Phylogenomic insights into evolutionary trajectories of multidrug resistant S. pneumoniae CC271 over a period of 14 years in China.

BACKGROUND: Streptococcus pneumoniae is a gram-positive opportunistic pathogen, and infection risks of S. pneumoniae can be profoundly augmented by its acquired multidrug-resistance (MDR). The rapid development of MDR in S. pneumoniae was attributed to the international dissemination of a small number of multidrug-resistant "clones." Clonal complex (CC) 271 is a prevalent MDR CC in the world and the most prevalent CC in China. However, the evolutionary trajectories of multidrug-resistant S. pneumoniae CC271 in China still are largely unknown. METHODS: We investigated a collection of 1312 S. pneumoniae isolates collected from 28 tertiary hospitals in China from 2007 to 2020. Recombination prediction and recombination-masked phylogenetic analysis were combined to determine the population structure and mode of evolution of CC271. Data from the Global Pneumococcal Sequencing program (GPS) were combined to understand the global distribution of clones identified in this study. Bayesian analysis were recruited to analysis the evolutionary dynamics of dominant clones within CC271 in China. RESULTS: The phylogenomic analysis resulted in the discovery of two globally distributed clones, ST271-A and ST271-B. ST271-A was a derivative of ST236 and an ancestor of ST271-B and ST320, refining the internal phylogenetic relationship of CC271. ST271-B was the most dominant clone in China, with higher ß-lactam resistance especially for cephalosporins comparing to other MDR clones. Bayesian skyline plot showed a rapid expansion of 19F ST271-B from 1995 to 2000, which correlates with the widespread use of cephalosporins in the 1990s in China. 19A ST320, a vaccine-escape clone, is the second largest population in China. The Bayesian skyline plot showed that the 19A ST320 began to expand rapidly around 2001, which appeared to coincide with the prevalence of 19A after application of PCV7 in 2000 in the USA. We also observed frequent transmission of 19A ST320 between countries. It suggests that mass vaccination in some countries could affect the prevalence of clones in unvaccinated countries in the context of high-frequency international transmission. CONCLUSIONS: Our results refined the internal phylogenetic relationship of CC271, showing that the 19F ST271-B and 19A ST320 evolved independently from ST271-A, with different histories and driving forces for their evolution and dissemination in China.

Synergism of eravacycline combined with other antimicrobial agents against carbapenem-resistant Enterobacteriaceae and Acinetobacter baumannii.

OBJECTIVES: This study aimed to investigate the synergistic activity of eravacycline combined with other antimicrobial agents against carbapenem-resistant Enterobacteriaceae and Acinetobacter baumannii collected from China. METHODS: Sixty carbapenem-resistant strains, including 20 Escherichia coli, 20 Klebsiella pneumoniae, and 20 Acinetobacter baumannii were investigated for the synergy analysis. Imipenem, ceftazidime, cefoperazone-sulbactam, ciprofloxacin, amikacin, and polymyxin B were selected to investigate their efficacy in combination with eravacycline against 60 carbapenem-resistant strains. Minimum inhibitory concentrations (MICs) of the drugs were determined by broth microdilution method. The efficacy of eravacycline in combination with these agents was determined by the chequerboard method. RESULTS: Antimicrobial susceptibility testing revealed that polymyxin B was most effective against all carbapenem-resistant strains, with resistance rates between 0% and 15%. Eravacycline showed potent activity against E. coli with an 85% susceptibility rate, and may also have activity against K. pneumoniae and A. baumannii with low MIC90 values. The chequerboard method showed that eravacycline-polymyxin B was the most effective combination against E. coli and K. pneumoniae, with more than 30% synergy. The most active combination against A. baumannii was eravacycline-ceftazidime and eravacycline-imipenem, which showed synergy in more than 50% of isolates. CONCLUSION: Eravacycline combined with ß-lactams or polymyxin B can lead to synergistic effects against clinically common carbapenem-resistant Gram-negative bacteria. The synergistic effects of eravacycline-based combinations varied in different species. A combination of eravacycline and polymyxin B may be considered for the treatment of carbapenem-resistant E. coli and K. pneumoniae; eravacycline in combination with ceftazidime or a carbapenem antimicrobial may be considered for the treatment of carbapenem-resistant A. baumannii.

