared to the sham group. The 25 cGy group exhibited deficits in recognition in SORM testing at day 7 postirradiation. Taken together, these results suggest a connection between GI microbiome composition, serotonin production, and neurobehavioral performance, and that this connection may be disrupted upon exposure to 25 cGy of 4He ions.

Pseudomonas aeruginosa: an antibiotic resilient pathogen with environmental origin

Pseudomonas aeruginosa, a bacterium characterized for its low antibiotics' susceptibility, is one of the most relevant opportunistic pathogens, causing infections at hospitals and in cystic fibrosis patients. Besides its relevance for human health, P. aeruginosa colonizes environmental ecosystems; therefore the elements driving its infectivity and antibiotic resistance must be analyzed from a One-Health perspective. Although some epidemic clones have been described, there are not specific lineages linked to infections, suggesting that P. aeruginosa virulence and antibiotic resistance determinants evolved in nature to play functions other than infecting the human host and avoiding antimicrobial treatment. Herein, we review current information on the population structure of P. aeruginosa and on the functional role that its resistance and virulence determinants have in non-clinical ecosystems.

Bloodstream infections' origins following fecal microbiota transplantation: a strain-level analysis

High rates of bloodstream infection (BSI) were seen after fecal microbiota transplantation (FMT) in patients with graft-versus-host disease.

Metagenomic analysis pointed to recipients’ indigenous microbiota as the BSI source, ruling out direct involvement of FMT donations.

We observed high rates of bloodstream infections (BSIs) following fecal microbiota transplantation (FMT) for graft-versus-host-disease (33 events in 22 patients). To trace the BSIs' origin, we applied a metagenomic bioinformatic pipeline screening donor and recipient stool samples for bacteremia-causing strains in 13 cases. Offending strains were not detected in FMT donations. Enterococcus faecium, Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii could be detected in stool samples before emerging in the blood. In this largest report of BSIs post-FMT, we present an approach that may be applicable for evaluating BSI origin following microbiota-based interventions. Our findings support FMT safety in immunocompromised patients but do not rule out FMT as an inducer of bacterial translocation.

Prevalence of multidrug-resistance and bla VIM and bla IMP genes among gram-negative clinical isolates in tertiary care hospital, Kathmandu, Nepal

Background and Objectives

Carbapenems have been the choice of antibiotics for the treatment of infections caused by multidrug-resistant bacteria. The main objective of this study was to determine the prevalence of carbapenemase (bla _VIM and bla _IMP ) producing isolates among Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii.

Materials and Methods

A total of 1,151 clinical samples were collected from the patients visiting Annapurna Neurological Institute and Allied Science and Annapurna Research Centre, Kathmandu, between June 2017 and January 2018. Antibiotic susceptibility testing (AST) was performed on the Enterobacteriaceae, P. aeruginosa and A. baumannii isolates using the Kirby-Bauer disk diffusion method. The modified Hodge test (MHT) was performed on the carbapenem-resistant isolates to confirm carbapenemase production. DNA was extracted and then screened for bla _VIM and bla _IMP genes by multiplex PCR.

Results

Of the total 1,151 clinical samples, 253 (22.0%) showed positive growth. Of them, 226 (89.3%) were identified as Enterobacteriaceae, P. aeruginosa, and A. baumannii. Among the 226 isolates, 106 (46.9%) were multidrug-resistant. Out of the 106, 97 (91.5%) isolates showed resistance to at least one of the carbapenem used. Among the 97 carbapenem-resistant isolates, 67 (69.1%) showed the modified Hodge test (MHT) positive results. bla _VIM and bla _IMP were detected in 40 and 38 isolates respectively using multiplex PCR assay.

Conclusion

This study determined a high prevalence of MDR and carbapenem resistance among Enterobacteriaceae, P. aeruginosa, and A. baumannii as detected by the presence of bla _VIM and bla _IMP genes. This study recommends the use of rapid and advanced diagnostic tools along with conventional phenotypic detection methods in the clinical settings for early detection and management of drug-resistant pathogens to improve treatment strategies.

