Comparison of influenza- and COVID-19-associated pulmonary aspergillosis in China.

PURPOSE: We conducted a monocentric retrospective study using the latest definitions to compare the demographic, clinical, and biological characteristics of influenza-associated pulmonary aspergillosis (IAPA) and COVID-19-associated pulmonary aspergillosis (CAPA). METHODS: The study retrospectively enrolled 180 patients, including 70 influenza/IPA patients (with positive influenza A/B and Aspergillus) and 110 COVID-19/IPA patients (with positive SARS-CoV-2 and Aspergillus). Among them, 42 (60%) and 30 (27.3%) patients fulfilled the definitions of IAPA and CAPA, respectively. RESULTS: The CAPA patients had significantly higher in-hospital mortality (13/31, 41.9%) than IAPA patients (8/42, 19%) with a P-value of 0.033. Kaplan-Meier survival curve also showed significantly higher 30-day mortality for CAPA patients (P = 0.025). Additionally, the CAPA patients were older, though insignificantly, than IAPA patients (70 (60-80) vs. 62 (52-72), P = 0.075). A lower percentage of chronic pulmonary disease (12.9 vs. 40.5%, P = 0.01) but higher corticosteroids use 7 days before and after ICU admission (22.6% vs. 0%, P = 0.002) were found in CAPA patients. Notably, there were no significant differences in the percentage of ICU admission or ICU mortality between the two groups. In addition, the time from observation to Aspergillus diagnosis was significantly longer in CAPA patients than in IAPA patients (7 (2-13) vs. 0 (0-4.5), P = 0.048). CONCLUSION: Patients infected with SARS-CoV-2 and Aspergillus during the concentrated outbreak of COVID-19 in China had generally higher in-hospital mortality but a lower percentage of chronic pulmonary disease than those infected with influenza and Aspergillus. For influenza-infected patients who require hospitalization, close attention should be paid to the risk of invasive aspergillosis upfront.

Molecular Characteristics of an NDM-4 and OXA-181 Co-Producing K51-ST16 Carbapenem-Resistant Klebsiella pneumoniae: Study of Its Potential Dissemination Mediated by Conjugative Plasmids and Insertion Sequences.

The carbapenem-resistant Klebsiella pneumoniae (CRKP) strain GX34 was recovered from the respiratory tract of an elderly male with severe pneumonia, and only susceptible to amikacin, tigecycline, and colistin. Complete genome suggested that it belonged to K51-ST16 and harbored plasmid-encoded NDM-4 and OXA-181, located on IncFIB plasmid GX34p1_NDM-4 and ColKP3/IncX3 plasmid GX34p4_OXA-181, respectively. A series of transconjugants generated in the plasmid conjugation assays, including Escherichia coli J53-N1 (harboring a self-transmissible and blaNDM-1-producing plasmid Eco-N-1-p), J53-N2 (harboring a blaNDM-4-producing plasmid and a helper plasmid GX34p5), and J53-O (harboring a blaOXA-181-producing plasmid), could be stably inherited after 10 days of serial passage and no significant biological fitness costs were detected. Furthermore, we first reported the blaNDM-1 gene, derived from blaNDM-4 mutation (460C>A) under meropenem pressure, could be in vitro transferred into a self-conjugative, recombined plasmid Eco-N-1-p of J53-N1. Eco-N-1-p was mainly recombined by GX34p4_OXA-181 (40,449 bp, 75.16%) and GX34p1_NDM-4 (8,553 bp, 15.89%), in which IS26 and IS5-like probably played a major role. Eco-N-1-p could be transferred into the conjugation recipient K. pneumoniae KP54 and make the latter sacrifice fitness. The retention rates of blaNDM-1 remained high stability (>80% after 200 generations). The comparative genomic analysis of GX34 and those carrying blaNDM-4 or blaOXA-181 genes retrieved from the NCBI RefSeq database showed all blaNDM-4 (26/26, 100.00%) and blaOXA-181 (13/13, 100.00%) were surrounded by IS26. The immediate environment of blaNDM-4 and blaOXA-181 in GX34 and some retrieved strains shared identical features, hinting at their possible dissemination. Effective measures should be taken to monitor the spread of this clone.

In vitro activity of cefiderocol, a siderophore cephalosporin, against carbapenem-resistant hypervirulent Klebsiella pneumoniae in China.