Streptococcus sputorum, a Novel Member of Streptococcus with Multidrug Resistance, Exhibits Cytotoxicity.

We describe the genomic and phenotypic characteristics of a novel member of Streptococcus with multidrug resistance (MDR) isolated from hospital samples. Strains SP218 and SP219 were identified as a novel Streptococcus, S. sputorum, using whole-genome sequencing and biochemical tests. Average nucleotide identity values of strains SP218 and SP219 with S. pseudopneumoniae IS7493 and S. pneumoniae ST556 were 94.3% and 93.3%, respectively. Genome-to-genome distance values of strains SP218 and SP219 with S. pseudopneumoniae IS7493 and S. pneumoniae ST556 were 56.70% (54-59.5%) and 56.40% (52.8-59.9%), respectively. The biochemical test results distinguished these strains from S. pseudopneumoniae and S. pneumoniae, particularly hydrolysis of equine urate and utilization of ribose to produce acid. These isolates were resistant to six major classes of antibiotics, which correlated with horizontal gene transfer and mutation. Notably, strain SP219 exhibited cytotoxicity against human lung epithelial cell line A549. Our results indicate the pathogenic potential of S. sputorum, and provide valuable insights into mitis group of streptococci.

Novel Plasmid-Mediated tet(X5) Gene Conferring Resistance to Tigecycline, Eravacycline, and Omadacycline in a Clinical Acinetobacter baumannii Isolate.

A novel, plasmid-mediated, high-level tigecycline resistance tet(X) gene variant, tet(X5), was detected in a clinical Acinetobacter baumannii isolate from China in 2017. Tet(X5) shows 84.5% and 90.5% amino acid identity to Tet(X3) and Tet(X4), respectively, with similar binding sites and a comparable affinity for tetracyclines. The tet(X5)-containing plasmid could only be transferred to A. baumannii via electrotransformation. This report follows the recent study describing the identification of tet(X3) and tet(X4).

A retrospective study on mcr-1 in clinical Escherichia coli and Klebsiella pneumoniae isolates in China from 2007 to 2016.

Objectives: To evaluate the prevalence of clinical mcr-1-positive Escherichia coli and Klebsiella pneumoniae and characterize the antimicrobial resistance profiles of mcr-1-positive E. coli and mcr-1-negative E. coli in China. Methods: A total of 6264 clinical E. coli (n = 3854) and K. pneumoniae (n = 2410) were collected from hospitalized patients from 18 to 20 hospitals as part of the China Antimicrobial Resistance Surveillance Trial (CARST) between January 2007 and June 2016. PCR was used to screen for the mcr-1 gene among all isolates. Antibiotic susceptibility testing was performed using the broth microdilution method. mcr-1-positive pathogens were then characterized by MLST and minimum spanning tree analysis using the BURST algorithm for related STs. Results: We examined 39 (0.62%) clinical isolates of mcr-1-positive E. coli and K. pneumoniae over a 10 year period. Resistance to antimicrobial agents was significantly more severe in mcr-1-positive isolates than mcr-1-negative isolates, particularly piperacillin (P = 0.008), amikacin (P < 0.0001), nitrofurantoin (P < 0.004) and fosfomycin (P < 0.0001). Among mcr-1-carrying isolates, ESBL production was as high as 84.6% (33 of 39) and 92.3% (36 of 39) of them displayed an MDR phenotype. STs suggested ubiquitous dissemination of mcr-1-carrying pathogens. Conclusions: mcr-1-carrying E. coli and K. pneumoniae displayed a lower prevalence and abundant phylogenetic diversity in mainland China. mcr-1-positive E. coli showed significant differences in antimicrobial resistance profiles compared with mcr-1-negative E. coli strains, suggesting physicians may consider prescribing different antibiotics when faced with infections caused by mcr-1-positive pathogens.