The Recovery, Interpretation and Use of Ancient Pathogen Genomes

The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biology and engaged considerable public interest. Although most studies of ancient genomes have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of microbial pathogens and microbiomes from ancient and historical human and non-human remains. This coming of age has been made possible by techniques that allow the preferential capture and amplification of discrete genomes from a background of predominantly host and environmental DNA. There are now near-complete ancient genome sequences for three pathogens of considerable historical interest — pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae) — and for three equally important endemic human disease agents — Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy) and Treponema pallidum pallidum (syphilis). Genomic data from these pathogens have extended earlier work by paleopathologists. There have been efforts to sequence the genomes of additional ancient pathogens, with the potential to broaden our understanding of the infectious disease burden common to past populations from the Bronze Age to the early 20^th century. In this review we describe the state-of-the-art of this rapidly developing field, highlight the contributions of ancient pathogen genomics to multidisciplinary endeavors and describe some of the limitations in resolving questions about the emergence and long-term evolution of pathogens.

Phase Variation in HMW1A Controls a Phenotypic Switch in Haemophilus influenzae Associated with Pathoadaptation during Persistent Infection

Genetic variants arising from within-patient evolution shed light on bacterial adaptation during chronic infection. Contingency loci generate high levels of genetic variation in bacterial genomes, enabling adaptation to the stringent selective pressures exerted by the host. A significant gap in our understanding of phase-variable contingency loci is the extent of their contribution to natural infections. The human-adapted pathogen nontypeable Haemophilus influenzae (NTHi) causes persistent infections, which contribute to underlying disease progression. The phase-variable high-molecular-weight (HMW) adhesins located on the NTHi surface mediate adherence to respiratory epithelial cells and, depending on the allelic variant, can also confer high epithelial invasiveness or hyperinvasion. In this study, we characterize the dynamics of HMW-mediated hyperinvasion in living cells and identify a specific HMW binding domain shared by hyperinvasive NTHi isolates of distinct pathological origins. Moreover, we observed that HMW expression decreased over time by using a longitudinal set of persistent NTHi strains collected from chronic obstructive pulmonary disease (COPD) patients, resulting from increased numbers of simple-sequence repeats (SSRs) downstream of the functional P2_hmw1A promoter, which is the one primarily driving HMW expression. Notably, the increased SSR numbers at the hmw1 promoter region also control a phenotypic switch toward lower bacterial intracellular invasion and higher biofilm formation, likely conferring adaptive advantages during chronic airway infection by NTHi. Overall, we reveal novel molecular mechanisms of NTHi pathoadaptation based on within-patient lifestyle switching controlled by phase variation.

Antibiotic susceptibility of human gut-derived facultative anaerobic bacteria is different under aerobic versus anaerobic test conditions

Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, including deep wound, vagina, periodontal pockets, gastrointestinal tract, genitourinary tract and lungs. Generally, antibiotic susceptibility tests (AST) for facultative anaerobes are performed under aerobic conditions due to ease of handling and rapid growth. However, variation in susceptibility of facultative anaerobes to antibiotics under aerobic and anaerobic conditions can lead to failure of antibiotic treatment. Our study evaluated the susceptibility of facultative anaerobic microorganisms to antibiotics during growth under anaerobic or aerobic conditions. We compared the resistance patterns of representatives from 15 bacterial genera isolated from the human-gastrointestinal tract against 22 different antibiotics from six classes under aerobic and anaerobic conditions. Preliminary results obtained by a disc diffusion method were verified using minimum inhibitory concentration (MIC) testing. The results demonstrated that 7-strains had a similar pattern of drug resistance under both conditions, while the remaining ten strains had significant differences in resistance patterns between aerobic and anaerobic conditions for at least one antibiotic. We conclude that successful antibiotic therapy for host-associated pathogens requires proper assessment of the oxygen condition of the growth environment and MIC testing of each pathogen under anaerobic and aerobic conditions.

