The variants of polymyxin susceptibility in different species of genus Aeromonas

The aquatic environment is an important medium for the accumulation and dissemination of antibiotic-resistant bacteria as it is often closely related to human activities. Previous studies paid little attention to the prevalence and mechanism of polymyxin-resistant bacteria in the aquatic environment. As a Gram-negative opportunistic pathogen widely distributed in aquatic ecosystems, the antibiotic-resistant profile of Aeromonas spp. deserves much attention. In this study, we identified 61 Aeromonas spp. isolates from water samples in the section of the Yangtze River. The total polymyxin B (PMB) resistance rate of these strains was 49.18% (30/61), showing a high level of polymyxin resistance in Aeromonas spp. The MIC50 and MIC90 for PMB exhibited a significant discrepancy among different species (p < 0.001). The MIC50 and MIC90 for PMB in the Aeromonas hydrophila were 128 mg/L and above 128 mg/L while in Aeromonas caviae and Aeromonas veronii, the MIC50 and MIC90 value were both 2 mg/L. Only two A. veronii strains (MIC = 2 mg/L) and one A. caviae strain (MIC = 0.5 mg/L) were identified as carrying mobilized polymyxin resistant gene mcr-3.42, and mcr-3.16. All mcr genes were located in the chromosome. This is the first report that the downstream region of mcr-3.42 was the truncated mcr-3-like gene separated by the insertion sequences of ISAs20 (1,674 bp) and ISAs2 (1,084 bp). Analysis of epidemiology of mcr-positive Aeromonas genomes from GenBank database showed that the genus Aeromonas and the aquatic environment might be the potential container and reservoir of mcr-3. By the whole-genome sequencing and qRT-PCR, we inferred that the sequence differences in the AAA domain of MlaF protein and its expression level among these three species might be involved in the development of polymyxin resistance. Our study provided evidences of the possible mechanism for the variety of polymyxin susceptibility in different species of the genus Aeromonas and a theoretical basis for the surveillance of the aquatic environment.

Inhibition of coagulation factor XI attenuates inflammation in myocardial ischemia/reperfusion injury

Background

Increasing evidence suggests that FXI is an attractive target for antithrombotic therapy because it reduces thrombosis without increasing bleeding risk. Patients with decreased levels of FXI are at reduced risk of cardiovascular diseases and thromboembolic events. We have already revealed that depletion of FXI inhibits the vascular coagulation-inflammatory circuit in angiotensin II-induced arterial hypertension. However, the effect of FXI depletion on cardiac inflammation and vascular function in ischemia/reperfusion (I/R) injury is unknown.

Purpose

Using FXI-depleted mice to investigate the role of FXI in inflammation response post cardiac I/R injury.

Methods

8–12 weeks old C57BL/6J male mice were injected intraperitoneally with FXI antisense oligonucleotide (FXI ASO) or scrambled controls for a period of 2 weeks. Then we temporarily ligated the left anterior descending (LAD) for 45 minutes to induce myocardial ischemia, followed by the reperfusion for 72 hours (ischemia/reperfusion injury, IRI). Myocardial inflammation and vascular function were analyzed by flow cytometry, real-time PCR, vascular relaxation studies from isolated aortic segment in organ chamber and chemiluminescence photon counting of oxidative burst in whole blood.

Results

FXI ASO treatment reduced hepatic FXI mRNA levels and prolonged activated partial thromboplastin time. Compared to scrambled ASO injected mice, oxidative burst from whole blood and endothelial dysfunction were decreased in FXI ASO injected mice with IRI. Compared to control groups, depletion of FXI attenuated cardiac infiltration of CD45+CD11b+ cells, especially LyG-LyChigh monocytes and LyG+ neutrophils at day 3 in I/R injury. Furthermore, the expression levels of adhesion molecules and expression of pro-inflammatory cytokines, such as Vcam-1, CCL2, IL-6 and IL-1b, in ischemic myocardium were significantly decreased in the FXI depleted mice of I/R injury.

Conclusion

Our results suggest that Inhibition of FXI leads to reduction of vascular dysfunction and ROS production in I/R injury, as well as attenuation of the inflammatory response and the influx of inflammatory cells in ischemic myocardium. This indicates that FXI could be a potential target for further treatment in cardiac IRI.

