Enterobacter aerogenes and Enterobacter cloacae; versatile bacterial pathogens confronting antibiotic treatment

Bacterial and Protozoan Lipoxygenases Could be Involved in Cell-to-Cell Signaling and Immune Response Suppression

Lipoxygenases are found in animals, plants, and fungi, where they are involved in a wide range of cell-to-cell signaling processes. The presence of lipoxygenases in a number of bacteria and protozoa has been also established, but their biological significance remains poorly understood. Several hypothetical functions of lipoxygenases in bacteria and protozoa have been suggested without experimental validation. The objective of our study was evaluating the functions of bacterial and protozoan lipoxygenases by evolutionary and taxonomic analysis using bioinformatics tools. Lipoxygenase sequences were identified and examined using BLAST, followed by analysis of constructed phylogenetic trees and networks. Our results support the theory on the involvement of lipoxygenases in the formation of multicellular structures by microorganisms and their possible evolutionary significance in the emergence of multicellularity. Furthermore, we observed association of lipoxygenases with the suppression of host immune response by parasitic and symbiotic bacteria including dangerous opportunistic pathogens.

Subdural Empyema by Enterobacter cloacae: Case Report

Infections of the central nervous system are a medical emergency, potentially lethal and associated with increased morbidity and mortality. We present the case of a male with risk factors and clinical deterioration, in which the brain computed tomography scan showed a subdural collection following a head injury, which underwent surgical evacuation revealing a subdural empyema. The culture of the subdural collection yielded a positive result to Enterobacter cloacae.

Synthesis of substituted N-(2'-nitrophenyl)pyrrolidine-2-carboxamides towards the design of proline-rich antimicrobial peptide mimics to eliminate bacterial resistance to antibiotics

The treatment of diseases is under threat due to the increasing resistance of disease-causing bacteria to antibiotics. Likewise, free radical-induced oxidative stress has been implicated in several human disease conditions, such as cancer, stroke and diabetes. In the search for amino acid analogues with antibacterial and antioxidant properties as possible mimics of antimicrobial peptides, substituted N-(2'-nitrophenyl)pyrrolidine-2-carboxamides 4a-4k and N-(2'-nitrophenyl)piperidine-2-carboxamides 4l-4n have been synthesized via a two-step, one-pot amidation of the corresponding acids, using thionyl chloride with different amines in dichloromethane. The carboxamides were characterized by infrared and nuclear magnetic resonance spectroscopy, mass spectrometry and elemental analysis. Carboxamides 4a-4n were assayed against five Gram-positive and five Gram-negative bacterial strains using the broth micro-dilution procedure and compared to standard antibiotic drugs (streptomycin and nalidixic acid). 4b showed the highest antibacterial activity with a minimum inhibitory concentration (MIC) value of 15.6 µg/mL against Staphylococcus aureus. Pertinently, 4b and 4k are promising candidates for narrow-spectrum (Gram-positive) and broad-spectrum antibiotics, respectively. The antioxidant properties of the carboxamides were also evaluated using the 1,1-diphenyl-2-picryl hydrazyl (DPPH) radical and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) radical cation. 4a and 4k recorded the lowest IC₅₀ values of 1.22 × 10^-3 mg/mL (with DPPH) and 1.45 × 10^-4 mg/mL (with ABTS), respectively. Notably, 4k recorded about 2.5 times better antioxidant capacity than the positive controls - ascorbic acid and butylated hydroxyanisole. These results bode well for N-aryl carboxamides as good mimics and substitutes for antimicrobial peptides towards mitigating bacterial resistance to antibiotics as well as ameliorating oxidative stress-related diseases.

Bacteriophage Infections of Biofilms of Health Care-Associated Pathogens: Klebsiella pneumoniae

Members of the family Enterobacteriaceae, such as Klebsiella pneumoniae, are considered both serious and urgent public health threats. Biofilms formed by these health care-associated pathogens can lead to negative and costly health outcomes. The global spread of antibiotic resistance, coupled with increased tolerance to antimicrobial treatments in biofilm-associated bacteria, highlights the need for novel strategies to overcome treatment hurdles. Bacteriophages (phages), or viruses that infect bacteria, have reemerged as one such potential strategy. Virulent phages are capable of infecting and killing their bacterial hosts, in some cases producing depolymerases that are able to hydrolyze biofilms. Phage therapy does have its limitations, however, including potential narrow host ranges, development of bacterial resistance to infection, and the potential spread of phage-encoded virulence genes. That being said, advances in phage isolation, screening, and genome sequencing tools provide an upside in overcoming some of these limitations and open up the possibilities of using phages as effective biofilm control agents.

β-Lactamase triggered visual detection of bacteria using cephalosporin functionalized biomaterials

We report the conjugation of a chromogenic cephalosporin β-lactamase (βL) substrate to polymers and integration into biomaterials for facile, visual βL detection. Identification of these bacterial enzymes, which are a leading cause of antibiotic resistance, is critical in the treatment of infectious diseases. The βL substrate polymer conjugate undergoes a clear to deep yellow color change upon incubation with common pathogenic Gram-positive and Gram-negative bacteria species. We have demonstrated the feasibility of formulating hydrogels with the βL substrate covalently tethered to a poly(ethylene glycol) (PEG) polymer matrix, exhibiting a visible color change in the presence of βLs. This approach has the potential to be used in diagnostic biomaterials for point-of-care detection of βL-producing bacteria, helping combat the spread of drug resistant microbes.

The Great ESKAPE: Exploring the Crossroads of Bile and Antibiotic Resistance in Bacterial Pathogens

Throughout the course of infection, many pathogens encounter bactericidal conditions that threaten the viability of the bacteria and impede the establishment of infection. Bile is one of the most innately bactericidal compounds present in humans, functioning to reduce the bacterial burden in the gastrointestinal tract while also aiding in digestion. It is becoming increasingly apparent that pathogens successfully resist the bactericidal conditions of bile, including bacteria that do not normally cause gastrointestinal infections. This review highlights the ability of Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, Enterobacter (ESKAPE), and other enteric pathogens to resist bile and how these interactions can impact the sensitivity of bacteria to various antimicrobial agents. Given that pathogen exposure to bile is an essential component to gastrointestinal transit that cannot be avoided, understanding how bile resistance mechanisms align with antimicrobial resistance is vital to our ability to develop new, successful therapeutics in an age of widespread and increasing antimicrobial resistance.

Characterization of a New Transposon, Tn6696, on a bla NDM- 1-Carrying Plasmid From Multidrug-Resistant Enterobacter cloacae ssp. dissolvens in China

Background

Enterobacter cloacae is an opportunistic pathogen which is responsible for serious nosocomial infections. A gene which plays an important role in resistance to carbapenems is the New Delhi metallo-β-lactamase 1 (NDM-1). Currently, the spread of NDM-1-producing E. cloacae strains is a serious public threat.

Methods

A multidrug-resistant E. cloacae ssp. dissolvens strain CBG15936 was recovered in 2017 in Guangzhou, China. PCR, S1-pulsed-field gel electrophoresis, and Southern blotting were performed to locate the bla_NDM–1 gene. Susceptibility testing and conjugation experiments were also performed. Illumina HiSeq and Nanopore sequencers were used to perform whole-genome sequencing.

Results

Strain CBG15936 belongs to ST932 and is resistant to carbapenems. The bla_NDM–1 gene was found on a ∼62-kb plasmid, which has a conjugation frequency of 1.68 × 10^–3 events per donor cell. Genome sequencing and analysis revealed that the NDM-1-carrying IncN1 plasmid contained a new transposon Tn6696, which consists of an intact qnrS1-carrying Tn6292 element, an inverted 8.3-kb Tn3000 remnant, ISkpn19, ΔtnpA, and IS26.

Conclusion

A new transposon, Tn6696, has been detected on a bla_NDM–1-carrying plasmid recovered from multidrug-resistant E. cloacae ssp. dissolvens CBG15936 from China. This finding provides a new perspective regarding the potential for bla_NDM–1 to undergo horizontal transfer among drug-resistant bacteria.

Green Synthesis of Silver Nanoparticles Using Artocarpus hirsutus Seed Extract and its Antibacterial Activity

Aims:

To evaluate the antibacterial activity of Artocarpus hirsutus mediated seed extract for nanoparticle synthesis.

Background:

Gastrointestinal bacteria are known for causing deadly infections in humans. They also possess multi-drug resistance and interfere with clinical treatments. Applied nanotechnology has been known to combat such infectious agents with little interference from their special attributes. Here we synthesize silver nanoparticles from Artocarpus hirsutus seed extract against two gastro-intestinal bacterial species: Enterobacter aerogenes and Listeria monocytogenes.

Objective:

To collect, dry, and process seeds of Artocarpus hirsutus for nanoparticle synthesis. To evaluate the morphological interaction of silver nanoparticles with bacteria.

Methods:

Artocarpus hirsutus seeds were collected and processed and further silver nanoparticles were synthesized by the co-precipitation method. The synthesized nanoparticles were characterized using XRD, UV, FTIR, and SEM. These nanoparticles were employed to study the antibacterial activity of nanoparticles against Enterobacter aerogenes and Listeria monocytogenes using well diffusion method. Further, morphological interaction of silver nanoparticles on bacteria was studied using SEM.

