Characterization and dynamics of intestinal microbiota in patients with Clostridioides difficile colonization and infection.

Gut microbiota dysbiosis increases the susceptibility to Clostridioides difficile infection (CDI). In this study, we monitored C. difficile colonization (CDC) patients from no CDC status (CDN) to CDC status (CDCp) and CDI patients from asymptomatic status before CDI (PRECDI), CDI status (ONCDI), to asymptomatic status after CDI (POSTCDI). Based on metagenomic sequencing, we aimed to investigate the interaction pattern between gut microbiota and C. difficile. There was no significant difference of microbiota diversity between CDN and CDCp. In CDCp, Bacteroidetes and short-chain fatty acid (SCFA)-producing bacteria increased, with a positive correlation between SCFA-producing bacteria and C. difficile colonization. Compared with PRECDI, ONCDI and POSTCDI showed a significant decrease in microbiota diversity, particularly in Bacteroidetes and SCFA-producing bacteria, with a positive correlation between opportunistic pathogen and C. difficile. Fatty acid metabolism, and amino acid biosynthesis were enriched in CDN, CDCp, and PRECDI, while bile secretion was enriched in ONCDI and POSTCDI. Microbiota and metabolic pathways interaction networks in CDN and CDCp were more complex, particularly pathways in fatty acid and bile acid metabolism. Increasing of Bacteroidetes and SCFA-producing bacteria, affecting amino acid and fatty acid metabolism, is associated with colonization resistance to C. difficile and inhibiting the development of CDI.

Photosensitizer-Amplified Antimicrobial Materials for Broad-Spectrum Ablation of Resistant Pathogens in Ocular Infections.

The emergence of multidrug resistant (MDR) pathogens and the scarcity of new potent antibiotics and antifungals are one of the biggest threats to human health. Antimicrobial photodynamic therapy (aPDT) combines light and photosensitizers to kill drug-resistant pathogens; however, there are limited materials that can effectively ablate different classes of infective pathogens. In the present work, a new class of benzodiazole-paired materials is designed as highly potent PDT agents with broad-spectrum antimicrobial activity upon illumination with nontoxic light. The results mechanistically demonstrate that the energy transfer and electron transfer between nonphotosensitive and photosensitive benzodiazole moieties embedded within pathogen-binding peptide sequences result in increased singlet oxygen generation and enhanced phototoxicity. Chemical optimization renders PEP3 as a novel PDT agent with remarkable activity against MDR bacteria and fungi as well as pathogens at different stages of development (e.g., biofilms, spores, and fungal hyphae), which also prove effective in an ex vivo porcine model of microbial keratitis. The chemical modularity of this strategy and its general compatibility with peptide-based targeting agents will accelerate the design of highly photosensitive materials for antimicrobial PDT.

Comparison of in vitro synergy between polymyxin B or colistin in combination with 16 antimicrobial agents against multidrug-resistant Acinetobacter baumannii isolates.

PURPOSES: This study determined the synergy of polymyxin B (POLB) and colistin (COL) with 16 other tested antimicrobial agents in the inhibition of multidrug-resistant Acinetobacter baumannii (MDR-AB). METHODS: We used chequerboard assays to determine synergy between the drugs against 50 clinical MDR-AB from a tertiary hospital in the Zhejiang province in 2019, classifying combinations as either antagonistic, independent, additive, or synergistic. The efficacy of hit combinations which showed highest synergistic rate were confirmed using time-kill assays. RESULTS: Both POLB and COL displayed similar bactericidal effects when used in combination with these 16 tested drugs. Antagonism was only observed for a few strains (2%) exposed to a combination of POLB and cefoperazone/sulbactam (CSL). A higher percentage of synergistic combinations with POLB and COL were observed with rifabutin (RFB; 90%/96%), rifampicin (RIF; 60%/78%) and rifapentine (RFP; 56%/76%). Time-kill assays also confirmed the synergistic effect of POLB and rifamycin class combinations. 1/2 MIC rifamycin exposure can achieve bacterial clearance when combined with 1/2 MIC POLB or COL. CONCLUSION: Nearly no antagonism was observed when combining polymyxins with other drugs by both chequerboard and time-kill assays, suggesting that polymyxins may be effective in combination therapy. The combinations of POLB/COL with RFB, RIF, and RFP displayed neat synergy, with RFB showing the greatest effect.