Funding Acknowledgement

Type of funding sources: Public grant(s) – EU funding. Main funding source(s): TICARDIO project has received funding from the European Union's Horizon 2020 research and Innovation programme under the Marie Skłodowska-Curie grant agreement No 813409.

Efficacy and safety of novel carbapenem–β-lactamase inhibitor combinations: Results from phase II and III trials

Objectives

The addition of novel β-lactamase inhibitors to carbapenems restores the activity against multidrug-resistant Gram-negative bacteria. The aim of this study was to summarize the evidence on the efficacy and safety of novel carbapenem–β-lactamase inhibitor combinations.

Methods

We conducted a meta-analysis of clinical trials comparing novel carbapenem–β-lactamase inhibitor combinations with comparators to assess the clinical and microbiological responses, mortality, and adverse events (AEs).

Results

A total of 1,984 patients were included. The pooled risk ratios (RRs) of clinical cure, microbiological eradication, all-cause mortality, and 28-day mortality were 1.11 (95% CI: 0.98–1.26), 0.98 (95% CI: 0.82–1.16), 0.90 (95% CI: 0.49–0.94), and 0.68 (95% CI: 0.49–0.94) between the novel carbapenem–β-lactamase inhibitor combinations and control groups. Sensitivity analysis revealed that the phase II trial of imipenem–cilastatin/relebactam (ICR) against complicated urinary tract infections could be the most important factor of heterogeneity for the microbiological response. The therapeutic effect of novel carbapenem–β-lactamase inhibitor combinations was better in meropenem–vaborbactam (MEV), phase III trials, and number of patients less than 200. The RRs of AEs from any cause and serious adverse events (SAEs) for patients receiving novel carbapenem–β-lactamase inhibitor combinations were 0.98 (95% CI: 0.93–1.04) and 1.01 (95% CI: 0.75–1.36), respectively.

Conclusions

ICR and MEV were superior to comparators for clinical cure and survival rate in the treatment of complicated infections, and both were as tolerable as the comparators.

[Correlation between heart rate index, SBPpeak-to-SBPrest ratio and peak oxygen consumption in patients with chronic heart failure]

Objective: To investigate the correlation between heart rate index (HRI), systolic blood pressure(SBP) peak-to-SBPrest ratio (SBPR) and peak oxygen consumption (peakVO₂) in patients with chronic heart failure (CHF), and discuss the possibility of using HRI and SBPR collected during exercise to assess the exercise tolerance of CHF patients in the absence of gas analysis. Methods: In this cross-sectional study, a total of 547 patients with CHF who underwent cardiopulmonary exercise test(CPET) in Tongji Hospital Heart Rehabilitation Center Affiliated to Tongji University from March 2007 to December 2018 were collected retrospectively, focusing on their clinical data including age, gender, type of heart failure,BMI as well as data collected during their CPETs, such as peakVO₂, HRI and SBPR. Spearman univariate correlation analysis was used for statistical analysis, to unveil the correlations between peakVO₂ and those parameters, and multiple linear regression analysis was also conducted. Results: A total of 547 CHF patients conducting CPET were included in this research, of which 447 were male, at age of 63(56, 69). Univariate analysis indicates that HRI, SBPR and peakVO₂ showed significant positive correlation (r=0.323, 0.263, respectively, all P<0.001); Age and peak VO₂ showed significant negative correlation(r=-0.207, P<0.001); Male patients showed peakVO₂ higher than female(r=-0.229, P<0.001); PeakVO₂ of heart failure with reduced ejection fraction(HFrEF) was lower than heart failure with mid-range ejection fraction(HFmrEF)and heart failure with preserved ejection fraction(HFpEF) (r=0.181, P<0.001). Body mass index (BMI) had no significant correlation with peakVO₂ (P>0.05). Multivariate linear regression analysis showed that the HRI, SBPR were positively correlated with peakVO₂(t=7.68, 5.08, respectively, all P<0.05), while age and BMI showed negative correlation with peakVO₂(t=-5.43, -0.31, respectively, all P<0.05). PeakVO₂ of male was higher than female(t=-6.03, P<0.05), and peakVO₂ of HFrEF was lower than those of HFmrEF and HFpEF(t=3.17, 4.48, respectively, all P<0.05). A linear equation (F=33.52, adjusted R²=0.29) could be constructed: peakVO₂=10.65(male) or 8.53(female)+4.26HRI+3.31SBPR-0.07age-0.13BMI+0(HFrEF) or 1.05 (HFmrEF) or 1.62(HFpEF). Conclusion: HRI and SBPR are positively correlated with peakVO₂. In the absence of gas analysis, it is possible to apply HRI and SBPR during exercise to predict exercise tolerance in patients with CHF.