Effects of Nemonoxacin on Thorough ECG QT/QTc Interval: A Randomized, Placebo- and Positive-controlled Crossover Study in Healthy Chinese Adults.

PURPOSE: Nemonoxacin, a nonfluorinated quinolone, has been approved in Taiwan and mainland China for the treatment of bacterial infection. Whether nemonoxacin is associated with the adverse events of other quinolones, such as the risk for QT-interval prolongation, which has led to the withdrawal of several fluoroquinolones from the market, needs to be elucidated. METHODS: The effects of nemonoxacin on thorough QT/QTc interval was investigated in this randomized, placebo- and positive-controlled crossover study conducted according to the International Conference on Harmonisation E14 guideline. Forty-eight healthy adults received a single oral dose of nemonoxacin 500 mg (therapeutic dose), nemonoxacin 750 mg (supratherapeutic dose), moxifloxacin 400 mg (positive control), or placebo in 1 of 4 cohorts (Williams Latin square design) in the fasted condition. After a 7-day washout, 6 male and 6 female subjects were orally administered a 500-mg dose of nemonoxacin after high-fat food intake. The primary end point was the change in QT interval corrected for heart rate using the Fridericia formula (QTcF). The secondary end point was the change in QT interval corrected for heart rate using the Bazett formula (QTcB). FINDINGS: The study revealed that nemonoxacin was classified as not likely dangerous at the therapeutic dose (500 mg) and as potentially dangerous at the supratherapeutic dose (750 mg). The Tmax of nemonoxacin was 1 to 2 hours after administration, and the elimination half-life was 5 to 7 hours, in the fasted conditions. High-fat food intake had significant effects on the Tmax, Cmax, AUC0-∞, and QT/QTc interval of nemonoxacin compared with these values in the fasted condition. A correlation between QTcF and the plasma drug concentration of nemonoxacin was not observed. IMPLICATIONS: Nemonoxacin at the clinically therapeutic and supratherapeutic doses had a prolongation effect on QT/QTc. ClinicalTrials.gov identifier: NCT03362853.

blaNDM-1-producing multidrug-resistant Escherichia coli isolated from a companion dog in China.

OBJECTIVES: This study characterised a blaNDM-1-producing Escherichia coli isolate from a companion dog. METHODS: The E. coli strain was isolated from a surveillance study of carbapenem-resistant Gram-negative bacteria from companion animals in the Animal Teaching Hospital of China Agricultural University (Beijing, China) in 2013. Species identification was performed using an API 20E system and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Minimum inhibitory concentrations (MICs) of various antimicrobial agents were determined by agar dilution. Multilocus sequence typing (MLST) was performed and various carbapenemase genes, including blaNDM, blaIMP, blaVIM, blaSME, blaIMI, blaKPC, blaGES, blaSPM, blaGIM, blaNMC, blaDIM, blaSIM, blaOXA-23, blaOXA-24, blaOXA-48, blaOXA-51 and blaOXA-58 were screened by PCR. S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern blotting as well as a modified random primer walking strategy were performed to analyse the location and genetic environment of blaNDM-1. RESULTS: An E. coli isolate belonging to ST167 was found to be positive for the blaNDM-1 gene and exhibited resistance to ß-lactams, tetracycline, gentamicin, fosfomycin and ciprofloxacin. The blaNDM-1 gene in this strain was located on an ca. 150-kb plasmid and the flanking sequences of the blaNDM-1-carrying region (a common gene cluster, ΔISAba125-blaNDM-1-ble-trpF-ΔdsbC) exhibited >99% identity to the corresponding regions of blaCTX-M-15-harboring plasmids in nosocomial E. coli ST131 isolates. CONCLUSIONS: This is the first report of blaNDM-1-producing ST167 E. coli in a companion dog. Companion animals harbouring carbapenemase-producing isolates are an upcoming public health threat and it is worthy paying attention to the emergence of carbapenem resistance in companion animals.