Sirtuin 6 ameliorates bleomycin-induced pulmonary fibrosis via activation of lipid catabolism.

Pulmonary fibrosis is a chronic and serious interstitial lung disease with little effective therapies currently. Our incomplete understanding of its pathogenesis remains obstacles in therapeutic developments. Sirtuin 6 (SIRT6) has been shown to mitigate multiple organic fibrosis. However, the involvement of SIRT6-mediated metabolic regulation in pulmonary fibrosis remains unclear. Here, we demonstrated that SIRT6 was predominantly expressed in alveolar epithelial cells in human lung tissues by using a single-cell sequencing database. We showed that SIRT6 protected against bleomycin-induced injury of alveolar epithelial cells in vitro and pulmonary fibrosis of mice in vivo. High-throughput sequencing revealed enriched lipid catabolism in Sirt6 overexpressed lung tissues. Mechanismly, SIRT6 ameliorates bleomycin-induced ectopic lipotoxicity by enhancing lipid degradation, thereby increasing the energy supply and reducing the levels of lipid peroxides. Furthermore, we found that peroxisome proliferator-activated receptor α (PPARα) was essential for SIRT6-mediated lipid catabolism, anti-inflammatory responses, and antifibrotic signaling. Our data suggest that targeting SIRT6-PPARα-mediated lipid catabolism could be a potential therapeutic strategy for diseases complicated with pulmonary fibrosis.

A New Full-Dimensional Ab Initio Intermolecular Potential Energy Surface and Rovibrational Energies of the H2O-H2 Complex.

H2O-H2 is a prototypical five-atom van der Waals system, and the interaction between H2O and H2 plays an important role in many physical and chemical environments. However, previous full-dimensional intermolecular potential energy surfaces (IPESs) cannot accurately describe the H2O-H2 interaction in the repulsive or van der Waals minimum region. In this work, we constructed a full-dimensional IPES for the title system with a small root-mean-square error of 0.252 cm-1 by using the permutation invariant polynomial neural network method. The ab initio calculations were performed by employing the explicitly corrected coupled cluster [CCSD(T)-F12a] method with the augmented correlation-consistent polarized valence quintuple-ζ basis set. Based on the newly developed IPES, the bound states of the H2O-H2 complex were calculated within the rigid-rotor approximation. The transition frequencies and band origins agreed well with the experimental values [Weida, M. J.; Nesbitt, D. J. J. Chem. Phys. 1999, 110, 156-167] with errors less than 0.1 cm-1 for most transitions. Those results demonstrate the high accuracy of our new IPES, which would build a solid foundation for the collisional dynamics of H2O-H2 at low temperatures.

Comparison of the inoculum effect of in vitro antibacterial activity of Imipenem/relebactam and Ceftazidime/avibactam against ESBL-, KPC- and AmpC-producing Escherichia coli and Klebsiella pneumoniae.

OBJECTIVE: To evaluate effect of inoculum size of extended-spectrum ß-Lactamase (ESBL)-producing-, AmpC-producing-, and KPC-producing Escherichia coli and Klebsiella pneumoniae on the in vitro antibacterial effects of imipenem/relebactam (IMR) and ceftazidime/avibactam (CZA). METHODS: We compared the impact of inoculum size on IMR and CZA of sixteen clinical isolates and three standard isolates through antimicrobial susceptibility tests, time-kill assays and in vitro PK/PD studies. RESULTS: When inoculum size increased from 105 to 107 CFU/mL, an inoculum effect was observed for 26.3% (5/19) and 52.6% (10/19) of IMR and CZA, respectively; time-kill assays revealed that the concentration of CZA increased from ≥ 4 × MIC to 16 × MIC to reach 99.9% killing rate against K. pneumoniae ATCC-BAA 1705 (KPC-2-, OXA-9- and SHV-182-producing) and 60,700 (SHV-27- and DHA-1-producing). While for IMR, a concentration from 1 × MIC to 4 × MIC killed 99.9% of the four strains. When the inoculum size increased to 109 CFU/mL, neither IMR nor CZA showed a detectable antibacterial effect, even at a high concentration. An in vitro PK/PD study revealed a clear bactericidal effect when IMR administered as 1.25 g q6h when inoculum size increased. CONCLUSION: An inoculum effect on CZA was observed more frequent than that on IMR. Among the ß-lactamase-producing strains, the inoculum effect was most common for SHV-producing and KPC-producing strains.