Psoriasis may increase the risk of lung cancer: a two-sample Mendelian randomization study

BACKGROUND

Although many studies have indicated that Psoriasis (PsO) could contribute to the risk of lung cancer, no study has reported a clear causal association between them. Our aim was to explore the potential causal association between PsO and the lung cancer risk using Mendelian randomization (MR) design.

METHODS

To explore a causal association between the PsO and lung cancer, we used large-scale genetic summary data from genome-wide association study (GWAS), including PsO (n = 337 159) and lung cancer (n = 361 586), based on previous observational studies. Our main analyses were conducted by inverse-variance weighted (IVW) method with random-effects model, with a complementary with the other two analyses: weighted median method and MR-Egger approach.

RESULTS

The results of IVW methods demonstrated that genetically predicted PsO was significantly associated with higher odds of lung cancer, with an odds ratio (OR) of 1.06 (95%CI, 1.01-1.12; P = 0.02). Weighted median method and MR-Egger regression also demonstrated directionally similar results (All P < 0.05). In addition, both funnel plots and MR-Egger intercepts indicated no directional pleiotropic effects between PsO and lung cancer.

CONCLUSIONS

Our study provided potential evidence between genetically predicted PsO and lung cancer, which suggested that enhanced screening for lung cancer allows early detection of lung cancer.

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.

Rifaximin Modulates the Gut Microbiota to Prevent Hepatic Encephalopathy in Liver Cirrhosis Without Impacting the Resistome

The gut microbiota has an important role in the pathogenesis of hepatic encephalopathy(HE). Rifaximin, an intestinal non-absorbable antibacterial agent, is effective in the treatment of HE. However, whether long-term prophylactic use induces antibacterial resistance and its mechanism for treating HE remains unclear. This prospective study assessed the impact of 12 weeks rifaximin administration on the gut microbiota and resistome in cirrhotic patients. Fecal sampling was conducted 1 day before the first rifaximin administration and at Weeks 1, 2, 4, 6, 8, 10, 12 of the study. Thirty cirrhotic patients who were in remission from recurrent HE was enrolled to receive rifaximin (400mg TID for 12 weeks). Rifaximin improved hyperammonemia and cognitive function in the 21 patients who completed rifaximin treatment. The dynamic observations showed the gut microbiota diversity, composition and the number of resistance genes, plasmids, insertion sequences did not change significantly during the period(P>0.05). Metabolic pathways such as aromatic amino acids, tryptophan synthesis, urea cycle, and LPS synthesis reduced. No new antimicrobial resistance genes was emergenced. However, the number of aminoglycosides, rifamycin and phenolic resistance genes increased, whereas tetracycline, fosfomycin and cephamycin decreased (P<0.05). Changes in the abundance of E. coli, K. pneumoniae, and B. longum strains correlated with changes of resistance genes. Prophylactic use of rifaximin for 12 weeks improved hyperammonemia and neurophysiological function, maintained gut microbiota diversity, composition and did not change the overall resistome. Rifaximin altered expression of HE-related metabolic pathways. All of these effects could play a key role in preventing HE. Clinical Trial Registration: ChiCTR1900022234 (registered at the Chinese Clinical Trial Registry).