Antibiotic resistance: Time of synthesis in a post-genomic age

Antibiotic resistance has been highlighted by international organizations, including World Health Organization, World Bank and United Nations, as one of the most relevant global health problems. Classical approaches to study this problem have focused in infected humans, mainly at hospitals. Nevertheless, antibiotic resistance can expand through different ecosystems and geographical allocations, hence constituting a One-Health, Global-Health problem, requiring specific integrative analytic tools. Antibiotic resistance evolution and transmission are multilayer, hierarchically organized processes with several elements (from genes to the whole microbiome) involved. However, their study has been traditionally gene-centric, each element independently studied. The development of robust-economically affordable whole genome sequencing approaches, as well as other -omic techniques as transcriptomics and proteomics, is changing this panorama. These technologies allow the description of a system, either a cell or a microbiome as a whole, overcoming the problems associated with gene-centric approaches. We are currently at the time of combining the information derived from -omic studies to have a more holistic view of the evolution and spread of antibiotic resistance. This synthesis process requires the accurate integration of -omic information into computational models that serve to analyse the causes and the consequences of acquiring AR, fed by curated databases capable of identifying the elements involved in the acquisition of resistance. In this review, we analyse the capacities and drawbacks of the tools that are currently in use for the global analysis of AR, aiming to identify the more useful targets for effective corrective interventions.

Driving Laboratory Standardization of Bacterial Culture and Antimicrobial Susceptibility Testing in Veterinary Clinical Microbiology in Europe and Beyond

Globally, antimicrobial resistance is one of the most important public health challenges in which the clinical microbiology laboratory plays a critical role by providing guidance for antimicrobial treatment. Despite the recognition of its importance, there is still a real need for the standardized training of clinical microbiologists and harmonization of diagnostic procedures. This is particularly true for veterinary clinical microbiology, where additional challenges exist when microbiologists are trying to fulfill a professional role very similar to that of their colleagues working in human microbiology laboratories. The specific points that need addressing to improve the outputs of veterinary microbiology laboratories discussed here include (i) harmonization of methodologies used by veterinary laboratories for antimicrobial susceptibility testing (AST); (ii) specific guidelines for interpretation and reporting of AST results for animal pathogens; (iii) guidelines for detection of antimicrobial resistance mechanisms in animal isolates; (iv) standardization of diagnostic procedures for animal clinical specimens; and (v) the need to train more veterinary clinical microbiology specialists. However, there is now a plan to address these issues, led by the European Network for Optimization of Veterinary Antimicrobial Treatment (ENOVAT), which is bringing together experts in veterinary microbiology, pharmacology, epidemiology, and antimicrobial stewardship from Europe and wider afield. ENOVAT is aiming to work with project partners toward standardization and harmonization of laboratory methodologies and optimization of veterinary antimicrobial treatment. Ultimately, the project may provide a mechanism for standardization and harmonization of veterinary clinical microbiology methodologies that could then be used as a template for implementation at a wider international level.

Antimicrobial resistance in clinical bacterial isolates from horses in the UK

BACKGROUND

Surveillance of antimicrobial resistance (AMR) in horses is important to aid empirical treatment decisions and highlight emerging AMR threats.

OBJECTIVE

To describe the AMR patterns of common groups of bacteria from clinical submissions from horses in the UK during 2018, and to determine how this varies by sample site and type of submitting veterinary practice.

STUDY DESIGN

Prospective observational study.

METHODS

All data on bacterial culture and subsequent antimicrobial susceptibility testing (AST) collected in 2018 from six large equine diagnostic laboratories were included. Resistance patterns were analysed including resistance to 1 or 2 antimicrobial classes, multidrug resistance (MDR), extensively drug resistant (XDR), resistance to highest priority critically important antimicrobials and isolates where there was no readily available treatment for adult horses in the UK. Submitting practices were classified according to whether they treated referral cases or not (first opinion). Comparisons between proportions and resistance for each bacterial group and sample site was performed using Chi-squared (or Fisher's exact test).