Result:

Silver nanoparticles were synthesized using Artocarpus hirsutus seed extract and characterization studies confirmed that silver nanoparticles were spherical in shape with 25-40 nm size. Antibacterial study exhibited better activity against Enterobacter aerogenes with a maximum zone of inhibition than on Listeria monocytogenes. SEM micrographs indicated that Enterobacter aerogenes bacteria were more susceptible to silver nanoparticles due to the absence of cell wall. Also, the size and charge of silver nanoparticles enable easy penetration of the bacterial cell wall.

Conclusion:

In this study, silver nanoparticles were synthesized using the seed extract of Artocarpus hirsutus for the first time exploiting the fact that Moraceae species have high phytonutrient content which aided in nanoparticle synthesis. This nanoparticle can be employed for large scale synthesis which when coupled with the pharmaceutical industry can be used to overcome the problems associated with conventional antibiotics to treat gastrointestinal bacteria.

Influence of Intratumor Microbiome on Clinical Outcome and Immune Processes in Prostate Cancer

Simple Summary

While the intratumor microbiome has been largely unexplored in relation to prostate cancer development, our research shows that microbes may play an anti-tumor or pro-tumor role to significantly alter clinical course in prostate cancer patients. We found that the presence and absence of specific microbes are strongly correlated with known biomarkers of prostate cancer, including increased androgen receptor expression, prostate-specific antigen level, immune-associated gene dysregulation, stem-cell related gene overexpression, cancer pathways, and known chromosomal alterations. Our results provide important insight on potential mechanisms by which intratumor microbes may greatly contribute to prostate cancer progression and prognosis. We hope our results can be validated in future studies, and the key microbes that we identified can be used as effective targets for more specialized prebiotic and probiotic treatments for prostate cancer.

Abstract

Although 1 in 9 American men will receive a diagnosis of prostate cancer (PC), most men with this diagnosis will not die from it, as most PCs are indolent. However, there is a subset of patients in which the once-indolent PC becomes metastatic and eventually, fatal. In this study, we analyzed microbial compositions of intratumor bacteria in PC to determine the influence of the microbiome on metastatic growth. Using large-scale RNA-sequencing data and corresponding clinical data, we correlated the abundance of microbes to immune pathways and PC risk factors, identifying specific microbes that either significantly deter or contribute to cancer aggressiveness. Interestingly, most of the microbes we found appeared to play anti-tumor roles in PC. Since these anti-tumor microbes were overrepresented in tumor samples, we believe that microbes thrive in the tumor microenvironment, outcompete cancer cells, and directly mitigate tumor growth by recruiting immune cells. These include Listeria monocytogenes, Methylobacterium radiotolerans JCM 2831, Xanthomonas albilineans GPE PC73, and Bradyrhizobium japonicum, which are negatively correlated with Gleason score, Tumor-Node-Metastasis (TNM) stage, prostate-specific antigen (PSA) level, and Androgen Receptor (AR) expression, respectively. We also identified microbes that contribute to tumor growth and are positively correlated with genomic alterations, dysregulated immune-associated (IA) genes, and prostate cancer stem cells (PCSC) genes.

Microbiological quality of kitchens sponges used in university student dormitories

Background

Kitchen sponges are a major source of cross-contamination as they can transfer foodborne pathogens, infectious agents and spoilage causing microorganisms to food contact surfaces. Several studies have revealed that university students adopt poor practices regarding food safety, hygiene, and the handling of kitchen cleaning equipment.

Methods

A total of fifty kitchen sponges were collected along with a questionnaire addressing social demographics and kitchen sponge usage by students living at the University of Sharjah dormitories. The effect of storage (3 and 10 days) on the microbial population of kitchen sponges at room temperature (21 °C) was assessed. Enterobacteriaceae isolated from sponges were identified and their antibiotic resistance determined.

Results

Student responses revealed that kitchen sponges used to clean food contact surfaces were also used to clean the oven (32%), sink (26%), refrigerator (10%), and to clean spills on the floor (4%). Kitchen sponges contained high counts of mesophilic aerobic bacteria (7.9 log₁₀/cm³), coliform (7.2 log₁₀/cm³), Enterobacteriaceae (7.3 log₁₀/cm³) and yeasts and molds (7.0 log₁₀/cm³). After storage of the sponges at room temperature (21 °C) for 3 and 10 days, the number of mesophilic aerobic bacteria, coliform, Enterobacteriaceae and yeasts and molds decreased by 0.4 and 1.3 log₁₀/cm³, 0.7 and 1.4 log₁₀/cm³, 0.4 and 1.1 log₁₀/cm³, and 0.6 and 1.3 log₁₀/cm³, respectively. The most frequently isolated Enterobacteriaceae were Enterobacter cloacae (56%) and Klebsiella oxytoca (16%). All E. cloacae isolates were resistant to amoxicillin, cefalotin, cefoxitin and cefuroxime axetil.

Conclusions

This study showed that students living in dormitories lacked good hygienic practices and were at increased risk of food poisoning. Kitchen sponges were highly contaminated with potentially pathogenic bacteria which could be transferred from the general kitchen environment to food contact surfaces and consequently lead to food contamination.

Venom peptides in association with standard drugs: a novel strategy for combating antibiotic resistance - an overview

Development of antibiotic resistance that leads to resurgence of bacterial infections poses a threat to disease-free existence for humankind and is a challenge for the welfare of the society at large. Despite research efforts directed towards treatment of pathogens, antibiotics within new improved classes have not emerged for years, a fact largely attributable to the pharmacological necessities compelling drug development. Recent reversion to the use of natural products alone or in combination with standard drugs has opened up new vistas for alternative therapeutics. The success of this strategy is evident in the sudden interest in plant extracts as additives/synergists for treatment of maladies caused by drug-resistant bacterial strains. Animal venoms have long fascinated scientists as sources of pharmacologically active components that can be exploited for the treatment of specific ailments and should be promoted further to clinical trials. In the present review, we outline the scope and possible methods for the applications of animal venoms in combination with commercial antibiotics to offer a better treatment approach against antibiotic-resistant infections.

Newly Named Klebsiella aerogenes (formerly Enterobacter aerogenes) Is Associated with Poor Clinical Outcomes Relative to Other Enterobacter Species in Patients with Bloodstream Infection

Enterobacter aerogenes was recently renamed Klebsiella aerogenes This study aimed to identify differences in clinical characteristics, outcomes, and bacterial genetics among patients with K. aerogenes versus Enterobacter species bloodstream infections (BSI). We prospectively enrolled patients with K. aerogenes or Enterobacter cloacae complex (Ecc) BSI from 2002 to 2015. We performed whole-genome sequencing (WGS) and pan-genome analysis on all bacteria. Overall, 150 patients with K. aerogenes (46/150 [31%]) or Ecc (104/150 [69%]) BSI were enrolled. The two groups had similar baseline characteristics. Neither total in-hospital mortality (13/46 [28%] versus 22/104 [21%]; P = 0.3) nor attributable in-hospital mortality (9/46 [20%] versus 13/104 [12%]; P = 0.3) differed between patients with K. aerogenes versus Ecc BSI, respectively. However, poor clinical outcome (death before discharge, recurrent BSI, and/or BSI complication) was higher for K. aerogenes than Ecc BSI (32/46 [70%] versus 42/104 [40%]; P = 0.001). In a multivariable regression model, K. aerogenes BSI, relative to Ecc BSI, was predictive of poor clinical outcome (odds ratio 3.3; 95% confidence interval 1.4 to 8.1; P = 0.008). Pan-genome analysis revealed 983 genes in 323 genomic islands unique to K. aerogenes isolates, including putative virulence genes involved in iron acquisition (n = 67), fimbriae/pili/flagella production (n = 117), and metal homeostasis (n = 34). Antibiotic resistance was largely found in Ecc lineage 1, which had a higher rate of multidrug resistant phenotype (23/54 [43%]) relative to all other bacterial isolates (23/96 [24%]; P = 0.03). K. aerogenes BSI was associated with poor clinical outcomes relative to Ecc BSI. Putative virulence factors in K. aerogenes may account for these differences.