Cefiderocol is a siderophore cephalosporin that binds ferric iron and utilizes iron transporters to cross the cell membrane. Hypervirulent Klebsiella pneumoniae (hvKp) is known to produce more siderophores; in this case, the uptake of cefiderocol may be decreased. Therefore, the objective of this study was to evaluate the in vitro activity of cefiderocol against hvKp isolates. A total of 320 carbapenem-resistant K. pneumoniae (CRKp) isolates were collected in China between 2014 and 2022, including 171 carbapenem-resistant hvKp (CR-hvKp) and 149 carbapenem-resistant classical K. pneumoniae (CR-cKp). Quantitative detection of siderophores showed that the average siderophore production of CR-hvKp (234.6 mg/L) was significantly higher than that of CR-cKp (68.9 mg/L, P < 0.001). The overall cefiderocol resistance rate of CR-hvKp and CR-cKp was 5.8% (10/171) and 2.7% (4/149), respectively. The non-susceptible rates of both cefiderocol and siderophore production of CR-hvKp isolates were higher than those of CR-cKp in either NDM-1- or KPC-2-producing groups. The MIC90 and MIC50 for CR-hvKp and CR-cKp were 8 mg/L and 2 mg/L and 4 mg/L and 1 mg/L, respectively. The cumulative cefiderocol MIC distribution for CR-hvKp was significantly lower than that of CR-cKp isolates (P = 0.003). KL64 and KL47 consisted of 53.9% (83/154) and 75.7% (53/70) of the ST11 CR-hvKp and CR-cKp, respectively, and the former had significantly higher siderophore production. In summary, cefiderocol might be less effective against CR-hvKp compared with CR-cKp isolates, highlighting the need for caution regarding the prevalence of cefiderocol-resistant K. pneumoniae strains, particularly in CR-hvKp isolates.

High concentration of Cas12a effector tolerates more mismatches on ssDNA.

Rapid pathogen detection is critical for prompt treatment, interrupting transmission routes, and decreasing morbidity and mortality. The V-type CRISPR system had been used for rapid pathogen detection. However, whether single-stranded DNA in CRISPR system can cause false positives remains undetermined. Herein, we show that high molar concentration of Cas12a effector tolerated more mismatches on ssDNA and activated its trans-cleavage activity at six base matches. Reducing Cas12a and crRNA molar concentration increased the minimal base-match number required for Cas12a ssDNA activation to 11, which reducing nonspecific activation. We then established a Cas12a-based M tuberculosis detection system with a primer having an 8 bp overlap with crRNA. This system did not exhibit primer-induced false positives, and minimum detection copy reached 1 copy/uL (inputting 1-µL sample) in standard strains. The Cas12a-based M tuberculosis detection system showed 80.0% sensitivity and 100.0% specificity in verification using clinical specimens, compared with Xpert MTB/RIF, which showed 72.0% sensitivity and 90.9% specificity. All these results prove that appropriate concentration of cas12a effector can effectively perform nucleic acid detection.

Clinical characteristics of patients with bronchiectasis with nontuberculous mycobacterial disease in Mainland China: a single center cross-sectional study.

BACKGROUND: The diagnosis and treatment of patients with bronchiectasis and nontuberculous mycobacterium (NTM) pulmonary disease are challenging issues and the treatment is also prolonged and depends on the species. There is limited information on patients with bronchiectasis and NTM pulmonary disease in Mainland China. METHODS: This cross-sectional study was conducted at the China-Japan Friendship Hospital, Beijing, China. Those adult patients who met the diagnostic criteria for bronchiectasis and obtained a culture result of mycobacteria from lower respiratory tract specimens or lung tissue were included in this study. A logistic regression model was used to identify the related factors in patients with NTM pulmonary disease. RESULTS: A total of 202 patients with bronchiectasis from 19 cities, 155 without and 47 (23.3%) with NTM pulmonary disease, were included. In all the 47 patients with NTM pulmonary disease, Mycobacterium avium complex was the most common species (66.0%), and 72.3% of them were initiated on standard anti-NTM treatment within 3 months after the diagnosis of NTM pulmonary disease. A larger proportion of patients with NTM pulmonary disease had acute exacerbations of ≥ 3 times within 1 year and were diagnosed bronchiectasis ≥ 50 years among patients with NTM pulmonary disease. The HRCT chest images revealed higher proportions of nodular shadow (100% vs. 35.3%), tree-in-bud sign (97.9% vs. 29.0%), cavities (29.8% vs. 5.8%), and airway dilation of the right middle lobe or the left lingular lobe (63.8% vs. 23.9%) in patients with NTM pulmonary disease than in those without NTM pulmonary disease (all P values = 0.001). The multivariable logistic regression model indicated that three and more abnormal features (OR 33.8; 95% CI 11.1-102.8) and main lesions of bronchial expansion in the middle or lingual lobe (OR 6.4; 95% CI 2.4-16.6) in HRCT chest images were independently associated with NTM pulmonary disease (P values = 0.001). CONCLUSION: In a single center of Mainland China, > 23% of patients with bronchiectasis had NTM pulmonary disease, and most patients were started on standard treatment within 3 months after the diagnosis of NTM pulmonary disease. These findings suggest that patients with bronchiectasis should be thoroughly examined for the presence of NTM pulmonary disease. TRIAL REGISTRATION: NCT03594032.

