Direct detection of Corynebacterium striatum, Corynebacterium propinquum, and Corynebacterium simulans in sputum samples by high-resolution melt curve analysis.

BACKGROUND: Pulmonary infections caused by non-diphtheriae corynebacteria are increasing. However, rapid identification of Corynebacterium species poses a challenge due to the low genetic variation within the genus. METHODS: Three reference strains and 99 clinical isolates were used in this study. A qPCR followed by high-resolution melting (HRM) targeting ssrA was performed to simultaneously identify C. striatum, C. propinquum and C. simulans. To further evaluate this assay's performance, 88 clinical sputum samples were tested by HRM and the detection results were compared with those of the traditional culture method and multiple cross-displacement amplification (MCDA) assay. RESULTS: The melting curve produced by a pair of universal primers generated species-specific HRM curve profiles and could distinguish the three target species from other related bacteria. The limit of detection of HRM assay for DNA from the three purified Corynebacterium species was 100 fg. Compared with the culture method, HRM detected 22 additional positive specimens, representing a 23.9% relative increase in detection rate. The HRM assay had 98.4% (95% confidence interval [CI], 90.5-99.9%) sensitivity and 100% (95% CI, 82.8-100%) specificity. Additionally, 95.5% concordance between HRM and MCDA (κ = 0.89 [95% CI, 0.79-0.99]) was noted. CONCLUSIONS: The HRM assay was a simple, rapid, sensitive, and specific diagnostic tool for detecting C. striatum, C. propinquum, and C. simulans, with the potential to contribute to early diagnosis, epidemiological surveillance, and rapid response to outbreak.

National Surveillance of Legionnaires' Disease, China, 2014-2016.

We report national surveillance of Legionnaires' disease in China. Urine samples from 11 (3.85%) of 286 patients with severe pneumonia of unknown cause were positive for the Legionella pneumophila serogroup 1 antigen. We isolated Legionella strains from 7 patients. Improved diagnostic testing is needed for this underestimated disease in China.

Whole-Genome Sequencing Reveals a Prolonged and Persistent Intrahospital Transmission of Corynebacterium striatum, an Emerging Multidrug-Resistant Pathogen.

Corynebacterium striatum is an emerging multidrug-resistant (MDR) pathogen that occurs primarily among immunocompromised and chronically ill patients. However, little is known about the genomic diversity of C. striatum, which contributes to its long-term persistence and transmission in hospitals. In this study, a total of 192 C. striatum isolates obtained from 14 September 2017 to 29 March 2018 in a hospital in Beijing, China, were analyzed by antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE). Whole-genome sequencing was conducted on 91 isolates. Nearly all isolates (96.3%, 183/190) were MDR. The highest resistance rate was observed for ciprofloxacin (99.0%, 190/192), followed by cefotaxime (90.6%, 174/192) and erythromycin (89.1%, 171/192). PFGE separated the 192 isolates into 79 pulsotypes, and differences in core genome single-nucleotide polymorphisms (SNPs) partitioned the 91 isolates sequenced into four clades. Isolates of the same pulsotype were identical or nearly identical at the genome level, with some exceptions. Two dominant subclones, clade 3a, and clade 4a, were responsible for the hospital-wide dissemination. Genomic analysis further revealed nine resistance genes mobilized by eight unique cassettes. PFGE and whole-genome sequencing revealed that the C. striatum isolates studied were the result mainly of predominant clones spreading in the hospital. C. striatum isolates in the hospital progressively acquired resistance to antimicrobial agents, demonstrating that isolates of C. striatum may adapt rapidly through the acquisition and accumulation of resistance genes and thus evolve into dominant and persistent clones. These insights will be useful for the prevention of C. striatum infection in hospitals.

Ribosomal protein L3 mutations are associated with cfr-mediated linezolid resistance in clinical isolates of Staphylococcus cohnii.