Prevalence of Aminoglycoside Resistance Genes and Molecular Characterization of a Novel Gene, aac(3)-IIg, among Clinical Isolates of the Enterobacter cloacae Complex from a Chinese Teaching Hospital

Members of the Enterobacter cloacae complex are important opportunistic human pathogens capable of causing a wide variety of infections. During recent decades, aminoglycoside-resistant E. cloacae complex isolates have increasingly been reported and have become a major concern. Here, we employed high-throughput sequencing in combination with specific PCR assays to investigate the prevalence of aminoglycoside resistance genes among 170 isolates of the E. cloacae complex collected from a teaching hospital in Wenzhou, China. A total of 12 known genes [aphA-1, strA, strB, aac(6')-IIc, aadA2, aac(3)-IId, aadB, aadA1, rmtB, armA, aadA5, and aac(6')-Ie-aph(2'')-Ia] and 1 novel gene [aac(3)-IIg] were identified, with aphA-1 (71.18%), strA (55.29%), and strB (52.35%) being the most prevalent, and aac(3)-IIg was detected with a positive rate of 21.76% (37/170). The aac(3)-IIg gene was 810 bp in length and encoded a protein that shared 72 to 78% identities with previously known AAC(3)-II aminoglycoside 3-N-acetyltransferases. The MICs of gentamicin and tobramycin were 512 μg/ml and 64 μg/ml, respectively, when aac(3)-IIg was cloned into Escherichia coli DH5α. All aac(3)-IIg-positive isolates exerted broad aminoglycoside resistance profiles, mediated by the coexistence of multiple resistance genes. Moreover, aminoglycoside resistance and resistance genes were found to be transferable in most strains (24/37). Nevertheless, pulsed-field gel electrophoresis (PFGE) and dendrogram analysis showed clonal diversity among these isolates. S1 nuclease PFGE, Southern hybridization, and whole-genome sequencing indicated that aac(3)-IIg was located on transferable as well as nontransferable plasmids of various sizes. The analysis of the genetic environment suggested that aac(3)-IIg is embedded within a class 1 integron, with IS26 playing an important role in its mobility.

In Vitro Pharmacodynamics of Fosfomycin against Carbapenem-Resistant Enterobacter cloacae and Klebsiella aerogenes

The increase of carbapenem-resistant Enterobacterales (CRE) and lack of therapeutic options due to the scarcity of new antibiotics has sparked interest toward the use of intravenous fosfomycin against systemic CRE infections. We aimed to investigate the in vitro pharmacodynamics of fosfomycin against carbapenem-resistant Enterobacter cloacae and Klebsiella aerogenes Time-kill studies and population analysis profiles were performed with eight clinical CRE isolates, which were exposed to fosfomycin concentrations ranging from 0.25 to 2,048 mg/liter. The 24-h mean killing effect was characterized by an inhibitory sigmoid maximum effect (E _max) model. Whole-genome sequencing was performed to elucidate known fosfomycin resistance mechanisms. Fosfomycin MICs ranged from 0.5 to 64 mg/liter. The isolates harbored a variety of carbapenemase genes including bla _IMP, bla _KPC, and bla _NDM Five out of eight isolates harbored the fosA gene, while none harbored the recently discovered fosL-like gene. Heteroresistant subpopulations were detected in all isolates, with two out of eight isolates harboring heteroresistant subpopulations at up to 2,048 mg/liter. In time-kill studies, fosfomycin exhibited bactericidal activity at 2 to 4 h at several fosfomycin concentrations (one isolate at ≥16 mg/liter, two at ≥32 mg/liter, two at ≥64 mg/liter, two at ≥128 mg/liter, and one at ≥512 mg/liter). At 24 h, bactericidal activity was only observed in two isolates (MICs, 0.5 and 4 mg/liter) at 2,048 mg/liter. From the E _max model, no significant bacterial killing was observed beyond 500 mg/liter. Our findings suggest that the use of fosfomycin monotherapy may be limited against CRE due to heteroresistance and rapid bacterial regrowth. Further optimization of intravenous fosfomycin dosing regimens is required to increase efficacy against such infections.

Evaluation of the Microbiological Profile of Alveolar Residual Screws and Cleft-Adjacent Teeth in Individuals With Complete Unilateral Fissures

OBJECTIVE

To evaluate the microbiota profile of residual alveolar slits and teeth adjacent to the cleft in fissured individuals.

DESIGNS

This study used a cross-sectional design.

PARTICIPANTS

Twenty individuals, aged 14 to 24 years, who had a residual fissure in the maxillary alveolar ridge region were selected.

MAIN OUTCOME MEASURES

Three sites per individual were selected for microbiological collection (the site of the residual cleft and the 2 nearest teeth). The samples were analyzed using the Checkerboard DNA-DNA hybridization technique for 73 species of bacteria.

RESULTS

All the species analyzed were found in the 2 niches (slits and teeth). The bacterial species present in the largest number in the residual cracks were Prevotella melaninogenica, Prevotella nigrescens, and Streptococcus mitis. With regard to the bacterial profiles in the mesial and distal faces, the most prevalent species were P nigrescens, Veillonella parvula, and Fusobacterium nucleatum sp vicentii. The analysis of all the collected samples demonstrated very similar profiles for the mesial and distal faces, with these 2 sites even presenting the same species in greater frequencies. Higher counts of 20 bacterial species (Wilcoxon test) were observed in the dental niche, in relation to the fissure, particularly, P nigrescens, V parvula, F nucleatum sp vicentii, and Neisseria mucosa.

CONCLUSION

Some species were significantly more prevalent in the residual alveolar fissures and in adjacent teeth. The comparison between the profiles of the 2 niches demonstrated large differences in the most frequent species in the teeth, and no qualitative differences with regard to specific pathogens.

Microbiota oral e retal de calitriquídeos (Callithrix sp.) em área antropizada de Mata Atlântica, Rio de Janeiro, Brasil

RESUMO A proximidade dos primatas não humanos (PNH) com o ser humano pode ser considerada um fator de risco para transmissão de bactérias entre essas duas populações. Neste estudo, foi investigada a microbiota anfibiôntica aeróbica oral e retal de calitriquídeos em um fragmento de Mata Atlântica localizado no Rio de Janeiro, Brasil, e foram realizados testes fenotípicos para detecção de bactérias multirresistentes nos isolados encontrados. Foram capturados 14 calitriquídeos e coletadas 21 amostras (14 de cavidade oral e sete de cavidade retal) em dois pontos da mata próximos às habitações humanas. As espécies mais frequentes, na cavidade oral, foram Klebsiella oxytoca (50,0%), K. pneumoniae (28,6%), Kluyvera ascorbata (21,4%) e Stenotrophomonas maltophilia (21,4%) e, na cavidade retal, K. pneumoniae (85,7%), Escherichia coli (28,6%) e Enterobacter spp. (42,9%). Todos os 48 isolados da família Enterobacteriaceae foram negativos para ESBL (betalactamase de espectro ampliado), mostrando-se não produtores da enzima nos dois métodos utilizados: disco-aproximação e método de detecção automatizado. Na pesquisa de ERC (enterobactérias resistentes a carbapenêmicos), esses mesmos isolados não apresentaram resistência aos antibióticos imipenem, meropenem e ertapenem. Todas as bactérias isoladas apresentam um potencial zoonótico, o que representa um risco à saúde pública e à conservação das espécies.

Isolation and characterization of an acid and metal tolerant Enterobacter cloacae NZS strain from former mining lake in Selangor, Malaysia

Background

Metal polluted environments have been found to harbor acid and metal tolerant bacterial communities. Metal oxidizing bacteria in particular are industrially important microorganisms that can be utilized for potential applications in biomining and bioremediation. However, some well-characterized strains are not readily culturable as they are obligate and fastidious chemolithotrophs requiring special techniques for their cultivation. Hence, this study was aimed at isolating, identifying, and characterizing indigenous metal tolerant heterotroph(s) from abandoned mines that can potentially be used for biomining or bioremediation processes in the future.

Results

Seventeen bacteria from former mining lakes were isolated and identified using 16S rRNA. Minimal inhibition concentration (MIC) and growth study of isolated bacteria carried out in Luria-Bertani media containing three different metals ions, zinc (II), copper (II), and iron (II), showed that a particular isolate termed Enterobacter cloacae NZS was found to exhibit better growth and tolerance for copper (up to 90 mM), zinc (up to 200 mM), and iron (up to 170 mM). Growth of the strain was notably well in the presence of iron (II). Compared to all the isolates, only E. cloacae NZS was able to be enumerated at pH lower than 5 while other strains were culturable only at pH 7. Its capability in iron (II) oxidation was preliminary assessed based on the pH, cell count, glucose consumption, and amount of iron oxidized throughout incubation in 9K media. E. cloacae NZS strain was found to be capable of oxidizing iron (II) supplied in 9K media to iron (III).

Conclusion

As preliminary investigation showed that E. cloacae NZS was able to oxidize iron (II) in 9K media at pH2, further optimization on the strain, medium, and culture conditions in future may be able to provide a better insight on this strain to be possibly used as an iron oxidizer for various applications.

Antimicrobial Resistance in ESKAPE Pathogens

Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.

Antimicrobial Resistance in ESKAPE Pathogens

Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.

Microbial Interaction Network Estimation via Bias-Corrected Graphical Lasso

With the increasing availability of microbiome 16S data, network estimation has become a useful approach to studying the interactions between microbial taxa. Network estimation on a set of variables is frequently explored using graphical models, in which the relationship between two variables is modeled via their conditional dependency given the other variables. Various methods for sparse inverse covariance estimation have been proposed to estimate graphical models in the high-dimensional setting, including graphical lasso. However, current methods do not address the compositional count nature of microbiome data, where abundances of microbial taxa are not directly measured, but are reflected by the observed counts in an error-prone manner. Adding to the challenge is that the sum of the counts within each sample, termed “sequencing depth,” is an experimental technicality that carries no biological information but can vary drastically across samples. To address these issues, we develop a new approach to network estimation, called BC-GLASSO (bias-corrected graphical lasso), which models the microbiome data using a logistic normal multinomial distribution with the sequencing depths explicitly incorporated, corrects the bias of the naive empirical covariance estimator arising from the heterogeneity in sequencing depths, and builds the inverse covariance estimator via graphical lasso. We demonstrate the advantage of BC-GLASSO over current approaches to microbial interaction network estimation under a variety of simulation scenarios. We also illustrate the efficacy of our method in an application to a human microbiome data set.