RESULTS

A total of 6,018 bacterial isolates from 4,038 diagnostic submissions were included from respiratory (n = 1555), urogenital (n = 1,010), skin/hair/wound/abscess (n = 753), surgical site infection (SSI) /catheter-related-infection (CRI) /orthopaedic infections (n = 347) and unknown/'other' submissions (n = 373). There were 2,711 Gram-negative isolates and 3,307 Gram-positive isolates. Prevalence of MDR for E. coli was 31.7%, Staphylococcus spp. 25.3% and > 25% for the majority of bacterial isolates from SSI/CRI/orthopaedic submissions. For Enterococcus spp. there was no readily available treatment for adult horses in the UK in 30.2% of positive submissions. MDR was significantly higher from referral hospital than first opinion submissions for the majority of pathogens (except Actinobacillus spp. and Pasteurella spp. and β-haemolytic Streptococcus spp.).

MAIN LIMITATIONS

Since culture and susceptibility results are not systematic analyses based on harmonised methods, selection bias could impact the findings.

CONCLUSIONS

Ongoing surveillance is essential to understand emerging patterns of resistance. MDR is high in SSI/CRI/orthopaedic infections, which is important for hospital biosecurity and guiding treatment decisions. Harmonisation of diagnostic procedures and interpretation of results amongst veterinary laboratories will improve AMR surveillance and data comparison among laboratories.

Effects of Antibiotic Treatment with Piperacillin/Tazobactam versus Ceftriaxone on the Composition of the Murine Gut Microbiota

Effective antimicrobial stewardship requires a better understanding of the impact of different antibiotics on the gut microflora. Studies with humans are confounded by large interindividual variability and difficulty in identifying control cohorts. However, controlled murine models can provide valuable information. In this study, we examined the impact of a penicillin-like antibiotic (piperacillin-tazobactam [TZP]) or a third-generation cephalosporin (ceftriaxone [CRO]) on the murine gut microbiota by analysis of changes in fecal microbiome composition by 16S rRNA amplicon sequencing and standard microbiology. Resistance to colonization by multidrug-resistant Escherichia coli sequence type 131 (ST131) and Klebsiella pneumoniae ST258 was also tested. Changes in microbiome composition and a significant (P < 0.05) decrease in diversity occurred in all treated mice, but dysbiosis was more marked and prolonged after CRO exposure, with a persistent rise in Proteobacteria Enterobacteriaceae blooms occurred in all antibiotic-treated mice, but for TZP, unlike CRO, these were significant only under direct antibiotic pressure. At the height of dysbiosis after antibiotic termination, the murine gut was highly susceptible to colonization with both multidrug-resistant enterobacterial pathogens. Cohabitation of treated mice with untreated individuals had a notable mitigating effect on dysbiosis of treated guts. The administration of a third-generation cephalosporin caused a more severe imbalance in the murine fecal microflora than that caused by a penicillin/β-lactam inhibitor combination with comparable activity against medically important virulent bacteria. At the height of dysbiosis, both antibiotic treatments equally led to microbial instability associated with loss of resistance to gut colonization by antibiotic-resistant pathogens.

Novel Detection of Nasty Bugs, Prevention Is Better than Cure

Hospital-acquired infections (HAIs) are a growing concern around the world. They contribute to increasing mortality and morbidity rates and are an economic threat. All hospital patients have the potential to contract an HAI, but those with weakened or inferior immune systems are at highest risk. Most hospital patients will contract at least one HAI, but many will contract multiple ones. Bacteria are the most common cause of HAIs and contribute to 80-90% of all HAIs, with Staphylococcus aureus, Clostridium difficile, Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae accounting for the majority. Each of these bacteria are highly resistant to antibiotics and can produce a protective film, known as a biofilm, to further prevent their eradication. It has been shown that by detecting and eradicating bacteria in the environment, infection rates can be reduced. The current methods for detecting bacteria are time consuming, non-specific, and prone to false negatives or false positives. Aptamer-based biosensors have demonstrated specific, time-efficient and simple detection, highlighting the likelihood that they could be used in a similar way to detect HAI-causing bacteria.