Characterisation of clinical isolates of oxacillin-susceptible mecA-positive Staphylococcus aureus in China from 2009 to 2014.

OBJECTIVES: The aim of this study was to investigate the prevalence and molecular characteristics of clinical oxacillin-susceptible mecA-positive Staphylococcus aureus (OS-MRSA) isolates in China from July 2009 to June 2014. METHODS: A total of 2068 non-duplicate S. aureus isolates were collected from 21 hospitals. Antimicrobial susceptibility testing was performed by the agar dilution method. All OS-MRSA strains were screened for the presence of the genes mecA, mecC and nuc as well as the Panton-Valentine leukocidin gene (pvl). Staphylococcal cassette chromosome mec (SCCmec) typing, staphylococcal protein A (spa) typing and multilocus sequence typing (MLST) were performed to analyse the isolate genotypes. RESULTS: A total of 34 S. aureus isolates were mecA-positive but were susceptible to oxacillin [minimum inhibitory concentration (MIC)≤2mg/L]. All OS-MRSA isolates were resistant to cefoxitin and most were also multiresistant to other antibiotics besides ß-lactams. Among the 34 OS-MRSA isolates, nine spa and three SCCmec types were detected and, combined with MLST, ST338/59-t437-SCCmecV (47%; 16/34) was the predominant clone. In addition, 17 strains (50%) carried the pvl gene. CONCLUSIONS: The most frequent clone of OS-MRSA isolates in China was ST338-t437-SCCmecV. Most of the OS-MRSA isolates were susceptible to the majority of antibacterial agents except macrolides, clindamycin and chloramphenicol.

cfr-mediated linezolid-resistant clinical isolates of methicillin-resistant coagulase-negative staphylococci from China.

Three linezolid-resistant coagulase-negative staphylococci (LR-CoNS), including two Staphylococcus cohnii and one Staphylococcus capitis, were isolated from 1104 clinical staphylococcal isolates across China in 2013-2014. Antibiotic susceptibilities of the bacteria were determined by the agar dilution method. PCR and DNA sequencing were performed to determine the potential molecular mechanism of linezolid resistance. The two linezolid-resistant S. cohnii isolates were subjected to pulsed-field gel electrophoresis (PFGE) to investigate their genetic relatedness. Primer walking, S1 nuclease PFGE and Southern blot hybridisation were conducted to ascertain the location and environment of the cfr gene. All three isolates were positive for the cfr gene. Amino acid mutations S158F and S158Y in the ribosomal protein L3 were identified in S. cohnii 13B289 and 13L105, respectively, both of which also had an additional substitution (D159Y) in L3. PFGE indicated that the two S. cohnii isolates belonged to diverse clonal strains. S1 nuclease PFGE and Southern blotting experiments indicated that the cfr gene of the three isolates resided on plasmids of similar size (ca. 35.4kb). The cfr-harbouring segments of S. capitis 13G350 and S. cohnii 13L105 were identical to plasmid pSS-01 reported previously. The cfr-carrying fragment of S. cohnii 13B289 was indistinguishable from the formerly described plasmid pSS-02. In conclusion, the presence of the cfr gene located on a plasmid was the main mechanism contributing to resistance to linezolid in the three staphylococcal isolates. Hence, timely detection and judicious use of antibiotics are essential to prevent further transmission of this resistance mechanism.

Nationwide Surveillance of Novel Oxazolidinone Resistance Gene optrA in Enterococcus Isolates in China from 2004 to 2014.