Comparative Effectiveness of Combined Favipiravir and Oseltamivir Therapy Versus Oseltamivir Monotherapy in Critically Ill Patients With Influenza Virus Infection.

BACKGROUND: A synergistic effect of combination therapy with favipiravir and oseltamivir has been reported in preclinical models of influenza. However, no data are available on the clinical effectiveness of combination therapy in severe influenza. METHODS: Data from 2 separate prospective studies of influenza adults were used to compare outcomes between combination and oseltamivir monotherapy. Outcomes included rate of clinical improvement (defined as a decrease of 2 categories on a 7-category ordinal scale) and viral RNA detectability over time. Subhazard ratios (sHRs) were estimated by the Fine and Gray model for competing risks. RESULTS: In total, 40 patients were treated with combination therapy and 128 with oseltamivir alone. Clinical improvement on day 14 in the combination group was higher than in the monotherapy group (62.5% vs 42.2%; P = .0247). The adjusted sHR for combination therapy was 2.06 (95% confidence interval, 1.30-3.26). The proportion of undetectable viral RNA at day 10 was higher in the combination group than the oseltamivir group (67.5% vs 21.9%; P < .01). No significant differences were observed in mortality or other outcomes. CONCLUSIONS: Favipiravir and oseltamivir combination therapy may accelerate clinical recovery compared to oseltamivir monotherapy in severe influenza, and this strategy should be formally evaluated in a randomized controlled trial.

Co-infection with SARS-CoV-2 and Influenza A Virus in Patient with Pneumonia, China.

We report co-infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus in a patient with pneumonia in China. The case highlights possible co-detection of known respiratory viruses. We noted low sensitivity of upper respiratory specimens for SARS-CoV-2, which could further complicate recognition of the full extent of disease.

Multilocus sequence analysis for the taxonomic updating and identification of the genus Proteus and reclassification of Proteus genospecies 5 O'Hara et al. 2000, Proteus cibarius Hyun et al. 2016 as later heterotypic synonyms of Proteus terrae Behrendt et al. 2015.

BACKGROUND: Members of the genus Proteus are mostly opportunistic pathogens that cause a variety of infections in humans. The molecular evolutionary characteristics and genetic relationships among Proteus species have not been elucidated to date. In this study, we developed a multilocus sequence analysis (MLSA) approach based on five housekeeping genes (HKGs) to delineate phylogenetic relationships of species within the genus Proteus. RESULTS: Of all 223 Proteus strains collected in the current study, the phylogenetic tree of five concatenated HKGs (dnaJ, mdh, pyrC, recA and rpoD) divided 223 strains into eleven clusters, which were representative of 11 species of Proteus. Meanwhile, the phylogenetic trees of the five individual HKGs also corresponded to that of the concatenated tree, except for recA, which clustered four strains at an independent cluster. The evaluation of inter- and intraspecies distances of HKG concatenation indicated that all interspecies distances were significantly different from intraspecies distances, which revealed that these HKG concatenations can be used as gene markers to distinguish different Proteus species. Further web-based DNA-DNA hybridization estimated by genome of type strains confirmed the validity of the MLSA, and each of eleven clusters was congruent with the most abundant Proteus species. In addition, we used the established MLSA method to identify the randomly collected Proteus and found that P. mirabilis is the most abundant species. However, the second most abundant species is P. terrae but not P. vulgaris. Combined with the genetic, genomic and phenotypic characteristics, these findings indicate that three species, P. terrae, P. cibarius and Proteus genospecies 5, should be regarded as heterotypic synonyms, and the species should be renamed P. terrae, while Proteus genospecies 5 has not been named to date. CONCLUSIONS: This study suggested that MLSA is a powerful method for the discrimination and classification of Proteus at the species level. The MLSA scheme provides a rapid and inexpensive means of identifying Proteus strains. The identification of Proteus species determined by the MLSA approach plays an important role in the clinical diagnosis and treatment of Proteus infection.