Alteration of Bacterial Communities in Anterior Nares and Skin Sites of Patients Undergoing Arthroplasty Surgery: Analysis by 16S rRNA and Staphylococcal-Specific tuf Gene Sequencing

The aim was to study alterations of bacterial communities in patients undergoing hip or knee arthroplasty to assess the impact of chlorhexidine gluconate soap decolonisation and systemic antibiotic prophylaxis. A Swedish multicentre, prospective collection of samples obtained from elective arthroplasty patients (n = 83) by swabbing anterior nares, skin sites in the groin and the site of planned surgery, before and after arthroplasty surgery, was analysed by 16S rRNA (V3-V4) gene sequencing and a complementary targeted tuf gene sequencing approach to comprehensively characterise alterations in staphylococcal communities. Significant reductions in alpha diversity was detected for both bacterial (p = 0.04) and staphylococcal (p = 0.03) groin communities after arthroplasty surgery with significant reductions in relative Corynebacterium (p = 0.001) abundance and Staphylococcus hominis (p = 0.01) relative staphylococcal abundance. In nares, significant reductions occurred for Staphylococcus hominis (p = 0.02), Staphylococcus haemolyticus (p = 0.02), and Staphylococcus pasteuri (p = 0.003) relative to other staphylococci. Staphylococcus aureus colonised 35% of anterior nares before and 26% after arthroplasty surgery. Staphylococcus epidermidis was the most abundant staphylococcal species at all sampling sites. No bacterial genus or staphylococcal species increased significantly after arthroplasty surgery. Application of a targeted tuf gene sequencing approach provided auxiliary staphylococcal community profiles and allowed species-level characterisation directly from low biomass clinical samples.

Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health

Antibiotic resistance is a problem for human health, and consequently, its study had been traditionally focused toward its impact for the success of treating human infections in individual patients (individual health). Nevertheless, antibiotic-resistant bacteria and antibiotic resistance genes are not confined only to the infected patients. It is now generally accepted that the problem goes beyond humans, hospitals, or long-term facility settings and that it should be considered simultaneously in human-connected animals, farms, food, water, and natural ecosystems. In this regard, the health of humans, animals, and local antibiotic-resistance-polluted environments should influence the health of the whole interconnected local ecosystem (One Health). In addition, antibiotic resistance is also a global problem; any resistant microorganism (and its antibiotic resistance genes) could be distributed worldwide. Consequently, antibiotic resistance is a pandemic that requires Global Health solutions. Social norms, imposing individual and group behavior that favor global human health and in accordance with the increasingly collective awareness of the lack of human alienation from nature, will positively influence these solutions. In this regard, the problem of antibiotic resistance should be understood within the framework of socioeconomic and ecological efforts to ensure the sustainability of human development and the associated human-natural ecosystem interactions.

Broad-Spectrum Cephalosporin-Resistant and/or Fluoroquinolone-Resistant Enterobacterales Associated with Canine and Feline Urogenital Infections

The aim of the present study was to characterize Enterobacterales resistant to 3rd and 4th generation cephalosporins, carbapenems and/or fluoroquinolones, isolated from dogs and cats with urogenital infections. In total, 36 strains (Escherichia coli (n = 28), Klebsiella pneumoniae (n = 3), Serratia marcescens, Raoultella ornithinolytica, Proteus mirabilis, Citrobacter portucalensis and Enterobacter cloacae (each n = 1)) were included in the present study, 28 from Austria and 8 from Serbia. Isolates were characterized by a polyphasic approach including susceptibility pheno- and genotyping and microarray-based assays. Escherichia (E.) coli isolates were additionally characterized by two-locus (fumC and fimH) sequence phylotyping and multi-locus sequence typing (MLST) of selected isolates. MLST of carbapenem-resistant Enterobacter cloacae isolates was also performed. Among E. coli, the most dominant phylogenetic group was B1 (27.8%), followed by C, (16.6%), A and Clade II (5.5% each), B2 and F (2.77% each). The most predominant β-lactam resistance genes were blaTEM (70%) and blaCTX-M (38.8%), blaCMY (25%). blaNDM was detected in one carbapenem-resistant Enterobacter cloacae ST114. The most common ST among selected E. coli was 744 (10.7% isolates). The pandemic clones ST131 and ST648 carrying CTX-M-15 were also detected. Remaining STs belonged to 469, 1287, 1463 and 1642. E. coli clonotyping revealed 20 CH types. Based on the presence of certain virulence genes, three isolates were categorized as ExPEC/UPEC. The most prevalent virulence factors were fimH detected in 61%, iucD and iss both in 55%, iroN in 27.8%, papC in 13.8% and sat in 8.3% isolates.