A total of 2,201 nonduplicate enterococcal isolates collected from 29 hospitals in 23 cities in China between 2004 and 2014 were screened for the oxazolidinone resistance gene optrA; 45 isolates (2.0%) were optrA positive with 11 OptrA variants identified. The positive rate of optrA increased from 0.4% to 3.9% during the 10-year surveillance period. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence type (MLST) analysis revealed that 37 optrA-positive Enterococcus faecalis isolates clustered into 25 PFGE patterns and 21 sequence types, while 6 Enterococcus faecium isolates represented 6 PFGE patterns and 6 sequence types. The present study underscores the importance of routine and persistent monitoring of oxazolidinone resistance and optrA gene.

A novel gene, optrA, that confers transferable resistance to oxazolidinones and phenicols and its presence in Enterococcus faecalis and Enterococcus faecium of human and animal origin.

OBJECTIVES: The oxazolidinone-resistant Enterococcus faecalis E349 from a human patient tested negative for the cfr gene and 23S rRNA mutations. Here we report the identification of a novel oxazolidinone resistance gene, optrA, and a first investigation of the extent to which this gene was present in E. faecalis and Enterococcus faecium from humans and food-producing animals. METHODS: The resistance gene optrA was identified by whole-plasmid sequencing and subsequent cloning and expression in a susceptible Enterococcus host. Transformation and conjugation assays served to investigate the transferability of optrA. All optrA-positive E. faecalis and E. faecium isolates of human and animal origin were analysed for their MICs and their genotype, as well as the location of optrA. RESULTS: The novel plasmid-borne ABC transporter gene optrA from E. faecalis E349 conferred combined resistance or elevated MICs (when no clinical breakpoints were available) to oxazolidinones (linezolid and tedizolid) and phenicols (chloramphenicol and florfenicol). The corresponding conjugative plasmid pE349, on which optrA was located, had a size of 36 331 bp and also carried the phenicol exporter gene fexA. The optrA gene was functionally expressed in E. faecalis, E. faecium and Staphylococcus aureus. It was detected more frequently in E. faecalis and E. faecium from food-producing animals (20.3% and 5.7%, respectively) than from humans (4.2% and 0.6%, respectively). CONCLUSIONS: Enterococci with elevated MICs of linezolid and tedizolid should be tested not only for 23S rRNA mutations and the gene cfr, but also for the novel resistance gene optrA.

Antimicrobial resistance surveillance of flomoxef in China.

The aim of this study was to investigate the susceptibility of flomoxef against clinical isolates collected from China and understand the trend of antimicrobial resistance. A total of 2955 pathogenic strains isolated from 18 tertiary hospitals in 18 cities of China over the period from July 2011 to June 2012 were studied. And the susceptibility tests were performed using agar dilution method recommended by CLSI in central laboratory. Flomoxef showed good potency against Enterobacteriaceae with susceptibility rate 85%-100%. The susceptibility rates of flomoxef against Staphylococcus spp. isolates were 63.9%-92.2%; 98.8% of MSSA and 88.2% of MSSE were susceptible to this drug. For other tested bacteria including Moraxella catarrhalis, Haemophilus spp., and Streptococcus spp. (except Viridans group streptococci) flomoxef showed good potency with susceptibility rate more than 95%. All these results strongly suggest that flomoxef is a potent antibacterial agent against major pathogens in China.

[Study on the molecular epidemiology of bacterial infection in patients in cardiac surgical intensive care unit].

OBJECTIVE: To investigate the molecular epidemiology of acinetobacter baumannii and pseudomonas aeruginosa isolated from clinical specimens from patients on mechanical ventilation. METHODS: From October to December, 2012, acinetobacter baumannii and pseudomonas aeruginosa strains were isolated from patients on mechanical ventilation. Antibiotic susceptibility data of all strains was collected. Homology of the strains was analyzed by the methods of pulsed field gel electrophoresis (PFGE) genotype, meanwhile, the clinical data was also analyzed. RESULTS: Of the 15 pathogens isolated from patients on mechanical ventilation, 7 acinetobacter baumannii strains had different genotypes, indicating specific clustering in a specific location, so acinetobacter baumannii should be a scattered infection or colonized strains. Parts of 8 pseudomonas aeruginosa strains came from the same clone and confirm the existence of cross-infection of nosocomial infections. CONCLUSION: The result shows that nosocomial infection outbreak doesn't occur, there is a small range of cross-infection of pseudomonas aeruginosa.