Single-cell landscape of peripheral immune response in patients with anti-melanoma differentiation-associated gene 5 dermatomyositis.

OBJECTIVE: Anti-melanoma differentiation-associated gene 5 (MDA5)-positive dermatomyositis (DM) is a rare but life-threatening autoimmune disorder with a high risk to develop rapidly progressive interstitial lung disease. Current empirical therapies have limited improvement on patients' survival, as little is known about the aetiology of MDA5 DM. To best understand its immune landscape, we applied single-cell RNA sequencing (scRNA-seq) to peripheral blood samples from DM patients and healthy controls. METHODS: Peripheral blood mononuclear cells (PBMCs) from eight DM patients, comprising three distinct subtypes, as well as two healthy donors, were sequenced by 10X Genomics platform. Additional scRNA-seq data of four healthy donors were incorporated for further bioinformatic analysis. RESULTS: Aberrant increased proportions of CD14+ monocyte and plasma cells were observed in MDA5 DM samples. Moreover, we found overactivated type I interferon response and antiviral immunity in both innate and adaptive immune cells derived from MDA5 DM patients, which was positively correlated with disease severity. Importantly, a unique subset of CD14+ monocyte that highly expressed interferon alpha-inducible protein 27 (IFI27, a biomarker for viral infection) and interferon induced with helicase C domain 1 (IFIH1, encodes MDA5) was specifically identified in MDA5 DM samples for the first time. CONCLUSION: Our study demonstrates the peripheral immune cell atlas of different DM subtypes, provides compelling evidence for viral infection-derived origin of MDA5 DM, and offers potential targets for innovative therapeutic interventions.

Full quantum scattering calculations of the line-shape parameters for the P and R branches of HF perturbed by Ar.

This work studied the rovibrational absorption spectral line-shape parameters of the P(1)-P(10) and R(0)-R(9) lines for Hydrogen fluoride perturbed by argon in the 0-0, 1-0, and 2-0 vibrational bands at 20-1000 K. A dataset of beyond-Voigt line-shape parameters (pressure broadening and shifting parameters, their speed dependencies, and the complex Dicke parameters) has been theoretically determined for the first time from generalized spectroscopic cross-section calculated by the full quantum scattering calculations. Then these parameters were employed to predict the line shape and asymmetry based on the partially-correlated speed-dependent hard-collision and the partially-correlated quadratic-speed-dependent hard-collision profiles. The effect of each parameter on the line shape and line asymmetry was further studied, which revealed that the beyond-Voigt effects were indispensable to accurately describe the line shape contour. Our results are in good agreement with the available experimental observations and provide a comprehensive set of theoretical references for further experimental measurements.

Clinical, biological and genome-wide comparison of carbapenem-resistant Klebsiella pneumoniae with susceptibility transformation to polymyxin B during therapy.