Microbiome analysis of healthy and diseased sponges Lubomirskia baicalensis by using cell cultures of primmorphs

Endemic sponges (Demosponges, Lubomirskiidae) dominate the fauna of the littoral zone of Lake Baikal. These freshwater sponges live in symbiosis with diverse eukaryotes and prokaryotes, including chlorophyll-containing microalgae. Within the last 5 years, the incidence of sponge disease and mortality events in Lake Baikal has increased. The etiology and ecology of these events remain unknown, in part because of the lack of models to study sponge-microbe interactions. In this work, we tested the use of primmorph cell cultures of Lubomirskia baicalensis as a tool for investigating the microbiomes of sponges. We infected primmorphs, cultured in vitro, with samples from diseased sponges and observed, by microscopy, disease symptoms, including loss of green symbionts, associated with mass die-off events. Subsequent sequencing of 16S rRNA gene fragments revealed that the microbiome community of healthy sponge and primmorphs formed a group separate from the community of diseased sponges and infected primmorphs. This confirms the suitability of the primmorph cell culture as a model sponge system. We also discovered mass mortality of green symbionts (Chlorophyta) was associated with a shift in the microbial communities of sponges/primmorphs. Microbes in diseased sponges, and infected primmorphs, belonged mainly to the phyla Bacteroidetes and Proteobacteria and these families Flavobacteriaceae, Burkholderiaceae, and Moraxellaceae. Primmorphs cell culture may provide a model to study interactions between these bacteria and their host and elucidate the cause of mass mortality events.

Mucosal microbial parasites/symbionts in health and disease: an integrative overview

Microbial parasites adapted to thrive at mammalian mucosal surfaces have evolved multiple times from phylogenetically distant lineages into various extracellular and intracellular life styles. Their symbiotic relationships can range from commensalism to parasitism and more recently some host-parasites interactions are thought to have evolved into mutualistic associations too. It is increasingly appreciated that this diversity of symbiotic outcomes is the product of a complex network of parasites-microbiota-host interactions. Refinement and broader use of DNA based detection techniques are providing increasing evidence of how common some mucosal microbial parasites are and their host range, with some species being able to swap hosts, including from farm and pet animals to humans. A selection of examples will illustrate the zoonotic potential for a number of microbial parasites and how some species can be either disruptive or beneficial nodes in the complex networks of host-microbe interactions disrupting or maintaining mucosal homoeostasis. It will be argued that mucosal microbial parasitic diversity will represent an important resource to help us dissect through comparative studies the role of host-microbe interactions in both human health and disease.

Factors Obscuring the Role of E. coli from Domestic Animals in the Global Antimicrobial Resistance Crisis: An Evidence-Based Review

Recent studies have found limited associations between antimicrobial resistance (AMR) in domestic animals (and animal products), and AMR in human clinical settings. These studies have primarily used Escherichia coli, a critically important bacterial species associated with significant human morbidity and mortality. E. coli is found in domestic animals and the environment, and it can be easily transmitted between these compartments. Additionally, the World Health Organization has highlighted E. coli as a "highly relevant and representative indicator of the magnitude and the leading edge of the global antimicrobial resistance (AMR) problem". In this paper, we discuss the weaknesses of current research that aims to link E. coli from domestic animals to the current AMR crisis in humans. Fundamental gaps remain in our understanding the complexities of E. coli population genetics and the magnitude of phenomena such as horizontal gene transfer (HGT) or DNA rearrangements (transposition and recombination). The dynamic and intricate interplay between bacterial clones, plasmids, transposons, and genes likely blur the evidence of AMR transmission from E. coli in domestic animals to human microbiota and vice versa. We describe key factors that are frequently neglected when carrying out studies of AMR sources and transmission dynamics.