From June, 2012 to November, 2013 five linezolid-resistant Staphylococcus cohnii isolates were identified in our hospital in Beijing, China. The investigation of the resistance mechanisms confirmed that the cfr-carrying plasmids were the main cause of linezolid resistance in those clinical isolates. Moreover, all the five isolates had ribosomal protein L3 mutations, which had different coordinate effect on cfr-mediated linezolid resistance directly through the substitution of serine 158 by phenylalanine or tyrosine in L3 protein. In this study, two types of plasmids (p432, p438) (Accession No. KM114207) were found, which share high sequence identity with previously reported cfr-carrying pRM01 and pMHZ plasmids originated from northern and southern China, showing wide regional dissemination in China. The stability of linezolid resistance was studied by passaging single colonies serially on antibiotic-free blood medium, which showed that the susceptible derivatives emerged until the passages 39-42 with the elimination of cfr-carrying plasmid. Thus the high stability of this plasmid may pose a risk for the transmission among patients or even cause an outbreak in clinical settings.

[Mechanism of hetero-erythromycin resistant Staphylococcus aureus and a comparison of detection methods].

OBJECTIVE: To explore the phenotypes and genotypes of Staphylococcus aureus (S. aureus) hetero-resistant to erythromycin and clindamycin and compare their detection methods so as to report results accurately to guide clinical rational use of antibiotics. METHODS: D test was used to detect the phenotypes of S. aureus hetero-resistant to erythromycin. And then the results of two methods (automated instrument and disk diffusion) were analyzed. All strains were continuously passaged for 50 generations to verify the phenotypic and genotypic stability of hetero-resistance. ErmA, ermC and msrA genes were amplified by multiplex polymerase chain reaction (PCR). RESULTS: Among 95 erythromycin-sensitive strains, there were 70 strains hetero-resistant to erythromycin (73.7%). The primary 70 strains were all susceptive to erythromycin (MIC ≤ 0.25 µg/ml) and clindamycin (MIC ≤ 0.25 µg/ml) with the cards of GP-67 of VITEK2 Compact. With D tests, the results were difficult to observe. The passaged 70 strains were all resistant to erythromycin (MIC >8 µg/ml) and susceptible to clindamycin (MIC ≤ 0.25 µg/ml) and D test positive with the cards of GP-67 of VITEK2 Compact. The primary and 50(th) generation of herero-erythromycin resistant strains were stable in susceptibility test results. The primary and the 50(th)th generation strains were all ermA gene positive, ermC and msrA negative with PCR results. CONCLUSIONS: The phenotypes and genotypes of hetreo-erythromycin resistant S. aureus strains were stable. Missed detection with VITEK2 Compact may affect the proper use of erythromycin and clindamycin. Laboratory technicians should identify the erythromycin-susceptible strains by disk diffusion method.

Cystoisospora belli infection in an AIDS patient in China: Need for cautious interpretation of mNGS.

Cystoisospora belli (C. belli) is an opportunistic coccidian parasite. This case is the first reported C. belli infection associated with AIDS in China. C. belli infection of this case was diagnosed with the presence of oocysts using direct wet mount and Ziehl-Neelsen acid-fast stain method, and confirmed by polymerase chain reaction (PCR) and Sanger sequencing, ruling out the result of metagenomic next-generation sequencing (mNGS). This case demonstrates that C. belli infection in AIDS could be a potential risk factor for persistent diarrhea, and should not be neglected in non-endemic area and emphaise the necessity of accurate mNGS databases.

Electrical and magnetic properties of antiferromagnetic semiconductor MnSi2N4 monolayer.

Two-dimensional antiferromagnetic semiconductors have triggered significant attention due to their unique physical properties and broad application. Based on first-principles calculations, a novel two-dimensional (2D) antiferromagnetic material MnSi2N4 monolayer is predicted. The calculation results show that the two-dimensional MnSi2N4 prefers an antiferromagnetic state with a small band gap of 0.26 eV. MnSi2N4 has strong antiferromagnetic coupling which can be effectively tuned under strain. Interestingly, the MnSi2N4 monolayer exhibits a half-metallic ferromagnetic properties under an external magnetic field, in which the spin-up electronic state displays a metallic property, while the spin-down electronic state exhibits a semiconducting characteristic. Therefore, 100% spin polarization can be achieved. Two-dimensional MnSi2N4 monolayer has potential application in the field of high-density information storage and spintronic devices.

Epidemiology and Antimicrobial Resistance Profiles of the Nocardia Species in China, 2009 to 2021.