OBJECTIVES: The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major clinical concern, and polymyxin B (PMB) is a 'last resort' antibiotic for its treatment. Understanding the effects of drug susceptibility transformation in CRKP-infected patients undergoing PMB treatment would be beneficial to optimize PMB treatment strategies. METHODS: We retrospectively collected data from patients infected with CRKP and treated with PMB from January 2018 to December 2020. CRKPs were collected before and after PMB therapy, and patients were classified into the 'transformation' group (TG) and 'non-transformation' group (NTG) by the shift of susceptibility to PMB. We compared clinical characteristics between these groups, and further analysed the phenotypic and genome variation of CRKP after PMB susceptibility transformation. RESULTS: A total of 160 patients (37 in the TG and 123 in the NTG) were included in this study. The duration of PMB treatment before PMB-resistant K. pneumoniae (PRKP) appearance in TG was even longer than the whole duration of PMB treatment in NTG (8 [8] vs. 7 [6] days; p 0.0496). Compared with isogenic PMB-susceptible K. pneumoniae (PSKP), most PRKP strains had missense mutations in mgrB (12 isolates), yciC (10 isolates) and pmrB (7 isolates). The competition index of 82.4% (28/34) of PRKP/PSKP pairs was <67.6% (23/34), and 73.5% (25/34) of PRKP strains showed a higher 7-day lethality in Galleria mellonella and a greater ability to resist complement-dependent killing than their corresponding PSKP, respectively. CONCLUSION: Low dose with longer PMB treatment durations may be associated with the emergence of polymyxin resistance. The evolution of PRKP is predominantly mediated by an accumulation of mutations, including those in mgrB, yciC, and pmrB. Lastly, PRKP exhibited reduced growth and increased virulence compared with parental PSKP.

Computational investigation on the binding modes of PET polymer to PETase.

Poly(ethylene terephthalate) (PET) has been widely utilized in daily life, but its non-degradability has induced severe environmental and health problems. Recently, PETase, which has been isolated from bacterium Ideonella sakaiensisis, was reported to have the highest PET degradation activity and specificity under room temperature, but no crystal structure for PET in complex with PETase has been reported. To provide deep insight into the binding mode of PET polymer on PETase and the binding interactions, we employed molecular docking and molecular dynamics simulations to study the substrate binding at the atomic level. Different PET oligomers have been studied with chain lengths varying from 2 to 8. In addition, the binding energies and hot-spot residues were analyzed to gain better insights into the binding mechanism by MM/GBSA approach. The PET oligomers adopt stable and reactive conformations in a shallow cleft on a flat surface of PETase. The binding cleft can only accommodate four moieties, and others beyond the region will be stabilized by the π-stacking interactions with Trp156 at the terephthalic acid terminal. Our studies provide a clear picture of how the binding mode of PET polymer and its interactions with PETase change with the chain length. Those studies would provide useful information for the rational design of catalytically more efficient PETase variants toward plastic degradation.Communicated by Ramaswamy H. Sarma.

Mechanisms of ceftazidime/avibactam resistance in drug-naïve bacteraemic Enterobacterales strains without metallo-beta-lactamase production: Associated with ceftazidime impedance.

In order to investigate ceftazidime/avibactam (CZA) resistance characteristics and mechanisms of bacteraemic Enterobacterales strains that had not been treated previously with CZA, 9708 strains were collected from 43 hospitals in 18 provinces across China from January 2019 to June 2020. The minimum inhibitory concentration (MIC) values of CZA in 165 (1.70%) strains were ≥8/4 mg/L. Ten (6.06%) CZA-resistant strains without metallo-ß-lactamase production were obtained from the individuals without prior exposure to CZA, including six Escherichia coli isolates, three Klebsiella pneumoniae isolates and one Enterobacter cloacae isolate. Whole-genome sequencing revealed that ECB88611, ECB142593 and ECB144539 had encoded disrupted OmpF loss of function. OmpF of ECB126041 had a 2_9 MKRNILAV deletion; OmpK35 of three K. pneumoniae isolates harboured amino acid fragment deletions from positions 1 to 38; and ELB117287 had encoded disrupted OmpF. The G132D amino acid substitution of OmpC of ECB88611, ECB142593 and ECB144539, and the 134_135GD insertion of OmpK36 of three K. pneumoniae isolates were predicted to alter ceftazidime permeability. 333_334 YRIK or YRIN insertions occurred in PBP3 of six E. coli isolates. The relative expression of blaKPC-2 in KPB125108 was 4.527 ± 0.2166 times higher than the control strain, and the relative expression of acrF in six E. coli isolates was 2-3 times higher than the control strain. The addition of phenylalanine-arginine-ß-naphthylamine at 100 mg/L decreased the MIC values of CZA against nine strains significantly. In conclusion, the antimicrobial resistance mechanisms in 10 isolates included increased expression of blaKPC-2, non-functional OMPs, upregulation of efflux pump activity, and variants of PBP3. Most of these mechanisms affected the antimicrobial activity of CZA by impeding ceftazidime.