Genomic epidemiology and characterisation of penicillin-sensitive Staphylococcus aureus isolates from invasive bloodstream infections in China: an increasing prevalence and higher diversity in genetic typing be revealed

Many countries have reported increasing rates of penicillin-susceptible methicillin-sensitive Staphylococcus aureus (MSSA-PEN^S). To date, there is relatively little known about the current situation and molecular characteristics of MSSA-PEN^S in China. In this study, we carried out a laboratory-based multi-region retrospective study to investigate the genomic epidemiology and characterisation of MSSA-PEN^S isolated from invasive bloodstream infections (BSIs) across 17 provinces. The prevalence of MSSA-PEN^S isolates increased significantly over the 6-year period, with the proportion increasing from 3.51% in 2014-8.80% in 2019, an average relative increase of 22.14% per year (95% confidence interval 9.67%-34.61%, P for trend <0.001), suggesting that China is experiencing a resurgence of MSSA-PEN^S. Phylogenetic analysis showed a higher strain diversity occurred; the most frequent clonal complexes (CCs) identified were CC188 (17.14%), CC398 (15.71%) and CC5 (15.71%). Over half of MSSA-PEN^S strains were pan-susceptible, with erythromycin the most frequent resistance observed. Moreover, 25 isolates were identified as immune evasion cluster negative, including CC15, CC188 and CC1, and 6 strains encoded the Panton-Valentine leucocidin gene. Importantly, virulence assays showed that MSSA-PEN^S exhibited a level of virulence comparable to that of penicillin-resistant MSSA (MSSA-PEN^R), indicating that more-sensitive strains should not be mistaken for lacking aggressiveness in vivo. Furthermore, 11 of these isolates were confirmed as blaZ positive but phenotype sensitive, with different amino acid changes in blaZ. Our data support the recommendation to clinicians regarding the usage of penicillin in invasive BSIs caused by MSSA-PEN^S, which might create a novel opportunity for better antimicrobial stewardship in the future.

Socioeconomic Burden of Bloodstream Infections Caused by Carbapenem-Resistant Enterobacteriaceae

Background

Although infection with carbapenem-resistant Enterobacteriaceae (CRE) has become an urgent public health threat worldwide, the socioeconomic burden of CRE bloodstream infection (BSI) remains to be clarified.

Methods

This retrospective study included all patients infected with Escherichia coli or Klebsiella pneumoniae who were hospitalized for BSI from 2013 to 2015. Socioeconomic burden, including direct and indirect economic burden, was compared in patients infected with carbapenem-sensitive Enterobacteriaceae (CSE) and CRE following 1:1 propensity score matching (PSM) to control for confounding variables.

Results

Data from 879 patients with Enterobacteriaceae BSI were evaluated, including 152 (17.3%) patients infected with CRE and 727 (82.7%) infected with CSE. PSM yielded 112 pairs of 224 patients. Median hospital length of stay did not differ significantly in the CRE and CSE groups (35 vs 29 days, P = 0.089), but in-hospital 28-day mortality rate was significantly higher in patients infected with CRE than with CSE (45.5% vs 32.1%, P = 0.040). Median direct economic burden was significantly greater in patients with CRE-BSI than with CSE-BSI during hospitalization ($24,940.1 vs 16,864.0, P = 0.017) but not during the period after infection ($10,403.4 vs 8498.0, P = 0.178). Drug expenditure accounted for the largest proportion of costs in both groups. The median disability-adjusted life year (DALY) was higher in CRE-BSI than in CSE-BSI patients, but the difference was not statistically significant (7.9 vs 6.7 years, P = 0.190). Median indirect economic burden did not differ significantly in these two groups ($3848.5 vs 1139.9, P = 0.304), although indirect economic burden increased significantly from 2013 to 2015 in patients with CRE-BSI.

Conclusion

Carbapenem resistance had a major impact on the clinical and socioeconomic burden of patients with Enterobacteriaceae BSI. The higher mortality rate in patients with CRE-BSI was associated with increased direct healthcare burden and indirect socioeconomic loss.

Biomimetic hybrid hydrogel for hemostasis, adhesion prevention and promoting regeneration after partial liver resection

Partial liver resection is an established treatment for hepatic disorders. However, surgical bleeding, intra-abdominal adhesion and rapid liver regeneration are still major challenges after partial liver resection, associated with morbidity and mortality. Herein, a biomimetic hybrid hydrogel, composed of oxidized hyaluronic acid, glycol chitosan and MenSCs-derived conditioned medium (CM), is presented to address these issues. The hybrid hydrogel is formed through reversible Schiff base, and possesses injectability and self-healing capability. Moreover, hybrid hydrogel exhibits the capabilities of hemostasis, anti-infection, tissue adhesion and controllable release of cargoes. Based on in vivo studies of the multifunctional hybrid hydrogel, it is demonstrated that acute bleeding in partial liver resection can be ceased immediately by virtue of the hemostasis features of hybrid hydrogel. Also, a significant reduction of intra-abdominal adhesion is confirmed in hybrid hydrogel-treated resection surface. Furthermore, upon the treatment of hybrid hydrogel, hepatic cell proliferation and tissue regeneration can be significantly improved due to the controllably released cytokines from MenSCs-derived CM, exerting the effects of mitogenesis and anti-inflammation in vivo. Thus, the biomimetic hybrid hydrogel can be a promising candidate with great potential for application in partial liver resection.