The genus Nocardia includes ubiquitous environmental saprophytes and the most frequently isolated aerobic actinomycete human pathogen responsible for localized or disseminated infection. Herein, the species distribution and antimicrobial susceptibility profiles of 441 nonrepetitive Nocardia strains are reported, collected from 21 provinces/cities in China over 13 years (from 2009 to 2021). These isolates were identified to species level by mass spectrometry or targeted DNA sequencing. The susceptibility profiles of Nocardia species for 15 antibiotics were determined by the broth microdilution method. Among these Nocardia isolates, Nocardia farcinica was the most commonly isolated species (39.9%, 176 of 441), followed by Nocardia cyriacigeorgica (28.6%, 126), Nocardia abscessus (6.6%, 29), and Nocardia otitidiscaviarum (5.9%, 26). Furthermore, 361 Nocardia strains (81.9%) were collected from lower respiratory tract (sputum, lung tissue, and bronchoalveolar lavage fluid), 50 (11.3%) were collected from skin and soft tissues, 9 were collected from blood, 9 were collected from eye, 4 were collected from cerebrospinal fluid and brain abscesses, and 2 were collected from pleural effusion. All of the Nocardia strains were susceptible to linezolid, followed by amikacin (99.3%) and trimethoprim-sulfamethoxazole (TMP-SMX) (99.1%). The antibiotic resistance profiles of other antibiotics varied tremendously among different Nocardia species. This demonstrated that accurate species identification and/or antibiotic susceptibility testing should be performed before the usage of these antibiotics. In summary, this is the largest study on the species and antibiotic resistance profiles of the genus Nocardia circulating in China, and our data will contribute to a better understanding of clinical nocardiosis. IMPORTANCE The genus Nocardia has the potential to cause nocardiosis, which might be underrecognized and underdiagnosed. Herein, the demographical features of 441 nonrepetitive nocardiosis cases and species distribution of their Nocardia strains in China, 2009 to 2021, are summarized. The susceptibility profiles for 15 antibiotics against all of the above Nocardia strains were also determined by the broth microdilution method. To date, this is the largest study on the genus Nocardia contributing to nocardiosis in China. Our study will be helpful for understanding the species diversity of Nocardia isolates distributed in China and for decision-making in the context of nocardiosis diagnosis and treatment.

A biological and genomic comparison of a drug-resistant and a drug-susceptible strain of Candida auris isolated from Beijing, China.

The fungal pathogen Candida auris has emerged as a new threat to human health. We previously reported the first isolate of C. auris (BJCA001) in China, which belongs to the South Asian clade (I) and was susceptible to all antifungals tested. In this study, we report the isolation of a drug-resistant C. auris strain (BJCA002) from the same city (Beijing). Strain BJCA002 belongs to the South African clade (III) and is resistant to fluconazole and amphotericin B based on the tentative MIC breakpoints. Taking advantage of the two isolates with distinct antifungal susceptibility and genetic origins, we performed a biological and genomic comparative study. Besides antifungal susceptibility, strains BJCA001 and BJCA002 showed differences in multiple aspects including morphologies, expression of virulence factors, virulence, mating type, and genomic sequence and organization. Notably, strain BJCA002 was less virulent than BJCA001 in both the Galleria mellonella and mouse systemic infection models. Genomic analysis demonstrated that strain BJCA002 but not BJCA001 had multiple mutations in drug resistance-associated genes, including a hot-spot mutation of ERG11 (VF125AL, namely V125A and F126L) and some missense mutations in CDR1, MDR1, and TAC1. Notably, strain BJCA001 carried 64 copies of the Zorro3 retrotransposon, whereas BJCA002 had only 3 copies in the genome. Taken together, our findings not only reveal the genetic and phenotypic diversities of the two isolates from Beijing, China, but also shed new light on the genetic basis of the antifungal resistance and virulence of C. auris.

A Nosocomial Respiratory Infection Outbreak of Carbapenem-Resistant Escherichia coli ST131 With Multiple Transmissible bla KPC-2 Carrying Plasmids.