Phenotypic and genomic comparison of dominant and nondominant sequence-type of Acinetobacter baumannii isolated in China.

A. baumannii is a common clinical pathogen that often causes pneumonia and bloodstream infections in ICU patients. Sequence types (ST) are used to investigate the distribution and spread of A. baumannii. Biological characteristics such as virulence and resistance may play a role in A. baumannii becoming a specific dominant ST(DST,ST191, ST195 and ST208) strain. To characterize the biological, genetic, and transcriptomic differences between the DST and non-dominant ST(NST,ST462 and ST547,etc.) strains in A. baumannii, we performed several biological experiments and genetic, and transcriptomic analyses. The DST group displayed more resistance ability to desiccation, oxidation, multiple antibiotics, and complement killing than the NST group. However, the latter had higher biofilm formation ability than the former. The genomic analysis showed the DST group exhibited more capsule-related and aminoglycoside-resistant genes. Besides, GO analysis indicated that functions involved in lipid biosynthetic, transport, and the metabolic process were up-regulated in the DST group, while KEGG analysis manifested that the two-component system related to potassium ion transport and pili were down-regulated. In short, resistance to desiccation, oxidation, multiple antibiotics, and serum complement killing are important reasons for the formation of DST. Genes related to capsule synthesis and lipid biosynthesis and metabolism play an important role at the molecular level in the formation of DST.

Accelerated Quantum Mechanics/Molecular Mechanics Simulations via Neural Networks Incorporated with Mechanical Embedding Scheme.

A powerful tool to study the mechanism of reactions in solutions or enzymes is to perform the ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations. However, the computational cost is too high due to the explicit electronic structure calculations at every time step of the simulation. A neural network (NN) method can accelerate the QM/MM-MD simulations, but it has long been a problem to accurately describe the QM/MM electrostatic coupling by NN in the electrostatic embedding (EE) scheme. In this work, we developed a new method to accelerate QM/MM calculations in the mechanic embedding (ME) scheme. The potentials and partial point charges of QM atoms are first learned in vacuo by the embedded atom neural networks (EANN) approach. MD simulations are then performed on this EANN/MM potential energy surface (PES) to obtain free energy (FE) profiles for reactions, in which the QM/MM electrostatic coupling is treated in the mechanic embedding (ME) scheme. Finally, a weighted thermodynamic perturbation (wTP) corrects the FE profiles in the ME scheme to the EE scheme. For two reactions in water and one in methanol, our simulations reproduced the B3LYP/MM free energy profiles within 0.5 kcal/mol with a speed-up of 30-60-fold. The results show that the strategy of combining EANN potential in the ME scheme with the wTP correction is efficient and reliable for chemical reaction simulations in liquid. Another advantage of our method is that the QM PES is independent of the MM subsystem, so it can be applied to various MM environments as demonstrated by an SN2 reaction studied in water and methanol individually, which used the same EANN PES. The free energy profiles are in excellent accordance with the results obtained from B3LYP/MM-MD simulations. In future, this method will be applied to the reactions of enzymes and their variants.

Recombination Drives Evolution of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 KL47 to KL64 in China.