Proteus faecis sp. nov., and Proteus cibi sp. nov., two new species isolated from food and clinical samples in China.

Eight swarming motile bacteria were isolated from food and clinical samples in China. Cells were Gram-stain-negative, facultatively anaerobic and rod-shaped (0.5-0.8×1.0-3.0 µm) with hairlike pili and flagella. The 16S rRNA and partial rpoB housekeeping gene sequence analyses indicated that the strains belong to the genus Proteusin the family Enterobacteriaceae. Of the eight strains studied, seven and a single isolate formed two separate clades in the phylogeny of Proteusspecies, indicating two separate species. Both the in silico DNA-DNA hybridization and the average nucleotide identity values between these two groups and to the type strains of the genus Proteuswere below the recommended threshold for signifying their candidature as two separate species. The DNA G+C contents of strains TJ1636T and FJ2001126-3T were 37.8 and 38.1 mol%, respectively. The major cellular fatty acids of the two novel type strains were C16:0, cyclo C17:0, summed feature 3 and summed feature 8. The results supported that the strains belong to different taxonomic positions in the genus Proteus. The isolates were named Proteus faecis sp. nov., with type strain TJ1636T (=DSM 106180T=GDMCC 1.1245T), and Proteuscibi sp. nov., with type strain FJ2001126-3T (=DSM 106178T =GDMCC 1.1244T).

Infection due to Mycoplasma hominis after left hip replacement: case report and literature review.

BACKGROUND: Hip replacement is generally conducted in those with prolonged arthritis pain or hip fractures, and postoperative infection is a serious complication. Mycoplasma hominis, belonging to mycoplasma species, exists mainly in the genitourinary tract. M. hominis infection after total hip replacement was rarely documented in literature. CASE PRESENTATION: A 59-year-old male was febrile after left total hip replacement. Empiric therapy with cefepime for suspected infection was ineffective. Specimens at the infection site were collected for culture, and pinpoint colonies grew after incubation at 35 °C for 48 h on blood agar plate. They grew to approximately 0.5 mm colonies in diameter after 7-day incubation, and were identified as M. hominis. Sequentially, combination therapy with clindamycin hydrochloride and moxifloxacin was initiated, and the patient defervesced within 3 days and was discharged home. CONCLUSIONS: The study highlighted the potential pathogenicity of M. hominis in postoperative infection. The possibility of this microorganism involvement should be valued if the patients who experienced the hip or joint replacement had inexplicable fever.

Fatal deep venous thrombosis and pulmonary embolism secondary to melioidosis in China: case report and literature review.

BACKGROUND: Burkholderia pseudomallei is a gram-negative bacterium and the causative pathogen of melioidosis, which manifests a variety ranges of infection symptoms. However, deep venous thrombosis (DVT) and pulmonary embolism (PE) secondary to bacteremic melioidosis are rarely documented in the literature. Herein, we reported a fatal case of melioidosis combined with DVT and PE. CASE PRESENTATION: A 54-year-old male construction worker and farmer with a history of diabetes was febrile, painful in left thigh, swelling in left lower limb, with chest tightness and shortness of breath for 4 days. He was later diagnosed as DVT of left lower extremity and PE. The culture of his blood, sputum and bone marrow samples grew B. pseudomallei. The subject was administrated with antibiotics (levofloxacin, cefoperazone/tazobactam, and imipenem) according to antimicrobial susceptibility testing and low molecular heparin for venous thrombosis. However, even after appropriate treatment, the patient deteriorated rapidly, and died 2 weeks after admission. CONCLUSIONS: This study enhanced awareness of the risk of B. pseudomallei bloodstream infection in those with diabetes. If a patient has predisposing factors of melioidosis, when DVT is suspected, active investigation and multiple therapeutic interventions should be implemented immediately to reduce mortality rate.