In Vitro Activity Comparison of Ceftazidime-Avibactam and Aztreonam-Avibactam Against Bloodstream Infections With Carbapenem-Resistant Organisms in China

Objectives

The aim of this work was to investigate the activity of ceftazidime–avibactam (CZA) and aztreonam–avibactam (AZA) against bloodstream infections caused by carbapenem-resistant organisms (CROs).

Methods

Non-duplicate CROs, including 56 carbapenem-resistant Escherichia coli (CR-Eco), 318 carbapenem-resistant Klebsiella pneumoniae (CR-Kpn), and 65 carbapenem-resistant Pseudomonas aeruginosa (CR-Pae), were collected using the Blood Bacterial Resistant Investigation Collaborative System (BRICS) program in China. The minimum inhibitory concentrations (MICs) of 24 antibiotics were tested. Carbapenemase genes were amplified for CZA-resistant CROs by PCR. The MICs of CZA and AZA were further determined with avibactam at 8 and 16 mg/L, respectively.

Results

The resistance rate of polymyxin B against CROs was less than 5%. Only one CR-Kpn was resistant to tigecycline. The resistance rates of CZA against CR-Eco, CR-Kpn, and CR-Pae were 75.0%, 12.6%, and 18.5%, respectively. The MIC₉₀ values of AZA against CR-Eco, CR-Kpn, and CR-Pae were 2/4, 1/4, and 64/4 mg/L, respectively. Among the CZA-resistant CROs, 42 (100%) CR-Eco, 24 (60%) CR-Kpn, and 1 (8.3%) CR-Pae isolates harbored metallo-β-lactamase genes. The increase of avibactam concentration enhanced the susceptibility of CZA and AZA against CROs, especially for CR-Eco and CR-Kpn.

Conclusions

The in vitro activity of AZA was superior to that of CZA against CR-Eco and CR-Kpn, whereas CZA showed better effect against CR-Pae.

[The value of renal color Doppler ultrasound in evaluating the severity and prognosis of patients with acute organophosphorus pesticide poisoning complicated by acute kidney injury]

Objective: To analyze the value of renal color Doppler ultrasound examination and clinical indicators in evaluating the severity and prognosis of acute organophosphorus pesticide poisoning (AOPP) complicated by acute kidney injury (AKI) . Methods: In November 2019, 86 AOPP patients complicated by AKI who were admitted from May 2018 to May 2019 were selected as the observation group, and they were divided into AKI stage 1 group (n=37) , AKI stage 2 group (n=32) and AKI stage 3 group (n=17) . 40 healthy people were selected as the control group. The differences in power Doppler ultrasound (PDU) score, renal interlobular artery resistance index (RI) value and related clinical indicators of each group were measured and analyzed, and the correlations between the indicators were analyzed. At the same time, binary logistic regression was used to analyze the risk factors of death in AOPP patients complicated by AKI. Results: There were statistically significant differences in Acute Physiology and Chronic Health Evaluation (APACHE) Ⅱscore, mean arterial pressure (MAP) , serum creatinine (SCr) and the length of continuous renal replacement therapy (CRRT) between different groups (P<0.05) . Compared with the control group, the APACHE Ⅱscores and SCr of patients in the AKI stage 2 and resistance index AKI stage 3 groups increased, while the MAP decreased (P<0.05) . Compared with the control group, AKI stage 1 group and AKI stage 2 group, the PDU score of patients in the AKI stage 3 group was significantly decreased, and the renal interlobular artery RI value was significantly increased (P<0.05) . SCr was positively correlated with the RI value of renal interlobular arteries and CRRT days (r=0.435, 0.713, P<0.05) , and was negatively correlated with renal PDU score (r=-0.643, P<0.05) . The renal PDU score was negatively correlated with the RI value of renal interlobular arteries and CRRT days (r=-0.350, -0.556, P<0.01) . Binary logistic regression analysis showed that SCr (OR=1.017, 95%CI: 1.004-1.041) and APACHE Ⅱ score (OR=1.289, 95%CI: 1.019-1.827) were risk factors for death in patients with AOPP complicated by AKI (P<0.05) . Conclusion: Both PDU score and the RI value of renal interlobular artery can reflect the severity and stage of patients with AOPP complicated by AKI to a certain extent, but neither of them is a key factor affecting the death of patients.