Carbapenem-resistant Enterobacteriaceae, especially carbapenemase-producing Klebsiella pneumoniae, is an urgent problem in health care facilities worldwide. K. pneumoniae isolates classified as sequence type 11 (ST11) are largely responsible for the spread of carbapenem-resistant K. pneumoniae (CRKP) in China. Our previous phylogenetic reconstruction suggested that CRKP ST11 capsular locus 64 (KL64) was derived from an ST11-KL47 ancestor through recombination. However, the molecular origin of KL64 remains largely unknown, and our understanding of the recombination is incomplete. Here, we screened a global sample of 22,600 K. pneumoniae genomes and searched for KL64-harboring STs, which were found to be ST1764, ST3685, ST1764-1LV, ST30, ST505, ST147, and ST11, wherein ST1764, ST3685, ST1764-1LV, and ST30 belonged to a clonal complex, CC1764. We compared the genetic structures of representative strains from ST11-KL47, ST11-KL64, CC1764-KL64, ST505-KL64, and ST147-KL64 and further performed phylogenetic analysis and single-nucleotide polymorphism analysis among 248 isolates from all these STs. The results suggested a recombination event has occurred in a homologous ~154-kb region covering KL and the lipopolysaccharide biosynthesis locus (OL) between a recipient ST11-KL47-OL101 and a donor CC1764 (except ST30), giving rise to ST11-KL64-O2v1 strains (recombination I). Furthermore, we also found an infrequent ST11-KL64-O2v1 subclone which was not produced by recombination I but was hybridized from ST11-KL47-OL101 and ST147-KL64-O2v1 strains through recombination of a homologous ~485-kb region covering KL and OL (recombination II). Our findings provide important insights into the role of recombination in the evolution of clinical strains and the diversity of capsule and lipopolysaccharide of widely distributed KPC-associated ST11 K. pneumoniae in China. IMPORTANCE Chromosomal recombination events are considered to contribute to the genetic diversification and ultimate success of many bacterial pathogens. A previous study unravelled the molecular evolution history of ST258 strains, which have been largely responsible for the spread of KPC in the United States. Here, we used comparative genomic analyses to discover two recombination events in ST11 CRKP strains, which is a predominant KPC-associated CRKP clone in China. Two new ST11-CRKP subclones with altered capsule and lipopolysaccharide, which are two primary determinants of antigenicity and antigenic diversity among K. pneumoniae, were produced through these two recombination events, respectively. Horizontal transfer of the KL and OL appears to be a crucial element driving the molecular evolution of K. pneumoniae strains. These findings not only extend our understanding of the molecular evolutionary history of ST11 but also are an important step toward the development of preventive, diagnostic, and therapeutic strategies for CRKP.

Fully quantum calculations of the line shape parameters for 1-0 P(22) and P(31) lines of CO perturbed by He or Ar.

This work reports the full quantum calculations of the spectral line shape parameters for the P(22) line of 13CO and the P(31) line of 12CO in the fundamental band perturbed by He or Ar from 20 to 1000 K for the first time. The generalized spectroscopic cross sections of CO-He/Ar indicate that the Dicke narrowing effect competes with the pressure broadening effect. The pressure broadening can be explained by the dynamic behaviors of intermolecular collisions. The intermolecular inelastic collisions contribute more than 95% to the pressure broadening in both CO-He and CO-Ar systems at high temperatures. Regarding the state-to-state inelastic contributions to pressure broadening, the maximum contribution out of the final state of a given line is close to that out of the initial state. The Dicke narrowing effect influences the line shape profile significantly at high temperatures, which suggests that it is indispensable for reproducing the spectral line profile. With the Dicke narrowing effect, the calculated pressure-broadening coefficients and spectral intensity distribution are in good agreement with the available experimental observations.

Small wards in the ICU: a favorable measure for controlling the transmission of carbapenem-resistant Klebsiella pneumoniae.

PURPOSE: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is one of the leading causes of healthcare-associated infections (HAIs) and is particularly pervasive in intensive care units (ICUs). This study takes ICU layout as the research object, and integrates clinical data and bacterial genome analysis to clarify the role of separate, small wards within the ICU in controlling the transmission of CRKP. METHODS: This study prospectively observed the carriage and spread of CRKP from a long-term in-hospital patient (hereafter called the Patient) colonized with CRKP in the gut and located in a separate, small ward within the ICU. The study also retrospectively investigated CRKP-HAIs in the same ICU. The relationship and transmission between CRKP isolates from the Patient and HAI events in the ICU were explored with comparative genomics. RESULTS: In this study, 65 CRKP-HAI cases occurred during the investigation period. Seven CRKP-HAI outbreaks were also observed. A total of 95 nonrepetitive CRKP isolates were collected, including 32 strains from the Patient in the separate small ward. Phylogenetic analysis based on core genome single-nucleotide polymorphism (cgSNP) showed that there were five possible CRKP clonal transmission events and two clonal outbreaks (A1, A2) during the study. CRKP strains from the Patient did not cause CRKP between-patient transmission or outbreaks in the ICU during the 5-year study period. CONCLUSION: The presence of a long-term hospitalized patient carrying CRKP and positioned in a separate, small ward did not lead to CRKP transmission or infection outbreaks in the ICU. Combining a small-ward ICU layout with normative HAI control measures for multidrug-resistant pathogen infection was effective in reducing CRKP transmission.