High Levels of Oxidative Stress Create a Microenvironment That Significantly Decreases the Diversity of the Microbiota in Diabetic Chronic Wounds and Promotes Biofilm Formation

Diabetics chronic wounds are characterized by high levels of oxidative stress (OS) and are often colonized by biofilm-forming bacteria that severely compromise healing and can result in amputation. However, little is known about the role of skin microbiota in wound healing and chronic wound development. We hypothesized that high OS levels lead to chronic wound development by promoting the colonization of biofilm-forming bacteria over commensal/beneficial bacteria. To test this hypothesis, we used our db/db^−/− mouse model for chronic wounds where pathogenic biofilms develop naturally after induction of high OS immediately after wounding. We sequenced the bacterial rRNA internal transcribed spacer (ITS) gene of the wound microbiota from wound initiation to fully developed chronic wounds. Indicator species analysis, which considers a species' fidelity and specificity, was used to determine which bacterial species were strongly associated with healing wounds or chronic wounds. We found that healing wounds were colonized by a diverse and dynamic bacterial microbiome that never developed biofilms even though biofilm-forming bacteria were present. Several clinically relevant species that are present in human chronic wounds, such as Cutibacterium acnes, Achromobacter sp., Delftia sp., and Escherichia coli, were highly associated with healing wounds. These bacteria may serve as bioindicators of healing and may actively participate in the processes of wound healing and preventing pathogenic bacteria from colonizing the wound. In contrast, chronic wounds, which had high levels of OS, had low bacterial diversity and were colonized by several clinically relevant, biofilm-forming bacteria such as Pseudomonas aeruginosa, Enterobacter cloacae, Corynebacterium frankenforstense, and Acinetobacter sp. We observed unique population trends: for example, P. aeruginosa associated with aggressive biofilm development, whereas Staphylococcus xylosus was only present early after injury. These findings show that high levels of OS in the wound significantly altered the bacterial wound microbiome, decreasing diversity and promoting the colonization of bacteria from the skin microbiota to form biofilm. In conclusion, bacteria associated with non-chronic or chronic wounds could function as bioindicators of healing or non-healing (chronicity), respectively. Moreover, a better understanding of bacterial interactions between pathogenic and beneficial bacteria within an evolving chronic wound microbiota may lead to better solutions for chronic wound management.

Systematic Review and Meta-Analysis of the Occurrence of ESKAPE Bacteria Group in Dogs, and the Related Zoonotic Risk in Animal-Assisted Therapy, and in Animal-Assisted Activity in the Health Context

Animal-assisted interventions are widely implemented in different contexts worldwide. Particularly, animal-assisted therapies and animal-assisted activities are often implemented in hospitals, rehabilitation centers, and other health facilities. These interventions bring several benefits to patients but can also expose them to the risk of infection with potentially zoonotic agents. The dog is the main animal species involved used in these interventions. Therefore, we aimed at collecting data regarding the occurrence of the pathogens ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) in dogs, in order to draft guidelines concerning the possible monitoring of dogs involved in animal-assisted therapies and animal-assisted activities in healthcare facilities. We performed a literature search using the PRISMA guidelines to examine three databases: PubMed, Web of Science, and Scopus. Out of 2604 records found, 52 papers were identified as eligible for inclusion in the review/meta-analysis. Sixteen papers reported data on E. faecium; 16 on S. aureus; nine on K. pneumoniae; four on A. baumannii; eight on P. aeruginosa; and six on Enterobacter spp. This work will contribute to increased awareness to the potential zoonotic risks posed by the involvement of dogs in animal-assisted therapies, and animal-assisted activities in healthcare facilities.

Spread of chloramphenicol and tetracycline resistance genes by plasmid mobilization in agricultural soil

Spread of antibiotic resistance genes (ARGs) poses a worldwide threat to public health and food safety. However, ARG spread by plasmid mobilization, a broad host range transfer system, in agricultural soil has received little attention. Here, we investigated the spread of chloramphenicol resistance gene (CRG) and tetracycline resistance gene (TRG) in agricultural soil by mobilization of pSUP106 under different conditions, including different concentrations of nutrients, temperatures, soil depths, rhizosphere soils, and soil types. The number of resistant bacteria isolated in non-sterilized soil from the experiments was approximately 10⁴ to 10⁷ per gram of soil, belonging to 5-10 species from four genera, including nonpathogen, opportunistic pathogen, pathogen bacteria, and gram-positive and gram-negative bacteria, depending on the experiment conditions. In sterilized soil, higher levels of nutrients and higher temperatures promoted plasmid mobilization and ARG expression. Topsoil and deep soil might not support the spread of antibiotic resistance, while ARG dissemination by plasmid mobilization was better supported by maize rhizosphere and loam soils. All these factors might change bacterial growth and the activity of bacteria and lead to the above influence. Introduction of only the donor and helper, or the donor alone also resulted in the transfer of ARGs and large numbers of antibiotic resistant bacteria (ARB), indicating that some indigenous bacteria contain the elements necessary for plasmid mobilization. Our results showed that plasmid mobilization facilitated dissemination of ARGs and ARB in soil, which led to the disturbance of indigenous bacterial communities. It is important to clear ARG dissemination routes and inhibit the spread of ARGs.

Genetic Characterization of the O-Antigen and Development of a Molecular Serotyping Scheme for Enterobacter cloacae

Enterobacter cloacae is a well-characterized opportunistic pathogen that is closely associated with various nosocomial infections. The O-antigen, which is one of the most variable constituents on the cell surface, has been used widely and traditionally for serological classification of many gram-negative bacteria. E. cloacae is divided into 30 serotypes, based on its O-antigen diversity. In this study, by using genomic and comparative-genomic approaches, we analyzed the O-antigen gene clusters of 26 E. cloacae serotypes in depth. We also identified the sero-specific gene for each serotype and developed a multiplex polymerase chain reaction (PCR) method. The sensitivity of the assay was 0.1 ng for genomic DNA and 10³ colony forming units for pure cultures. The assay reliability was evaluated by double-blinded testing with 81 clinical strains. Furthermore, we established a valid, genome-based tool for in silico serotyping of E. cloacae. By screening 431 E. cloacae genomes deposited in GenBank, 304 were classified into current antigenic scheme, and 112 were allocated into 55 putative novel serotypes. Our results represent the first genetic basis of the O-antigen diversity and variation of E. cloacae, providing a rationale for studying the O-antigen associated evolution and pathogenesis of this bacterium. In addition, we extended the current serotyping system for E. cloacae, which is important for detection and epidemiological surveillance purposes for this important pathogen.

Vaccinomics to design a novel single chimeric subunit vaccine for broad-spectrum immunological applications targeting nosocomial Enterobacteriaceae pathogens

Healthcare associated infections (HAIs) are major cause of elevated mortality, morbidity, and high healthcare costs. Development of a vaccine targeting these pathogens could benefit in reducing HAIs count and excessive use of antibiotics. This work aimed to design a multi-epitope based prophylactic/ therapeutic vaccine directing against carbapenem resistant Enterobacter cloacae and other leading nosocomial members of Enterobacteriaceae group. Based on subtractive proteomics and immunoinformatics in-depth investigation of E. cloacae reference proteome, we prioritize four targets: outer membrane usher protein-lpfC, putative outer membrane protein A-OmpA, putative outer membrane protein-FimD, and arginine transporter fulfilling criteria of vaccine candidacy. A multi-epitope peptide vaccine construct is then formulated comprising predicted epitopes with potential to evoke both innate and adaptive immunity and B-subunit of cholera toxin as an adjuvant. The construct is modelled, loop refined, improved for stability via disulfide engineering and optimized for codon usage as per Escherichia coli expression system to ensure its maximum expression. Cross-conservation analysis carried out to evaluate broad-spectrum applicability by providing cross protection against nosocomial pathogens. A blind docking method is applied further to predict predominant binding mode of the construct with TLR4 innate immune receptor, followed by molecular dynamics simulation protocol to probe complex dynamics and exposed topology of the construct epitopes for recognition and immune processing by the host. Towards the end, binding free energies of the vaccine construct-TLR4 receptor were estimated to test docking predictions and affirm complex stability. We believe these findings to be highly useful for vaccinologists in making a highly effective vaccine for E. cloacae specifically, and other notorious Enterobacteriaceae nosocomial pathogens in general.