What is an appropriate caesarean delivery rate for China: a multicentre survey

Objective

To assess the current status of caesarean delivery (CD) in China, propose reference CD rates for China overall, and by regions, investigate the main indications for CDs and identify possible areas for safe reduction.

Design

A multicentre cross‐sectional study.

Setting

A total of 94 hospitals across 23 provinces in China.

Population

A total of 73 977 randomly selected deliveries.

Methods

We used a modified Robson classification to characterise CDs in subgroups and by regions, and the World Health Organization (WHO) C‐Model to calculate reference CD rates.

Main outcome measures

CD rates in China.

Results

In 2015–2016, the overall CD rate in China was 38.9% (95% CI 38.6–39.3%). Considering the obstetric characteristics of the population, the multivariable model‐based reference CD rate was estimated at 28.5% (95% CI 28.3–28.8%). Accordingly, an absolute reduction of 10.4% (or 26.7% relative reduction) may be considered. The CD rate varied substantially by region. Previous CD was the most common indication in all regions, accounting for 38.2% of all CDs, followed by maternal request (9.8%), labour dystocia (8.3%), fetal distress (7.7%) and malpresentation (7.6%). Overall, 12.7% of women had prelabour CDs, contributing to 32.8% of the total CDs.

Conclusions

Nearly 39% of births were delivered by caesarean in China but a reduction of this rate by a quarter may be considered attainable. Repeat CD contributed more than one‐third of the total CDs. Given the large variation in maternal characteristics, region‐specific or even hospital‐specific reference CD rates are needed for precision management of CD.

Tweetable abstract

The caesarean rate in 2015–2016 in China was 38.9%, whereas the reference rate was 28.5%.

The caesarean rate in 2015–2016 in China was 38.9%, whereas the reference rate was 28.5%.

Linked article This article is commented on by M Varner, p. 148 in this issue. To view this mini commentary visit https://doi.org/10.1111/1471-0528.16953.

Trends towards revealing the genetic architecture of sheep tail patterning: Promising genes and investigatory pathways

Different sheep breeds have evolved after initial domestication, generating various tail phenotypic patterns. The phenotypic diversity of sheep tail patterns offers ideal materials for comparative analysis of its genetic basis. Evolutionary biologists, animal geneticists, breeders, and producers have been curious to clearly understand the underlying genetics behind phenotypic differences in sheep tails. Understanding the causal gene(s) and mutation(s) underlying these differences will help probe an evolutionary riddle, improve animal production performance, promote animal welfare, and provide lessons that help comprehend human diseases related to fat deposition (i.e., obesity). Historically, fat tails have served as an adaptive response to aridification and climate change. However, the fat tail is currently associated with compromised mating and animal locomotion, fat distribution in the animal body, increased raising costs, reduced consumer preference, and other animal welfare issues such as tail docking. The developing genomic approaches provide unprecedented opportunities to determine causal variants underlying phenotypic differences among populations. In the last decade, researchers have performed several genomic investigations to assess the genomic causality underlying phenotypic variations in sheep tails. Various genes have been suggested with the prominence of several potentially significant causatives, including the BMP2 and PDGFD genes associated with the fat tail phenotype and the TBXT gene linked with the caudal vertebrae number and tail length. Although the potential genes related to sheep tail characteristics have been revealed, the causal variant(s) and mutation(s) of these high-ranking candidate genes are still elusive and need further investigation. The review discusses the potential genes, sheds light on a knowledge gap, and provides possible investigative approaches that could help determine the specific genomic causatives of sheep tail patterns. Besides, characterizing and revealing the genetic determinism of sheep tails will help solve issues compromising sheep breeding and welfare in the future.