Microbiological and clinical characteristics of Streptococcus gallolyticus subsp. pasteurianus infection in China.

BACKGROUND: Infections by Streptococcus gallolyticus subsp. pasteurianus (SGSP) is often underestimated. Herein, the epidemiological features and resistant characteristics of SGSP in mainland China are characterized to enable a better understanding of its role in clinical infections. METHODS: In the present work, 45 SGSP isolates were collected from the samples of bloodstream, urine, aseptic body fluid, and fetal membrane/placenta from patients in 8 tertiary general hospitals of 6 cities/provinces in China from 2011 to 2017. The identification of all isolates was performed using traditional biochemical methods, 16S rRNA and gyrB sequencing, followed by the characterization of their antibiotic resistance profiling and involved genes. RESULTS: Among 34 non-pregnancy-related patients, 4 (4/34,11.8%) patients had gastrointestinal cancer, 10 (10/34, 29.4%) patients had diabetes, and one patient had infective endocarditis. Moreover, 11 cases of pregnant women were associated with intrauterine infection (9/11, 81.2%) and urinary tract infection (1/11, 9.1%), respectively. Except one, all other SGSP isolates were correctly identified by the BD Phoenix automated system. We found that all SGSP isolates were phenotypically susceptible to penicillin, ampicillin, cefotaxime, meropenem, and vancomycin. Forty strains (40/45, 88.9%) were both erythromycin and clindamycin-resistant, belonging to the cMLSB phenotype, and the majority of them carried erm(B) gene (39/40, 97.5%). Although the cMLSB/erm(B) constituted the most frequently identified phenotype/genotype combination (25/40, 62.5%) among all erythromycin-resistant cMLSB isolates, erm(B)/erm(A), erm(B)/mef(A/E), and erm(B)/erm(T) was detected in 7, 4, and 3 isolates, respectively. Furthermore, 43 strains (43/45, 95.6%) were tetracycline-resistant, and out of these, 39 strains (39/45, 86.7%) carried tet(L), 27(27/45, 60.0%) strains carried tet(O), and 7 (7/45, 15.6%) strains carried tet(M), alone or combined, respectively. All erythromycin-resistant isolates were also resistant to tetracycline. CONCLUSIONS: It is important to study and draw attention on SGSP, an underreported opportunistic pathogen targeting immunodeficient populations, notably elderly subjects, pregnant women and neonates.

Scopulariopsis/Microascus isolation in lung transplant recipients: A report of three cases and a review of the literature.

The current knowledge of invasive Scopulariopsis/Microascus infection in lung transplantation has been derived from only four case reports. Although these fungi are uncommon compared with Aspergillus, they are highly resistant to the current antifungal agents, and the mortality is extremely high. To explore the risk factors, clinical manifestations, notable diagnostic characteristics and outcomes of positive Scopulariopsis/Microascus isolation in lung transplantation patients. We included all cases with positive Scopulariopsis/Microascus isolation from lower respiratory tracts or bronchial mucosa biopsies in our lung transplantation centre. Proven cases from the literature were added. Positive isolation occurred in 2% (3/157) in our centre. Four cases from the literature were added. The mortality could be considered as high as 80%, once the two cases of colonisation were excluded. The average interval between transplantation and positive isolation was 106 (19-131) days. A total of 57.1% of patients had experienced a combination of infection with Aspergillus or other fungi as well as long-term azole antifungal agent treatment before the positive isolation, which may be possible risk factors. The combination of micafungin, posaconazole and terbinafine may be an effective treatment. The peak time of positive isolation was consistent with that of some opportunistic pathogens, and the possible risk factors were the infection of other fungi as well as prior long-term azole antifungal administration. In addition to its high mortality, Scopulariopsis/Microascus was also highly resistant to common antifungal agents and the combination of two or three drugs for therapy was recommended.

Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection.