Characterization of the Enterobacter Phage vB_EclM_CIP9

Enterobacter cloacae is an opportunistic pathogen that causes hospital-acquired infections in immunocompromised patients. Here, we describe vB_EclM_CIP9, a novel Enterobacter phage that infects a multidrug-resistant isolate of E. cloacae. Phage vB_EclM_CIP9 is a myovirus that has a 174,924-bp genome, with 296 predicted open reading frames.

Enterobacter cloacae is an opportunistic pathogen that causes hospital-acquired infections in immunocompromised patients. Here, we describe vB_EclM_CIP9, a novel Enterobacter phage that infects a multidrug-resistant isolate of E. cloacae. Phage vB_EclM_CIP9 is a myovirus that has a 174,924-bp genome, with 296 predicted open reading frames.

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of Non-Escherichia coli Enterobacterales from the Gut Microbiota of Healthy Subjects

Non-Escherichia coli Enterobacterales (NECE) can colonize the human gut and may present virulence determinants and phenotypes that represent severe heath concerns. Most information is available for virulent NECE strains, isolated from patients with an ongoing infection, while the commensal NECE population of healthy subjects is understudied. In this study, 32 NECE strains were isolated from the feces of 20 healthy adults. 16S rRNA gene sequencing and mass spectrometry attributed the isolates to Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter aerogenes, Enterobacter kobei, Citrobacter freundii, Citrobacter amalonaticus, Cronobacter sp., and Hafnia alvei, Morganella morganii, and Serratia liquefaciens. Multiplex PCR revealed that K. pneumoniae harbored virulence genes for adhesins (mrkD, ycfM, and kpn) and enterobactin (entB) and, in one case, also for yersiniabactin (ybtS, irp1, irp2, and fyuA). Virulence genes were less numerous in the other NECE species. Biofilm formation was spread across all the species, while curli and cellulose were mainly produced by Citrobacter and Enterobacter. Among the most common antibiotics, amoxicillin-clavulanic acid was the sole against which resistance was observed, only Klebsiella strains being susceptible. The NECE inhabiting the intestine of healthy subjects have traits that may pose a health threat, taking into account the possibility of horizontal gene transfer.

Large-sized planktonic bioaggregates possess high biofilm formation potentials: Bacterial succession and assembly in the biofilm metacommunity

Wanted and unwanted surface-attached growth of bacteria is ubiquitous in natural and engineered settings. Normally, attachment of planktonic cells to media surfaces initiates biofilm formation and fundamentally regulates biofilm assembly processes. Here, culturing biofilm with planktonic sludge as source community, we found distinct succession profiles of biofilm communities sourced from the size-fractionated sludge flocs (<25; 25-120; >120 μm). Null model analyses revealed that deterministic process dominated in biofilm community assemblies but decreased with decreasing floc size. Additionally, the relative importance of environmental selection increased with increasing floc size of the source sludge, whereas homogenizing dispersal and ecological drift followed opposite trends. Phylogenetic molecular ecological networks (pMENs) indicated that species interactions were intensive in biofilm microbiota developed from large-sized flocs (>120 μm), as evidenced by the low modularity and harmonic geodesic distance and the high average degree. Intriguingly, the keystone taxa in these biofilm ecological networks were controlled by distinct interaction patterns but all showed strong habitat characteristics (e.g., facultative anaerobic, motile, hydrophobic and involved in extracellular polymeric substance metabolism), corroborating the crucial roles of environmental filtering in structuring biofilm community. Taken together, our findings highlight the role of planktonic floc properties in biofilm community assembly and advance our understanding of microbial ecology in biofilm-based systems.

Carbapenem-Resistant Klebsiella aerogenes Clinical Isolates from a Teaching Hospital in Southwestern China: Detailed Molecular Epidemiology, Resistance Determinants, Risk Factors and Clinical Outcomes

Purpose

Little is known about the epidemiology and carbapenem-resistance determinants of carbapenem-resistant K. aerogenes (CRKA) isolated from a single medical center. The present study was initiated to characterize the molecular epidemiology and the carbapenem-resistance mechanisms of CRKA isolated during 2012–2018 from a teaching hospital in southwest China, and to investigate the risk factors and clinical outcomes of CRKA infections as well.

Methods

Pulsed-field gel electrophoresis (PFGE) was employed for epidemiological analysis. PCR amplification and DNA sequencing were used to examine the antibiotic-resistance determinants. Plasmids were extracted and characterized by PCR-based replicon typing and conjugation assays. In order to further investigate the risk factors and clinical outcomes of CRKA infections, a retrospective case–control study was also performed.

Results

PFGE analysis showed 32 different PFGE patterns among the 36 non-duplicated CRKA strains collected. Most of the isolates harbored multi-drug resistance (MDR) genes, including 2 (5.6%) carrying bla_NDM-1, 1 (2.8%) harboring bla_KPC-2, 13 (36.1%) carrying ESBL genes, 23 (63.9%) carrying ampC genes, 34 (94.4%) carrying quinolone resistance determinants (QRD) genes and 9 (25%) carrying aminoglycoside resistance determinants (ARD) genes. The outer membrane porins, OmpE35 and OmpE36, were, respectively, lost in 4 and 2 isolates. The efflux pump inhibition experiments were positive in 25 (69.4%) of the CRKA strains. Multivariate analysis indicated that hypo-albuminaemia, invasive procedures, and carbapenem exposure were independent risk factors for acquiring CRKA infections.

Conclusion

No clonality relationship was identified among most of the 36 CRKA isolates. The over-expression of ESBLs and AmpC coupled with the efflux pumps contributed to carbapenem resistance in K. aerogenes. Additionally, this is the first report of CRKA isolate co-harboring bla_NDM-1, bla_CTX-M-15, bla_EBC, bla_ACC, acc (6ʹ)-Ib, armA, qnrD and loss of OmpE36 in China. Hypo-albuminaemia, invasive procedures and carbapenem exposure were associated with acquisition of CRKA infections.

Complete genome of Enterobacter sichuanensis strain SGAir0282 isolated from air in Singapore

Background

Enterobacter cloacae complex (ECC) bacteria, such as E. cloacae, E. sichuanensis, E. kobei, and E. roggenkampii, have been emerging as nosocomial pathogens. Many strains isolated from medical clinics were found to be resistant to antibiotics, and in the worst cases, acquired multidrug resistance. We present the whole genome sequence of SGAir0282, isolated from the outdoor air in Singapore, and its relevance to other ECC bacteria by in silico genomic analysis.

Results

Complete genome assembly of E. sichuanensis strain SGAir0282 was generated using PacBio RSII and Illumina MiSeq platforms, and the datasets were used for de novo assembly using Hierarchical Genome Assembly Process (HGAP) and error corrected with Pilon. The genome assembly consisted of a single contig of 4.71 Mb and with a G+C content of 55.5%. No plasmid was detected in the assembly. The genome contained 4371 coding genes, 83 tRNA and 25 rRNA genes, as predicted by NCBI's Prokaryotic Genome Annotation Pipeline (PGAP). Among the genes, the antibiotic resistance related genes were included: Streptothricin acetdyltransferase (SatA), fosfomycin resistance protein (FosA) and metal-dependent hydrolases of the beta-lactamase superfamily I (BLI).

Conclusion

Based on whole genome alignment and phylogenetic analysis, the strain SGAir0282 was identified to be Enterobacter sichuanensis. The strain possesses gene clusters for virulence, disease and defence, that can also be found in other multidrug resistant ECC type strains.

Antibiotic Resistance Profile, Outer Membrane Proteins, Virulence Factors and Genome Sequence Analysis Reveal Clinical Isolates of Enterobacter Are Potential Pathogens Compared to Environmental Isolates

Outer membrane proteins (OMPs) of gram-negative bacteria play an important role in mediating antibacterial resistance, bacterial virulence and thus affect pathogenic ability of the bacteria. Over the years, prevalence of environmental antibiotic resistant organisms, their transmission to clinics and ability to transfer resistance genes, have been studied extensively. Nevertheless, how successful environmental bacteria can be in establishing as pathogenic bacteria under clinical setting, is less addressed. In the present study, we utilized an integrated approach of investigating the antibiotic resistance profile, presence of outer membrane proteins and virulence factors to understand extent of threat posed due to multidrug resistant environmental Enterobacter isolates. Also, we investigated clinical Enterobacter isolates and compared the results thereof. Results of the study showed that multidrug resistant environmental Enterobacter isolates lacked OmpC, lacked cell invasion abilities and exhibited low reactive oxygen species (ROS) production in neutrophils. In contrast, clinical isolates possessed OmpF, exhibited high invasive and adhesive property and produced higher amounts of ROS in neutrophils. These attributes indicated limited pathogenic potential of environmental Enterobacter isolates. Informations obtained from whole genome sequence of two representative bacterial isolates from environment (DL4.3) and clinical sources (EspIMS6) corroborated well with the observed results. Findings of the present study are significant as it highlights limited fitness of multidrug resistant environmental Enterobacter isolates.