Corrigendum: Comparative respiratory tract microbiome between carbapenem-resistant Acinetobacter baumannii colonization and ventilator associated pneumonia.

[This corrects the article DOI: 10.3389/fmicb.2022.782210.].

Molecular mechanisms underlying bacterial resistance to ceftazidime/avibactam.

Ceftazidime/avibactam (CAZ/AVI), a combination of ceftazidime and a novel ß-lactamase inhibitor (avibactam) that has been approved by the U.S. Food and Drug Administration, the European Union, and the National Regulatory Administration in China. CAZ/AVI is used mainly to treat complicated urinary tract infections and complicated intra-abdominal infections in adults, as well as to treat patients infected with Carbapenem-resistant Enterobacteriaceae (CRE) susceptible to CAZ/AVI. However, increased clinical application of CAZ/AVI has resulted in the development of resistant strains. Mechanisms of resistance in most of these strains have been attributed to blaKPC mutations, which lead to amino acid substitutions in ß-lactamase and changes in gene expression. Resistance to CAZ/AVI is also associated with reduced expression and loss of outer membrane proteins or overexpression of efflux pumps. In this review, the prevalence of CAZ/AVI-resistance bacteria, resistance mechanisms, and selection of detection methods of CAZ/AVI are demonstrated, aiming to provide scientific evidence for the clinical prevention and treatment of CAZ/AVI resistant strains, and provide guidance for the development of new drugs. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology.

Comparative Respiratory Tract Microbiome Between Carbapenem-Resistant Acinetobacter baumannii Colonization and Ventilator Associated Pneumonia.

Background: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a common cause of ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients, but its infection and colonization state are difficult to distinguish. If the judgment is wrong, it may aggravate the abuse of antibiotics and further accelerate the evolution of drug resistance. We sought to provide new clues for the diagnosis, pathogenesis and treatment of CRAB VAP based on lower respiratory tract (LRT) microbiota. Methods: A prospective study was conducted on patients with mechanical ventilation from July 2018 to December 2019 in a tertiary hospital. Multi-genomics studies (16S rRNA amplicon, metagenomics, and whole-genome sequencing [WGS]) of endotracheal deep aspirate (ETA) were performed. Results: Fifty-two ICU patients were enrolled, including 24 with CRAB VAP (CRAB-I), 22 with CRAB colonization (CRAB-C), and six CRAB-negative patients (infection-free) (CRAB-N). Diversity of pulmonary microbiota was significantly lower in CRAB-I than in CRAB-C or CRAB-N (mean Shannon index, 1.79 vs. 2.73 vs. 4.81, P < 0.05). Abundances of 11 key genera differed between the groups. Acinetobacter was most abundant in CRAB-I (76.19%), moderately abundant in CRAB-C (59.14%), and least abundant in CRAB-N (11.25%), but its interactions with other genera increased in turn. Metagenomics and WGS analysis showed that virulence genes were more abundant in CRAB-I than in CRAB-C. Multi-locus sequence typing (MLST) of 46 CRAB isolates revealed that the main types were ST208 (30.43%) and ST938 (15.22%), with no difference between CRAB-I and CRAB-C. Conclusion: Lower respiratory tract microbiota dysbiosis including elevated relative abundance of Acinetobacter and reduced bacterial interactions, and virulence enrichment may lead to CRAB VAP.