[Epidemiological characteristics of Chlamydia pneumoniae in cases with acute respiratory infection in Beijing, 2015-2019]

Objective: To analyze the epidemiological characteristics of Chlamydia pneumoniae infection among patients with acute respiratory infection in Beijing from 2015 to 2019. Methods: The epidemiological data of acute respiratory infection patients from 35 sentinel hospitals in Beijing were collected by the respiratory pathogen surveillance system in Beijing. The clinical samples were collected to detect Chlamydia pneumoniae, and the sequence of the VD4 region of the ompA gene in positive samples was analyzed. Results: From January 2015 to December 2019, the overall positive rate of Chlamydia pneumoniae among patients with acute respiratory infection in Beijing was 0.34% (129/37 460). The positive rate of Chlamydia pneumoniae generally increased in March, reaching the peak in May, and started to drop in July, with a duration of about 5-8 months. The epidemic season in different years fluctuated by 1-2 months. The positive monthly rate of Chlamydia pneumoniae was no less than 0.30% in every epidemic season. The positive rate of Chlamydia pneumoniae was the highest in the 5-44 years old group and the highest in 10-14 year-olds. The risk of Chlamydia pneumoniae infection increased with age in patients younger than 25 years old and decreased in those older one aged than 25 years of age. The positive rates in male and female patients were 0.33% (68/20 830) and 0.37% (61/16 528), respectively, and there was no significant difference between the two groups (χ²=0.486, P=0.486). The positive rate of Chlamydia pneumoniae in patients with common pneumonia was higher than that in patients with upper pneumonia and severe pneumonia (χ²=36.797, P<0.01). Other respiratory pathogens were also detected in the Chlamydia pneumoniae samples, and the top four pathogens appeared as Haemophilus influenzae (15 cases), Streptococcus pneumoniae (13 cases), Rhinovirus (8 cases), and Stenotrophomonas maltophilia (7 cases). 101 strains of 129 Chlamydia pneumoniae positive samples were identified as type A by sequencing. Conclusions: The annual epidemic pattern of Chlamydia pneumoniae in Beijing, is unimodal, and the epidemic season generally appears from March to July. The seasonal characteristics of Chlamydia pneumoniae in Beijing can be used for the differential diagnosis of Chlamydia pneumoniae from other respiratory pathogens. Chlamydia pneumoniae is most common in people aged 5-44 years, and the primary genotype is type A. People aged 10-44 years old suffer the highest incidence. If the nucleic acid positive rate of Chlamydia pneumoniae exceeds 0.30% for two consecutive months, the high prevalence period of Chlamydia pneumoniae can be preliminarily expected. Chlamydia pneumoniae infection has a higher probability of progressing to severe pneumonia from general pneumonia.

[Clinical characteristics of patients infected with Chlamydia pneumoniae in Beijing from 2015 to 2019]

Objective: To aralyze the clinical characteristics of Chlamydia pneumoniae infection in Beijing. Methods: Based on Beijing Respiratory Pathogen Surveillance System, acute respiratory infection patients were recruited from 35 different types of sentinel hospitals in Beijing. Their epidemiological and clinical data were systematically collected and clinical specimens were also obtained. Nuclear acid testing was performed for 30 types of respiratory pathogens (including Chlamydia pneumoniae). The identified patients of Chlamydia pneumoniae infection were divided into two groups, the acute upper respiratory tract infection (AURI) group and pneumoniae group. The differences in clinical characteristics, laboratory examination and prognosis were compared by using independent sample t test, Mann-Whitney U test, χ² test or Fisher's exact probability test. Results: A total of 119 patients of Chlamydia pneumoniae infection were included, including 12 patients in the AURI group and 107 patients in pneumoniae group. Chlamydia pneumoniae infection mainly occurred in people aged from 5 to 44 years, accounting for 81.5% (97/119). The three most common clinical symptoms were cough (92.4%, 110/119), fever (88.8%, 95/107), and sputum production (76.5%, 91/119). White blood cell counts increased in 39.3% (46/117) of patients. Neutrophile granulocyte proportion increased in 39.7% (46/116) of patients. Platelet count increased in 36.9% (41/111) of patients. An increase of the creatine kinase MB isoenzyme (CKMB) was observed in 12 pneumonia patients (24.5%, 12/49). Radiological examination showed that 90.6% (87/105) of patients in the pneumoniae group had pulmonary parenchymal changes; the lesion occurred most commonly in the lower right lung lobe (34.3%, 36/105) and the lower left lung lobe (27.6%, 29/105). Although 73.8% (79/107) of patients in the pneumoniae group were hospitalized, no case received intensive care unit or mechanical ventilation. As to outcomes, one patient developed respiratory failure and 6 patients suffered myocardial injury. No death was observed in this study. The median days of hospitalization and course of illness for pneumonia patients M(P₂₅,P₇₅) were 10.0 (7.0, 13.0) days and 18.0 (13.5, 22.0) days, respectively. Conclusion: Generally, Chlamydia pneumoniae infections in Beijing from 2015 to 2019 were mild, and the main clinical manifestations were cough, fever and sputum. However, most patients in the pneumoniae group caused by Chlamydia pneumoniae still required hospitalization but with a better outcome.