Escherichia coli sequence type 131 (ST131) is well known for its multidrug resistance profile. Carbapenems have been considered the treatment of choice for E. coli ST131 infections, and resistance to carbapenems is emerging due to the acquisition of carbapenemase-encoding genes. In this study, 45 carbapenem-resistant E. coli strains were collected in a hospital. The resistance mechanisms, plasmid profiles, and genetic relatedness of these strains were determined. Phylogenetic relationships between these strains were assessed by molecular profiling and aligned with patient clinical details. The genetic context of bla KPC-2 was analyzed to trace the potential dissemination of bla KPC-2. The 45 carbapenem-resistant E. coli ST131 strains were closely related. Initially prevalent only in a single ward, ST131 subsequently spread to other ward, resulting in a respiratory infection outbreak of carbapenem-resistant E. coli ST131. Eight of the 30 patients died within 28 days of the first isolation of E. coli ST131. The bla KPC-2-positive plasmid profiles suggest that the carbapenem resistance was due to the acquisition by E. coli ST131 of transmissible plasmids pE0272_KPC and pE0171_KPC carrying bla KPC-2. Additionally, diverse multidrug resistance elements were transferred and rearranged between these plasmids mediated by IS26. Our research indicates that clinical attention should be paid to the importance of E. coli ST131 in respiratory infections and the spread of bla KPC -carrying E. coli ST131.

A novel isothermal amplification-based method for detection of Corynebacterium striatum.

Corynebacterium striatum is an emerging multidrug-resistant pathogen causing increasing numbers of infections and nosocomial outbreaks worldwide. Thus, a simple, rapid and accurate method for C. striatum is urgently required for improving diagnosis efficiency. In this study, a C. striatum-multiple cross displacement amplification (MCDA) with visual detection reagent (VR) assay (C. striatum-MCDA-VR), which was a novel isothermal amplification-based method, was established to detect the species-specific ftr1 gene of C. striatum. Amplification was performed at a constant temperature (68 °C) for only 40 min, and the reaction results could be easily elucidated by observation of reaction mixture color when employing the VR. The limit of detection of this method was 10 fg of pure C. striatum DNA. No cross-reaction was observed with non-C. striatum strains. In testing of clinical sputum samples, the C. striatum-MCDA-VR assay showed excellent sensitivity and specificity when compared with sputum smear tests and PCR. The C. striatum-MCDA-VR assay is a simple, rapid and cost-effective approach for identifying C. striatum in microbiological laboratories, especially in resource-limited settings.

A case of Aspergillus salwaensis-induced spinal infection / 中国热带医学

@#Abstract: To report a case of Aspergillus salwaensis-induced spinal infection and its laboratory detection. The inflammatory granulation and necrotic tissue samples of a patient with spinal infection were collected from, the Affiliated Hospital of Chengde Medical College on June 17, 2020 for direct smear microscopy and culture, and the isolated strain was identified by microscopy by smear staining, matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF-MS), molecular identification and in vitro antifungal susceptibility test. The patient was 62 years old female and presented with recurrent chest and back pain with no obvious cause. The initial diagnosis was spinal infection, after 7 days of treatment with levofloxacin, the effect was not good. Surgery was then performed remove the lesion via posterior thoracic debridement, and fungal hypha was observed under microscope in tissue specimens. The isolated strains had no typical structure, MALDI-TOF-MS was used for identification for many times, but there was no identification result. After 7 days of fluconazole treatment, the patient's condition improved, and her chest and back pain were alleviated compared to before surgery. The patient was discharged and followed up in the outpatient department, the fungus was later identified as Aspergillus salwaensis by sequence analysis of the internal transcribed spacer (ITS) gene sequencing, and the patient's antifungal medication was changed to voriconazole after with the attending physician. The patient consciously recovered well with no pain in the operative area and normal spinal activity at 1 year follow-up. The possibility of spinal fungal infection should be considered in patients with back pain without a clear cause and poor response to routine antibiotic treatment. Direct smear report of microscopic results are very important for guiding clinical antibiotic selection for rare filament fungi with atypical colony and microscopic morphology and unsuccessful MALDI-TOF-MS identification, molecular biological methods such as ITS sequence analysis can be helpful for early identification of the fungal species, improving identification speed.

First emergence of acrAB and oqxAB mediated tigecycline resistance in clinical isolates of Klebsiella pneumoniae pre-dating the use of tigecycline in a Chinese hospital.