Background: Signature amino acids of H7N9 influenza A virus play critical roles in human adaption and pathogenesis, but their dynamic variation is unknown during disease development. Methods: We sequentially collected respiratory samples from H7N9 patients at different timepoints and applied next-generation sequencing (NGS) to the whole genome of the H7N9 virus to investigate the variation at signature sites. Results: A total of 11 patients were involved, from whom 29 samples were successfully sequenced, including samples from multiple timepoints in 9 patients. Neuraminidase (NA) R292K, basic polymerase 2 (PB2) E627K, and D701N were the 3 most dynamic mutations. The oseltamivir resistance-related NA R292K mutation was present in 9 samples from 5 patients, including 1 sample obtained before antiviral therapy. In all patients with the NA 292K mutation, the oseltamivir-sensitive 292R genotype persisted and was not eliminated by antiviral treatment. The PB2 E627K substitution was present in 18 samples from 8 patients, among which 12 samples demonstrated a mixture of E/K and the 627K frequency exhibited dynamic variation. Dual D701N and E627K mutations emerged but failed to achieve predominance in any of the samples. Conclusions: Signature amino acids in PB2 and NA demonstrated high polymorphism and dynamic variation within individual patients during H7N9 virus infection.

PCR-ESI/MS for Molecular Diagnosis of Bloodstream Infections Directly from Blood Samples: a Systematic Review and Meta-Analysis.

BACKGROUND: PCR-ESI/MS is a commercial molecular method that can identify bloodstream infection (BSI) pathogens directly from blood. Previous studies showed its sensitivity varied greatly. Its diagnostic accuracy has not been systematically evaluated yet, thus we aimed to assess its accuracy by systematic review and meta-analysis. METHODS: Studies were searched on PubMed and Embase up to November 2017, for studies using PCR/ESI-MS to diagnose BSI directly from blood and providing sufficient data to construct two-by-two tables. Subgroup analysis and meta-regression were used to assess heterogeneity. RESULTS: A total of nine studies including 3,392 patients met the inclusion criteria. Their pooled sensitivity and specificity was 0.66 (95% CI: 0.57 - 0.74) and 0.84 (95% CI: 0.78 - 0.89), respectively. The positive and negative likelihood ratios were 4.2 (95% CI: 3.0 - 5.9) and 0.40 (95% CI: 0.31 - 0.50), respectively. The diagnostic odds ratio (DOR) was 10.61 (95% CI: 6.67 - 16.88). The area under the SROC was 0.82 (95% CI: 0.78 - 0.85). High heterogeneity was found. Subgroup analysis and meta-regression showed that regions, BSI prevalence, blood volume, and settings may cause heterogeneity. CONCLUSIONS: PCR-ESI/MS using blood specimens directly has the potential for early diagnosis of BSI, compared with blood culture. Its rule-in value is higher than rule-out value. Due to the heterogeneity of currently available studies, further high-quality studies are still needed.

Shewanella carassii sp. nov., isolated from surface swabs of crucian carp and faeces of a diarrhoea patient.

Two strains, 08MAS2251T and LZ2016-166, were isolated from diverse samples in China collected from the surface of crucian carp and the faeces of a diarrhoea patient, respectively. Both strains were pink-orange coloured, Gram-negative, oxidase- and catalase-positive, facultative anaerobic and motile bacteria, produced H2S and reduced nitrates to nitrites. Growth occurred in the presence of 0-9 % (w/v) NaCl and at 10-42 °C. The optimum conditions were with 1 % (w/v) NaCl and at 35 °C. The phylogenetic tree of 16S rRNA gene demonstrated that strains 08MAS2251T and LZ2016-166 clustered in a distinctive clade next to the species Shewanella chilikensis JC5T within the genus Shewanella. Meanwhile, gyrB gene sequence analysis indicated that the two strains formed an independent branch that was clearly separate from all the other Shewanella species with sequence similarities from 68.49 to 95.74 %. The DNA G+C content of strain 08MAS2251T was 52.68 mol%. Genomic relatedness of in silico DNA-DNA hybridization between strain 08MAS2251T and phylogenetic neighbours ranged from 50.5-51.8 %, below the cutoff of 70 %. In addition, corresponding average nucleotide identity values were between 93.01 to 93.49%, which were lower than 95 % threshold. The major fatty acids of strain 08MAS2251T were C17 : 1ω8c (27.2 %), iso-C15 : 0 (22.5 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 8.7 %), C16 : 0 (6.2 %), iso-C13 : 0 (5.6 %) and C17 : 0 (4.5 %). Based on phenotypic and genetic analysis, strains 08MAS2251T and LZ2016-166 are identified as a novel species of the genus Shewanella, for which the name Shewanellacarassii sp. nov. is proposed. The type strain is 08MAS2251T (=DSM 104682T=CGMCC 1.16033T).