Horizontal transfer of antibiotic resistance genes in the human gut microbiome

Infections caused by antibiotic-resistant bacteria are a major threat to public health. The pathogens causing these infections can acquire antibiotic resistance genes in a process termed horizontal gene transfer (HGT). HGT is a common event in the human gut microbiome, that is, the microbial ecosystem of the human intestinal tract. HGT in the gut microbiome can occur via different mechanisms of which transduction and conjugation have been best characterised. Novel bioinformatic tools and experimental approaches have been developed to determine the association of antibiotic resistance genes with their microbial hosts and to quantify the extent of HGT in the gut microbiome. Insights from studies into HGT in the gut microbiome may lead to the development of novel interventions to minimise the spread of antibiotic resistance genes among commensals and opportunistic pathogens.

Interplay of Human Gut Microbiome in Health and Wellness

The gut microbiome analysis, with specific interest on their direct impact towards the human health, is currently revolutionizing the unexplored frontiers of the pathogenesis and wellness. Although in-depth investigations of gut microbiome, 'the Black Boxes', complexities and functionalities are yet at its infancy, profound evidences are being reported for their concurrent involvement in disease etiology and its treatment. Interestingly, studies from the 'minimal murine' (Oligo-MM12), 'humanized' microbiota gnotobiotic mice models and patient samples, combined with multi-omics and cell biology approaches, have been revealing the implications of these findings in the treatment of gut dysbiosis associated diseases. Nonetheless, due to the inherent heterogeneity of the gut commensals and their unified co-existence with opportunistic pathobionts, it is utmost essential to highlight their functionalities in 'good or bad' gut in human wellness. We have specifically reviewed dietary lifestyle and infectious diseases linked with the gut bacterial consortia to delineate the ecobiotic approaches towards their treatment. This notably includes gut mucosal immunity mediated diseases such as Tuberculosis, IBD, CDI, Type 2 Diabetes, etc. Alongside of each dysbiosis, we have described the current therapeutic advancements of the pre- and probiotics derived from human microbiome studies to restore gut microbial homeostasis. With a continuous running debate on the role of microbiota in above mentioned diseases, we have collected numerous scientific evidences highlighting a previously unanticipated complex involvement of gut microbiome in the potential of human health.

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering

Knowledge about the difference in the global distribution of pathogens and non-pathogens is limited. Here, we investigate it using a multi-sample metagenomics phylogeny approach based on short-read metagenomic sequencing of sewage from 79 sites around the world. For each metagenomic sample, bacterial template genomes were identified in a non-redundant database of whole genome sequences. Reads were mapped to the templates identified in each sample. Phylogenetic trees were constructed for each template identified in multiple samples. The countries from which the samples were taken were grouped according to different definitions of world regions. For each tree, the tendency for regional clustering was determined. Phylogenetic trees representing 95 unique bacterial templates were created covering 4 to 71 samples. Varying degrees of regional clustering could be observed. The clustering was most pronounced for environmental bacterial species and human commensals, and less for colonizing opportunistic pathogens, opportunistic pathogens and pathogens. No pattern of significant difference in clustering between any of the organism classifications and country groupings according to income were observed. Our study suggests that while the same bacterial species might be found globally, there is a geographical regional selection or barrier to spread for individual clones of environmental and human commensal bacteria, whereas this is to a lesser degree the case for strains and clones of human pathogens and opportunistic pathogens.

Challenges in the Diagnosis and Management of Bacterial Lung Infections in Solid Organ Recipients: A Narrative Review

Respiratory infections pose a significant threat to the success of solid organ transplantation, and the diagnosis and management of these infections are challenging. The current narrative review addressed some of these challenges, based on evidence from the literature published in the last 20 years. Specifically, we focused our attention on (i) the obstacles to an etiologic diagnosis of respiratory infections among solid organ transplant recipients, (ii) the management of bacterial respiratory infections in an era characterized by increased antimicrobial resistance, and (iii) the development of antimicrobial stewardship programs dedicated to solid organ transplant recipients.