Epidemiological characteristics of blaNDM-1 in Enterobacteriaceae and the Acinetobacter calcoaceticus-Acinetobacter baumannii complex in China from 2011 to 2012.

OBJECTIVES: The study aimed to investigate the prevalence and epidemiological characteristics of blaNDM-1 (encoding New Delhi metallo-ß-lactamase 1) in Enterobacteriaceae and the Acinetobacter calcoaceticus-Acinetobacter baumannii complex (ABC) in China from July 2011 to June 2012. METHODS: PCR was used to screen for the presence of blaNDM-1 in all organisms studied. For blaNDM-1-positive strains, 16S rRNA analysis and Analytical Profile Index (API) strips were used to identify the bacterial genus and species. The ABCs were reconfirmed by PCR detection of blaOXA-51-like. Antibiotic susceptibilities of the bacteria were assessed by determining minimum inhibitory concentration (MIC) of them using two-fold agar dilution test, as recommended by the Clinical and Laboratory Standards Institute (CLSI). Molecular typing was performed using pulsed-field gel electrophoresis (PFGE). S1 nuclease-pulsed-field gel electrophoresis (S1-PFGE) and Southern blot hybridization were conducted to ascertain the gene location of blaNDM-1. Conjugation experiments were conducted to determine the transmission of blaNDM-1-positive strains. RESULTS: Among 2,170 Enterobacteriaceae and 600 ABCs, seven Enterobacteriaceae strains and two A. calcoaceticus isolates from five different cities carried the blaNDM-1 gene. The seven Enterobacteriaceae strains comprised four Klebsiella pneumoniae, one Enterobacter cloacae, one Enterobacter aerogen and one Citrobacter freundii. All seven were non-susceptible to imipenem, meropenem or ertapenem. Two A. calcoaceticus species were resistant to imipenem and meropenem. Three K. pneumoniae showed the same PFGE profiles. The blaNDM-1 genes of eight strains were localized on plasmids, while one was chromosomal. CONCLUSIONS: Compared with previous reports, the numbers and species containing the blaNDM-1 in Enterobacteriaceae have significantly increased in China. Most of them are able to disseminate the gene, which is cause for concern. Consecutive surveillance should be implemented and should also focus on the dissemination of blaNDM-1 among gram-negative clinical isolates.

Cfr-mediated linezolid-resistance among methicillin-resistant coagulase-negative staphylococci from infections of humans.

Four methicillin-resistant coagulase-negative staphylococci (MRCoNS), one Staphylococcus haemolyticus and three Staphylococcus cohnii, from infections of humans collected via the Ministry of Health National Antimicrobial Resistance Surveillance Net (Mohnarin) program in China were identified as linezolid-resistant. These four isolates were negative for the 23S rRNA mutations, but positive for the gene cfr. Mutations in the gene for the ribosomal protein L3, which resulted in the amino acid exchanges Gly152Asp and Tyr158Phe, were identified in S. haemolyticus 09D279 and S. cohnii NDM113, respectively. In each isolate, the cfr gene was located on a plasmid of ca. 35.4 kb, as shown by S1 nuclease pulsed-field gel electrophoresis and Southern blotting experiments. This plasmid was indistinguishable from the previously described plasmid pSS-02 by its size, restriction pattern, and a sequenced 14-kb cfr-carrying segment. Plasmid pSS-02 was originally identified in staphylococci isolated from pigs. This is the first time that a cfr-carrying plasmid has been detected in MRCoNS obtained from intensive care patients in China. Based on the similarities to the cfr-carrying plasmid pSS-02 from porcine coagulase-negative staphylococci, a transmission of this cfr-carrying plasmid between staphylococci from pigs and humans appears to be likely.