Exiguobacterium sp. A1b/GX59 isolated from a patient with community-acquired pneumonia and bacteremia: genomic characterization and literature review.

BACKGROUND: Bacterial species belonging to the genus Exiguobacterium are facultative anaerobic, non-spore-forming, Gram-positive bacilli, and rarely associated with human infections. Herein, we reported the first case of community-acquired pneumonia (CAP) and bacteremia due to Exiguobacterium spp. in China. CASE PRESENTATION: An adult male with severe CAP was hospitalized. The pathogen was isolated from his bloodstream and broncho-alveolar lavage fluid. The correct identification of the micro-organism was achieved using 16S rRNA sequencing, and its antibiotic susceptibility test was performed by microdilution method. The Whole Genome Sequencing (WGS) was used to characterize its genetic features and to elucidate its potential pathogenic mechanisms. Furthermore, its genome sequence was also compared with those of 3 publicly-available Exiguobacterium strains. A PubMed search was performed for further understanding the features of Exiguobacterium infections. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain GX59 was most closely related to Exiguobacterium AT1b (99.7%). The genome of GX59 was 2,727,929 bp in size, harbouring 2855 putative protein-coding genes, 5 rRNA operons, 37 tRNA genes and 1 tmRNA. The multiple genome comparison of 4 Exiguobacterium strains demonstrated that Exiguobacterium contained 37 genes of secretion systems, including sec, tat, FEA, Type IV Pili and competence-related DNA transformation transporter (Com). Virulence factors of the micro-organism included tlyC, NprR, MCP, Dam, which might play a critical role in causing lethal infection. CONCLUSIONS: The study highlighted the potential pathogenicity of the genus Exiguobacterium for its unique genes encoding various virulence factors and those associated with antibiotic resistance, therefore, its clinical significance should be valued.

[The application and epidemiological research of xTAG GPP multiplex PCR in the diagnosis of infectious diarrhea].

OBJECTIVE: To investigate the application value of xTAG (®) gastrointestinal pathogen panel (xTAG9(®) GPP) multiplex PCR in the early diagnosis of infectious diarrhea, and understand the epidemiology of intestinal diarrhea pathogens. METHODS: Five hundred and ninety two specimens were collected in outpatient of Tongren Hospital, Capital Medical University, from 1st Oct 2013 to 30th Sep 2014, comparing the xTAG(®) GPP multiplex PCR assay with the traditional methods (culture, rapid enzyme immunoassay chromatography, microscopic examination, Real-time PCR) and mading the statistical analysis. RESULTS: The positive rate of 592 patients with diarrhea specimens was 47.8% (283/592), the proportion of male and female was 1: 1.02, the average age was 31years. The virus detection rate was 18.1%, Rotavirus A was the most common organism detected (8.8%), concentrated in winter, popular in children.Secondly,Norovirus GI/GII (8.4%),Adenovirus 40/41 was five cases. The positive rate of bacteria was 35.5%, Enterotoxigenic E.coli (8.4%, 50/592) was most frequently detected in summer, common in young adults. The other pathogens were Campylobacter 7.7%, Salmonella 7.0%, Clostridium difficile toxinA/B 3.5%, Shigella 3.3%,E.coli O157 3.3% and Shiga toxin-producing E.coli LT/ST 1.7%.None of Yersinia enterocolitica and Vibrio cholerae was detected. There were ten samples with parasitic (1.7%), five samples were positive for Cryptosporidium, three for Entamoeba histolytica and two for Giardia. All of them did not have obvious distribution followed by season and population. Totally 242(40.8%) infected specimens with single pathogen were detected. There were 41 (6.9%) co-infections samples, including two pathogens 36 cases (6.1%), three pathogens in 5 cases (0.8%). CONCLUSIONS: xTAG(®) GPP multiplex PCR is simple, sensitive, specific and can be used as a quick way to diagnose the infectious diarrhea. Diarrhea pathogen has significant characteristics with the season and crowd.