Tigecycline is one of the few therapeutic options for treating infections caused by some multi-drug resistant pathogens, such as Klebsiella pneumoniae. However, tigecycline-resistant K. pneumoniae has been discovered recently in China. From 2009 to 2013, nine tigecycline-resistant K. pneumoniae isolates were identified in our hospital. Six of nine strains were identified before using tigecycline. To investigate the efflux-mediated resistance mechanisms of K. pneumoniae, the expression of efflux pump genes (acrA, acrB, tolC, oqxA and oqxB) and pump regulators (acrR, marA, soxS, rarA, rob and ramA) were examined by real-time RT-PCR. Molecular typing of the tigecycline resistant strains was performed. ST11 was the predominant clone of K. pneumoniae strains, while ST1414 and ST1415 were novel STs. Efflux pump inhibitor (EPI)-carbonyl cyanide chlorophenylhydrazone (CCCP) was able to reverse the resistance patterns of 5 resistant K. pneumoniae strains. In comparison with strain A111, a tigecycline-susceptible strain (negative control), we found that the expression levels of efflux pump genes and pump regulators were higher in a majority of resistant strains. Higher expression levels of regulators rarA (2.41-fold, 9.55-fold, 28.44-fold and 18.31-fold, respectively) and pump gene oqxB (3.87-fold, 31.96-fold, 50.61-fold and 29.45-fold, respectively) were observed in four tigecycline resistant strains (A363, A361, A368, A373, respectively). Increased expression of acrB was associated with ramA and marA expression. To our knowledge, studies on tigecycline resistance mechanism in K. pneumoniae are limited especially in China. In our study, we found that both efflux pump AcrAB-TolC and OqxAB contributed to tigecycline resistance in K. pneumoniae isolates.

Subclinical infections of cardiac implantable electronic devices: insights into the host-bacteria dialog from blood and pocket tissue with pyrosequencing.

While bacteria exist in CIED patients without clinical signs of infection, the underlying bacterial community structure and diversity in the bloodstream and pocket tissue of asymptomatic CIED patients remain unknown. In this study, we performed high-throughput 454 pyrosequencing of bacterial 16S rDNA of blood and pocket tissue from 54 asymptomatic CIED patients as well as blood from 30 normal individuals (normal controls). Firstly, we observed a significant increase of blood bacterial diversity in patients as compared with blood of normal subjects or patient tissues. We also found significant differences in 13 blood-associated bacterial genera between patients and normal subjects, and 14 bacteria genera between blood and tissues within patients. Secondly, we found that the serum levels of four inflammatory markers (CRP, IL-1ß, IL-6, and MCP-1) in CIED patients were significantly higher than those in normal subjects. Thirdly, we found that there were significant correlations between 43 bacterial species and these inflammatory markers. Taken together, our results reveal a high diversity in the microbial community in CIED patients, and suggest the potential roles of multiple bacteria co-occurrence in the CIED subclinical infections.

Nosocomial spread of hospital-adapted CC17 vancomycin-resistant Enterococcus faecium in a tertiary-care hospital of Beijing, China.

BACKGROUND: The incidence of vancomycin-resistant enterococci (VRE) appeared to be increasing in China, but very few nosocomial outbreaks have been reported. Our hospital had experienced an outbreak of VRE since March 2008 to March 2009. The objective of this study was to analyze the molecular features of the isolates and the control measures used to eradicate a VRE outbreak in a tertiary institution in China. METHODS: We characterized VRE isolates from 21 infected and 11 colonized inpatients from a single hospital by pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), the analysis of Tn1546-like elements and virulence genes detection. Infection control measures, including more environmental disinfection, screening for VRE colonization, contact precautions, education and strict antibiotic restriction, were implemented to control the outbreak. RESULTS: During the outbreak, a total of 32 VRE strains were obtained. There were 21 strains found in Emergency Intensive Care Unit (EICU), 9 isolates from Geriatric Ward, and two from other units. All the isolates harbored the vanA gene, however, four of them exhibited the VanB phenotype. Meanwhile, MLST analysis revealed that all isolates belonged to clonal complex (CC) 17. With the infection-control measures, the epidemic was constrained in two units (EICU and Geriatric Ward). After March 2009, no further case infected with VRE was detected in the following one-year period. CONCLUSION: The outbreak was controlled by continuous implementation of the infection control programme, and more rigorous infection control policy is needed.