The Determinants of the Human Milk Metabolome and Its Role in Infant Health

Human milk is needed for optimal growth as it satisfies both the nutritional and biological needs of an infant. The established relationship between breastfeeding and an infant’s health is attributable to the nutritional and non-nutritional, functional components of human milk including metabolites such as the lipids, amino acids, biogenic amines and carbohydrates. These components have diverse roles, including protecting the infant against infections and guiding the development of the infant’s immature immune system. In this review, we provide an in-depth and updated insight into the immune modulatory and anti-infective role of human milk metabolites and their effects on infant health and development. We also review the literature on potential determinants of the human milk metabolome, including maternal infectious diseases such as human immunodeficiency virus and mastitis.

Carbapenem-Resistant Enterobacter hormaechei ST1103 with IMP-26 Carbapenemase and ESBL Gene bla SHV-178

Purpose

To investigate the occurrence and genetic characteristics of the bla_IMP-26-positive plasmid from a multidrug-resistant clinical isolate, Enterobacter hormaechei L51.

Methods

Species identification was determined by MALDI-TOF MS and Sanger sequencing. Antimicrobial susceptibility testing was performed by the agar dilution and broth microdilution. Whole-genome sequencing was conducted using Illumina HiSeq 4000-PE150 and PacBio Sequel platforms, and the genome was annotated by the RAST annotation server. The ANI analysis of genomes was performed using OAT. Phylogenetic reconstruction and analyses were performed using the Harvest suite based on the core-genome SNPs of 61 publicly available E. hormaechei genomes.

Results

The E. hormaechei L51 genome consists of a 5,018,729 bp circular chromosome and a 343,918 bp conjugative IncHI2/2A plasmid pEHZJ1 encoding bla_IMP-26 which surrounding genetic context was intI1-bla_IMP-26-ltrA-qacE∆1-sul1. A new sequence type (ST1103) was assigned for the isolate L51 which was resistant to cephalosporins, carbapenems, but sensitive to piperacillin-tazobactam, amikacin, tigecycline, trimethoprim-sulfamethoxazole and colistin. Phylogenetic analysis demonstrated that E. hormaechei L51 belonged to the same subspecies as the reference strain E. hormaechei SCEH020042, however 18,248 divergent SNP were identified. Resistance genes in pEHZJ1 including aac(3)-IIc, aac(6ʹ)-IIc, bla_SHV-178, bla_DHA-1, bla_TEM-1, bla_IMP-26, ereA2, catII, fosA5, qnrB4, tet(D), sul1 and dfrA19.

Conclusion

In our study, we identified a conjugative IncHI2/2A plasmid carrying bla_IMP-26 and bla_SHV-178 in E. hormaechei ST1103, a novel multidrug-resistant strain isolated from China, and describe the underlying resistance mechanisms of the strain and detailed genetic context of mega plasmid pEHZJ1.

Relationship between the Gut Microbiome and Energy/Nutrient Intake in a Confined Bioregenerative Life Support System

Recent studies have suggested that the gut microbiome is modified in space analogs and that human health can be affected during actual spaceflight. However, the relationship between the gut microbiome and dietary intake in simulator subjects and astronauts remains unclear. Bioregenerative life support systems (BLSSs) are confined and self-sufficient ecosystems that enable exploration of this issue. Here, we correlate changes in gut microbes to the nutrient types present in controlled diets within subjects cohabitating in a BLSS. A metagenome-wide association study (MWAS) was performed on 55 shotgun-sequenced fecal samples longitudinally obtained from healthy Chinese subjects (n = 4 in total, n = 2 per sex) subjected to a 60-day BLSS stay and a specialized diet. Each food item was categorized based on nutrient type according to the Chinese Food Ingredients List (https://wenku.baidu.com/view/3f2b628488eb172ded630b1c59eef8c75fbf9514.html?from=search). The physical parameters of each subject fluctuated within normal medical ranges. Sex- and individual-specific differences and a trend of individual convergence of the gut microbiome in the BLSS were observed. Depletion of bacterial taxa such as Faecalibacterium prausnitzii, Bifidobacterium longum, and Escherichia coli and functional modules such as short-chain fatty acid (SCFA) production, as well as an increase in an unidentified Lachnospiraceae and glutamate/tryptophan synthesis, were observed in the BLSS. Correlation analysis showed that these compositional and functional changes were associated with energy/nutrient intake during the BLSS stay. Our findings suggest that the gut microbiota is a useful indicator for monitoring health and that individual nutritive diets should be considered according to sex and individual differences in simulations or in spaceflight.IMPORTANCE The gut microbiome shows individual specificity and is affected by sex, environment, and diet; gut microbiome imbalance is related to cancer, cardiovascular diseases, and autoimmune diseases. Astronauts are faced with a challenging environment and limited diet in outer space. Recent studies indicate that the gut microbiome is altered in space simulators and space, but what happens to intestinal microorganisms when astronauts cohabitate in a self-sufficient ecosystem in which they plant and cook food is unclear. Bioregenerative life support systems (BLSSs) are ideal devices to investigate the above issues because they are closed and self-sufficient. Four healthy Chinese subjects cohabitated in a confined BLSS for 60 days, during which their physical parameters and energy/nutrient intake were recorded. We performed a metagenome-wide association study (MWAS) on 55 shotgun-sequenced fecal samples longitudinally obtained from the subjects. Alterations occurred in the gut microbial composition and function, and their relationships with energy/nutrient intake were explored.

Identification of Non- Streptococcus mutans Bacteria from Predente Infant Saliva Grown on Mitis-Salivarius-Bacitracin Agar

Objective: Although mitis-salivarius-bacitracin (MSB) agar is a commonly used selective medium for detecting Streptococcus mutans in clinical studies, non-S. mutans microorganisms are cultivatable on MSB agar. Since few studies have identified non-S. mutans bacteria grown on MSB, this study aimed to identify and differentiate MSB-grown non-S. mutans bacteria from predente infants' oral cavity. Study design: The saliva from 51 predente infants were plated on MSB agars. Bacteria colonies were characterized based on their morphology under direct visualization and light microscopic observation. Colony PCR targeting S. mutans htrA locus and 16S rRNA DNA sequencing were used for further bacteria identification. Results: Overall, 80% of the predente infants had oral bacteria grown on the MSB agar. Nine bacteria were identified, including S. mutans, Staphylococcus epidermidis, Klebsiella quasi-pneumoniae, Klebsiella pneumoniae, Enterobacter kobei, Enterococcus faecalis, Staphylococcus hominis, Streptococcus anginosus and Phytobacter. The most frequently detected bacteria were S. epidermidis (41.5%), followed by E. kobei (24.4%), K. pneumoniae (17.1%) and S. mutans (9.8%.) Conclusions: Multiple non-S. mutans bacteria from infants' oral cavity could grow on MSB agar. Caution should be exercised in counting the colony forming units of S. mutans from oral samples on MSB agar to avoid overestimation by assuming that all colonies on the MSB agar are S. mutans. Using the colony morphological guide we summarized, these non-S. mutans bacteria could be distinguished from S. mutans. Our study provides a key reference to pediatric cariology clinical-epidemiological studies that commonly use MSB to identify/quantify S. mutans in infants and young children.

Petting Zoo Animals as an Emerging Reservoir of Extended-Spectrum β-Lactamase and AmpC-Producing Enterobacteriaceae

Extended spectrum beta-lactamases and AmpC-producing Enterobacteriaceae (ESBL/AmpC-E) have become a great concern in both human and veterinary medicine. One setting in which this risk could be particularly prominent is petting zoos, in which humans, especially children, directly and indirectly interact with the animals. Yet, while the zoonotic transmission of various Enterobacteriaceae has been reported previously in petting zoos, reports on ESBL/AmpC-E shedding in this setting is currently lacking, despite the high potential risk. To fill this knowledge gap, we conducted a prospective cross-sectional study to explore the prevalence, molecular epidemiology, and risk for shedding of ESBL/AmpC-E in petting zoos. We performed a prospective cross-sectional study in eight petting zoos. Altogether, we collected 381 fecal and body-surface samples from 228 animals, broth-enriched them, and then plated them onto CHROMagar ESBL-plates for ESBL/AmpC-E isolation. Next, we identified the isolated species and tested their susceptibility to various antibiotics using the Vitek-2 system, determined bacterial relatedness by multilocus sequence typing (MLST), and identified ESBL/AmpC genes by using PCR and sequencing. Finally, we asked petting zoo owners and veterinarians to complete questionnaires, which we then analyzed to evaluate risk factors for ESBL/AmpC-E shedding. We found that ESBL/AmpC-E shedding is an important, currently oversighted risk in petting zoos, as the overall shedding rate was 12% (35 isolates, including 29% ESBL-producers, 34% AmpC-producers, and 37% ESBL and AmpC-producers). The isolated bacteria included Enterobacter cloacae (55%), Escherichia coli (31%), and Citrobacter freundii (14%), with diverse ESBL genes. MLST revealed diverse sequence types (STs), including the highly virulent Enterotoxigenic ST656 and the Uropathogenic ST127 E. coli strains, indicating complex epidemiology with inter-animal bacterial transmission. Shedding was associated with petting permission and antibiotic treatment in the petting zoo (OR = 7.34), which were identified as risk factors for ESBL/AmpC shedding. Our findings highlight petting zoos as a source for antibiotic-resistant ESBL/AmpC-producing bacteria, including highly virulent, disease-associated MDR E. coli strains. As this risk has not been previously described in detail, it calls for the implementation of infection control and active surveillance programs in petting zoos and raises the need for a comprehensive guideline to restrain this emerging concern.