Characterization of highly virulent community-associated methicillin-resistant Staphylococcus aureus ST9-SCCmec XII causing bloodstream infection in China

Previous studies have shown that livestock (LA)-MRSA ST398 evolved from a human-adapted methicillin-susceptible S. aureus (MSSA) clone. However, detailed information regarding ST9 is still unclear. Here, we characterized a community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) ST9-SCCmec XII isolate that has not been previously reported to cause serious disease in China. We obtained whole-genome sequences of one ST9-t899-XII isolate—ZY462471—from a patient with bloodstream infection without livestock contact. The antibiotic susceptibilities of ZY462471 were determined and the clinical information was extracted from medical notes and compared with twenty-seven previously sequenced genomes. Phylogenetic reconstruction was performed to investigate the probable host evolutionary origins of ZY462471, and the difference in resistome and virulence factors were investigated. Virulence assay was performed to evaluate the high virulence potential of ZY462471 and compare the virulence between the closest ST9 MSSA neighbours. Clinical data suggested that ZY462471 is a CA-MRSA. Phylogenetic analysis showed a much closer relationship of ZY462471 with human-associated MSSA ST9 isolates than other LA-MRSA ST9 isolates, suggesting that ZY462471 probably evolved from ST9 MSSA predecessors by acquiring an SCCmec cassette. Importantly, virulence assays indicated that ZY462471 was highly virulent and compared with the MSSA ST9 predecessors, ZY462471 did not show attenuated virulence. Finally, we found that ZY462471 harboured an immune evasion cluster (IEC)-carrying βC-Φ, which is typically found in human clinical S. aureus rather than LA-MRSA isolates, suggesting that ZY4762471 obtained the IEC-carrying βC-Φs from human clinical S. aureus strains. Considering its high virulence potential, this strain should be monitored to prevent more widespread dissemination.

Genomic and Transcriptomic Analysis of Colistin-Susceptible and Colistin-Resistant Isolates Identify Two-Component System EvgS/EvgA Associated with Colistin Resistance in Escherichia coli

Purpose

Colistin is one of the last-resort antimicrobial agents that combat the increasing threat of multi-drug resistant (MDR) gram-negative bacteria. Based on the known mechanism of colistin resistance which contributes to chromosomal mutations involved in the synthesis and modification of lipopolysaccharide (LPS), we explored the regulatory genes mediate colistin resistance, by whole genome sequencing and transcriptome analysis.

Materials and Methods

In this study, a colistin-resistant (Col^r) strain Escherichia coli ATCC 25922-R was generated from colistin-sensible (Col^s) strain E. coli ATCC 25922 by colistin induction. We compared the genome and transcriptome sequencing result from Col^s and Col^r strain. MALDI-TOF mass spectrometry was used to detect LPS.

Results

Genomic analysis and complementation experiment demonstrated the PmrB amino acid substitution in ATCC 25922-R (L14R) conferred the colistin resistance phenotype. Results of RNA sequencing (RNA-Seq) and comparative transcriptome analysis indicated that the two-component system EvgS/EvgA is highly involved in the global regulation of colistin resistance.

Conclusion

This study demonstrated that PmrB L14R amino acid substitution resulted in colistin resistance, and two-component system EvgS/EvgA might participate in colistin resistance in E. coli.