Microbial volatile compounds-induced cytotoxicity in the yeast Saccharomyces cerevisiae: The role of MAPK signaling and proteasome regulatory pathway

Microbial volatile organic compounds (mVCs) are formed in the metabolism of microorganisms and widely distributed in nature and pose threats to human health. However, the air pollution by microorganisms is a situation which is poorly understood. In this study, the cytotoxicity of E. aerogenes VCs was evaluated in the model organism Saccharomyces cerevisiae. E. aerogenes VCs inhibited the survival of yeast and triggered the formation of intracellular reactive oxygen species (ROS). The hypersensitive of MAP kinase mpk1/slt2 and 19S regulatory assembly chaperone adc17 mutants to the E. aerogenes VCs indicated cell wall integrity (CWI) pathway together with stress-inducible proteasome assembly regulation are essentially involved in mVCs tolerance mechanism. Furthermore, exposure to the mVCs resulted in the transcriptional upregulation of the CWI pathway, the regulatory particle assembly chaperones, and genes involved in proteasome regulations. Our research suggested that the ROS/MAPK signaling and proteasome regulatory pathway play pivotal roles in the integration and fine-tuning of the mVCs stress response. This study provides a molecular framework for future study of the effects of mVCs on more complex organisms, such as humans.

Enterobacter spp.: Update on Taxonomy, Clinical Aspects, and Emerging Antimicrobial Resistance

The genus Enterobacter is a member of the ESKAPE group, which contains the major resistant bacterial pathogens. First described in 1960, this group member has proven to be more complex as a result of the exponential evolution of phenotypic and genotypic methods. Today, 22 species belong to the Enterobacter genus. These species are described in the environment and have been reported as opportunistic pathogens in plants, animals, and humans. The pathogenicity/virulence of this bacterium remains rather unclear due to the limited amount of work performed to date in this field. In contrast, its resistance against antibacterial agents has been extensively studied. In the face of antibiotic treatment, it is able to manage different mechanisms of resistance via various local and global regulator genes and the modulation of the expression of different proteins, including enzymes (β-lactamases, etc.) or membrane transporters, such as porins and efflux pumps. During various hospital outbreaks, the Enterobacter aerogenes and E. cloacae complex exhibited a multidrug-resistant phenotype, which has stimulated questions about the role of cascade regulation in the emergence of these well-adapted clones.

Resistance Levels and Epidemiology of Non-Fermenting Gram-Negative Bacteria in Urinary Tract Infections of Inpatients and Outpatients (RENFUTI): A 10-Year Epidemiological Snapshot

Background: Urinary tract infections (UTIs) are one of the most common infections in the human medicine, both among outpatients and inpatients. There is an increasing appreciation for the pathogenic role of non-fermenting Gram-negative bacteria (NFGNBs) in UTIs, particularly in the presence of underlying illnesses. Methods: The study was carried out using data regarding a 10-year period (2008-2017). The antimicrobial susceptibility testing was performed using the disk diffusion method, E-tests, and broth microdilution. Results: NFGNB represented 3.46% ± 0.93% for the outpatients, while 6.43% ± 0.81% of all positive urine samples for the inpatients (p < 0.001). In both groups, Pseudomonas spp. (78.7% compared to 85.1%) and Acinetobacter spp. (19.6% compared to 10.9%), were the most prevalent. The Acinetobacter resistance levels were significantly higher in inpatients isolates (p values ranging between 0.046 and <0.001), while the differences in the resistance levels of Pseudomonas was not as pronounced. The β-lactam-resistance levels were between 15-25% and 12-28% for the Acinetobacter and Pseudomonas spp., respectively. 4.71% of Acinetobacter and 1.67% of Pseudomonas were extensively drug resistant (XDR); no colistin-resistant isolates were recovered. Conclusions: Increasing resistance levels of the Acinetobacter spp. from 2013 onward, but not in the case of the Pseudomonas spp. Although rare, the drug resistant NFGNB in UTIs present a concerning therapeutic challenge to clinicians with few therapeutic options left.

High distribution of 16S rRNA methylase genes rmtB and armA among Enterobacter cloacae strains isolated from an Ahvaz teaching hospital, Iran

The emergence of 16S rRNA methylase genes encoded on plasmids confers high-level aminoglycoside resistance (HLAR). This study aimed to investigate the prevalence of 16S rRNA methylases among Enterobacter cloacae strains isolated from an Ahvaz teaching hospital, Iran. A total of 68 E. cloacae clinical strains were collected between November 2017 and September 2018. The MICs of aminoglycosides were assessed using the agar dilution method. The presence of 16S rRNA methylase genes, including armA, rmtA to rmtH, and nmpA was evaluated by PCR. The transferability of 16S rRNA methylase-harboring plasmids was evaluated by conjugation assay. The genetic diversity of all isolates was evaluated by ERIC-PCR. The armA and rmtB genes were the only 16S rRNA methylase genes detected in this study (29 out of 68 isolates; 42.64%). The transferability by conjugation was observed in 23 rmtB or/and armA positive donors. HLAR phenotype was in 33 of 68 strains. Ten clonal types were obtained by ERIC-PCR and significant associations (p < 0.05) were between the clone types and aminoglycoside susceptibility, as well as with profile of the 16S rRNA methylase genes. In conclusion, both horizontal transfer and clonal spread are responsible for dissemination of the rmtB and armA genes among E. cloacae strains.

Going around in circles: virulence plasmids in enteric pathogens

Plasmids have a major role in the development of disease caused by enteric bacterial pathogens. Virulence plasmids are usually large (>40 kb) low copy elements and encode genes that promote host-pathogen interactions. Although virulence plasmids provide advantages to bacteria in specific conditions, they often impose fitness costs on their host. In this Review, we discuss virulence plasmids in Enterobacteriaceae that are important causes of diarrhoea in humans, Shigella spp., Salmonella spp., Yersinia spp and pathovars of Escherichia coli. We contrast these plasmids with those that are routinely used in the laboratory and outline the mechanisms by which virulence plasmids are maintained in bacterial populations. We highlight examples of virulence plasmids that encode multiple mechanisms for their maintenance (for example, toxin-antitoxin and partitioning systems) and speculate on how these might contribute to their propagation and success.

The prevalence of the culturable human skin aerobic bacteria in Riyadh, Saudi Arabia

Background

Human skin is an appropriate environment for the growth of different types of microbes that may inhabit the skin as commensal flora. This study aims at identifying the diversity of skin microbiota in healthy Saudi population. In this study, 80 Saudi subjects of both males and females, from different habitat, and different ages (elderly and young), were recruited to determine the aerobic bacterial flora from their three skin sites; hand, scalp and foot. A single colony obtained from aerobic culture was identified using Biomérieux VITEK® 2 system. For those not being identified by VITEK® 2 system, the identification was conducted using 16 s rRNA sequence.

Results

Thirty-three bacterial species were isolated from males, whilst 24 species were isolated from females. Micrococci are the predominant organisms, followed by Staphylococci, Pantoea species, and lastly Enterococcus faecium. Acinetobacter baumannii, Enterococcus faecalis, and Klebsiella pneumoniae were only found in elder subjects, while Pseudomonas aeruginosa was isolated from the young only. The number of bacterial isolates in the elders was higher that of the young. The average number of flora was larger in foot, then hand and lastly scalp.

Conclusion

Here we show the difference in the number of cultivable bacteria across age and gender that may result in the variety of local skin infection. This study paves the way to further investigation in the aspect of in-depth metagenomics analysis and host-pathogen interaction.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1569-5) contains supplementary material, which is available to authorized users.

High Prevalence of Metallo-β-Lactamase-Producing Enterobacter cloacae From Three Tertiary Hospitals in China

Enterobacter cloacae has recently emerged as one of the most common carbapenem-resistant Enterobacteriaceae. The emergence and spread of metallo-β-lactamase-producing E. cloacae have posed an immediate threat globally. Here, we investigated the molecular characteristics of 84 carbapenem-resistant Enterobacter cloacae (CREL) collected from three tertiary hospitals in China between 2012 and 2016. Species identification and antimicrobial susceptibility testing were performed using a VITEK-2 system. Carbapenems, polymyxins B, and tigecycline were tested by broth microdilution method. The carbapenem in activation method (CIM) and cefoxitin three-dimensional test were used to detect carbapenemase and AmpC β-lactamase, respectively. Isolates were screened for β-lactam resistance genes by PCR, and expression of ompC and ompF was determined by qRT-PCR. Genetic relatedness was performed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST), while selected isolates were subjected to whole-genome sequencing. Among the 84 CREL isolates, 50 (59.5%) were detected as carbapenemase producers. NDM-1 was the dominant carbapenemase (80.0%), followed by IMP-26 (8.0%) and IMP-4 (6.0%). Notably, we identified the first NDM-1 and IMP-1 co-producing E. cloacae, carrying plasmids of several incompatibility (Inc) groups, including IncHI2, IncHI2A, and IncN. Most isolates showed decreased expression of ompC and/or ompF, and contained a broad distribution of ESBLs and AmpC β-lactamases. These findings suggested that different molecular mechanisms, including carbapenemase, ESBL and/or AmpC plus loss of porins, have contributed to carbapenem resistance. The bla_NDM−1-harboring plasmids contained highly conserved gene environment around bla_NDM−1 (bla_NDM−1-ble_MBL-trpF-dsbD-cutA1-groES-groEL), which could be associated with the potential dissemination of bla_NDM−1. IMP-type MBL was located within a variety of integrons and usually contained various gene cassettes encoding multidrug resistance. These isolates produced 54 different pulsotypes, and were classified into 42 STs by MLST. Nineteen bla_NDM−1-positive E. cloacae isolates obtained from Ningxia had the same pulsotype (PFGE type 1), belonging to ST78 within clonal complex 74 (CC74). The plasmid-based replicon typing indicated that IncX3 plasmids mediated the dissemination of bla_NDM−1 among these homologous strains. This is the first report on the outbreak of NDM-1-producing E. cloacae ST78 with contribution of IncX3 plasmids in Northwestern China. There's an immediate need to intensify surveillance attentively to prevent and control the further spread of NDM-1 in China.

Antimicrobial susceptibility profile of selected Enterobacteriaceae in wastewater samples from health facilities, abattoir, downstream rivers and a WWTP in Addis Ababa, Ethiopia

Background

Evaluation of antimicrobial susceptibility profile of various bacterial pathogens in the health facilities, abattoirs and related environment is important to assess potential risk of dissemination of resistant pathogens to the environment. There is limited information about antimicrobial susceptibility profile of common Enterobacteriaceae in waste water samples from hospitals, abattoirs and the downstream water bodies in Addis Ababa. The present study assessed antimicrobial susceptibility of bacteria belonging to the family Enterobacteriaceae isolated from wastewater samples (WWS) of two hospitals: Tikur Anbessa Specialized Hospital (TASH) and Minilik II hospital, a wastewater treatment plant (WWTP) and an abattoir, and downstream rivers in Addis Ababa.

Results

A total of 54 bacterial isolates belonging to 6 species were identified: E.coli (32%), Salmonella 23%), Klebsiella pneumonia (15%), Enterobacter aerogenes (11%), Citrobacter (7%), Klebsiella oxytoca (6%) and Enterobacter cloacae (6%), respectively. Two strains of Citrobacter spp. isolated from TASH wastewater sample (WWS) were resistant to all 12 antimicrobials tested whereas an E. coli isolate from the same source was resistant to 11 antimicrobials. All isolates were resistant to 2 or more antimicrobials tested. Multi-drug resistance (MDR) to several antimicrobials was recorded, particularly in isolates obtained from hospital WWS and it was more common in Citrobacter and E. coli isolates. Extended spectrum betalactamase (ESBL) production was detected in 27.3% of MDR isolates, all of them obtained from hospital effluents whereas none of the isolates were carbapenemase producers.

Conclusion

The present study revealed that Enterobacteriaceae in wastewater from hospitals, abattoir and downstream water bodies are resistant to commonly used antimicrobials. Hospital effluents contained more of MDR bacteria, posing significant public health threat through dissemination to the downstream water bodies.

High prevalence and diversity of extended-spectrum β-lactamase and emergence of OXA-48 producing Enterobacterales in wildlife in Catalonia

Most of the studies focused on antimicrobial resistance (AMR) performed in wildlife describe Escherichia coli as the principal indicator of the selective pressure. In the present study, several species of Enterobacterales with a large panel of cephalosporin resistant (CR) genes have been isolated from wildlife in Catalonia. A total of 307 wild animals were examined to determine the prevalence of CR enterobacteria, AMR phenotypes and the presence of common carbapenem and CR genes. The overall prevalence of CR-phenotype was 13% (40/307): 17.3% in wild mammals (18/104) and 11.5% in wild birds (22/191) (p<0.01). Hedgehogs showed the highest prevalence (13.5% of 104) of the mammal specimens, and raptors the highest in bird specimen (7.3% of 191). Although CR E. coli was the most frequently isolated (45%), other CR- Enterobacterales like Klebsiella pneumoniae (20%), Citrobacter freundii (15%), Enterobacter cloacae (5%), Proteus mirabilis (5%), Providencia spp (5%) and Serratia marcescens (2.5%) were also isolated. A high diversity of CR genes was identified among the isolates, with 50% yielding blaCMY-2, 23% blaSHV-12, 20% blaCMY-1 and 18% blaCTX-M-15. Additionally, resistance to carbapenems associated to OXA-48 gene was found. Most of the CR isolates, principally K. pneumoniae and C. freundii, were multi-resistant with co-resistance to fluoroquinolones, tetracycline, sulphonamides and aminoglycosides. This study reports high prevalence of Enterobacterales harbouring a variety of CR genes and OXA-48 mediated-carbapenem resistance, all of them frequently associated to nosocomial human infections, for the first time in wild mammals and wild birds. Implementation of control measures to reduce the impact of anthropogenic pressure in the environment is urgently needed.

Genomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance in Klebsiella aerogenes

Klebsiella aerogenes is an important pathogen in healthcare-associated infections. Nevertheless, in comparison to other clinically important pathogens, K. aerogenes population structure, genetic diversity, and pathogenicity remain poorly understood. Here, we elucidate K. aerogenes clonal complexes (CCs) and genomic features associated with resistance and virulence. We present a detailed description of the population structure of K. aerogenes based on 97 publicly available genomes by using both multilocus sequence typing and single-nucleotide polymorphisms extracted from the core genome. We also assessed virulence and resistance profiles using Virulence Finder Database and Comprehensive Antibiotic Resistance Database, respectively. We show that K. aerogenes has an open pangenome and a large effective population size, which account for its high genomic diversity and support that negative selection prevents fixation of most deleterious alleles. The population is structured in at least 10 CCs, including two novel ones identified here, CC9 and CC10. The repertoires of resistance genes comprise a high number of antibiotic efflux proteins as well as narrow- and extended-spectrum β-lactamases. Regarding the population structure, we identified two clusters based on virulence profiles because of the presence of the toxin-encoding clb operon and the siderophore production genes, irp and ybt. Notably, CC3 comprises the majority of K. aerogenes isolates associated with hospital outbreaks, emphasizing the importance of constant monitoring of this pathogen. Collectively, our results may provide a foundation for the development of new therapeutic and surveillance strategies worldwide.

Cooccurrence of NDM-1, ESBL, RmtC, AAC(6')-Ib, and QnrB in Clonally Related Klebsiella pneumoniae Isolates Together with Coexistence of CMY-4 and AAC(6')-Ib in Enterobacter cloacae Isolates from Saudi Arabia

The aim of this study was to investigate the mechanisms responsible for resistance to antimicrobials in a collection of enterobacterial isolates recovered from two hospitals in Saudi Arabia. A total of six strains isolated from different patients showing high resistance to carbapenems was recovered in 2015 from two different hospitals, with four being Klebsiella pneumoniae and two Enterobacter cloacae. All isolates except one K. pneumoniae were resistant to tigecycline, but only one K. pneumoniae was resistant to colistin. All produced a carbapenemase according to the Carba NP test, and all were positive for the EDTA-disk synergy test for detection of MBL. Using PCR followed by sequencing, the four K. pneumoniae isolates produced the carbapenemase NDM-1, while the two E. cloacae isolates produced the carbapenemase VIM-1. Genotyping analysis by Multilocus Sequence Typing (MLST) showed that three out of the four K. pneumoniae isolates were clonally related. They had been recovered from the same hospital and belonged to Sequence Type (ST) ST152. In contrast, the fourth K. pneumoniae isolate belonged to ST572. Noticeably, the NDM-1-producing K. pneumoniae additionally produced an extended-spectrum ß-lactamase (ESBL) of the CTX-M type, together with OXA-1 and TEM-1. Surprisingly, the three clonally related isolates produced different CTX-M variants, namely, CTX-M-3, CTX-M-57, and CTX-M-82, and coproduced QnrB, which confers quinolone resistance, and the 16S rRNA methylase RmtC, which confers high resistance to all aminoglycosides. The AAC(6')-Ib acetyltransferase was detected in both K. pneumoniae and E. cloacae. Mating-out assays using Escherichia coli as recipient were successful for all isolates. The bla _NDM-1 gene was always identified on a 70-kb plasmid, whereas the bla _VIM-1 gene was located on either a 60-kb or a 150-kb plasmid the two E. cloacae isolates, respectively. To the best of our knowledge, this is the first report of the coexistence of an MBL (NDM-1), an ESBL (CTX-M), a 16S rRNA methylase (RmtC), an acetyltransferase (AAC[6']-Ib), and a quinolone resistance enzyme (QnrB) in K. pneumoniae isolates recovered from different patients during an outbreak in a Saudi Arabian hospital.