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The present study collected 280 isolates of Cryptococcus neoformans and 22 isolates of Cryptococcus gattii and evaluated the consistencies between Sensititre YeastOne (SYO), VITEK 2, and the reference broth microdilution (BMD) method for the antifungal susceptibility testing of fluconazole, voriconazole, and flucytosine. For amphotericin B, SYO was replaced with the BIO KONT amphotericin B microbroth dilution kit. The essential agreements (EAs) by SYO and VITEK 2 for C. neoformans var. grubii and C. neoformans var. neoformans were 98.15–99.63% and 88.89–100%, respectively, with fluconazole, voriconazole, and flucytosine. The EA for C. gattii VG Ⅰ against fluconazole was 29.41% by VITEK 2, while the other EAs for C. gattii strains were 100% by SYO and VITEK 2. The categorical agreements (CAs) by SYO and VITEK 2 for C. neoformans and C. gattii were 94.12–100%, while VITEK 2 failed to distinguish 5/6 fluconazole-resistant non-wild-type C. neoformans var. grubii isolates; this finding confirmed the limitation of testing fluconazole against C. neoformans as documented in the manufacturer's package insert. The EAs for amphotericin B were 97.42–100% for C. neoformans and C. gattii, but the CAs were 17.65–60% by BIO KONT and VITEK 2. Thus, SYO can be used for susceptibility testing of C. neoformans and C. gattii against fluconazole, voriconazole, and flucytosine, and VITEK 2 can be used for susceptibility testing of C. neoformans against voriconazole and flucytosine. Further studies using amphotericin B-resistant isolates are required to assess the agreement between VITEK 2, BIO KONT, and BMD. Lay Summary Sensititre YeastOne showed a good agreement with the CLSI broth microdilution method for C. neoformans and C. gattii against voriconazole and flucytosine. The limitation regarding fluconazole testing against C. neoformans documented in VITEK 2 manufacturer's package insert was confirmed.

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.

Nocardia spp. is a pathogen responsible for a variety of clinical infections, ranging from skin and soft tissue infections, to the respiratory tract and central nervous system infections. Its epidemiological characteristics, including species distribution, clinical features, and antimicrobial susceptibility profiles, should be under surveillance for the prevention and treatment of nocardiosis. In the present study, over a 9-year period (from 2009 to 2017), 53 non-repetitive Nocardia isolates were collected from 8 tertiary general hospitals of 7 cities in China. These isolates were identified to species level by multilocus sequence analysis(MLSA). The clinical data were also reviewed. The susceptibilities to 10 commonly-used antibiotics for Nocardia were determined by E-test stripes, and the resistance rates, MIC50 and MIC90 to each antibiotic by different species were analyzed. Of 53 Nocardia isolates, N. farcinica was the most common species (24.5%, 13/53), followed by N. cyriacigeorgica (20.8%, 11/53), N. terpenica (15.1%, 8/53), N. abscessus (9.43%, 5/53), N. otitidiscaviarum (7.55%, 4/53), respectively. Furthermore, 31 Nocardia (58.5%) isolates were recovered from lower respiratory tract (sputum and BALF), 15 (28.3%) from superficial Infection, 3 (5.7%) from pleural effusion, 2 (3.8%) from CSF, and 1 from bone marrow and 1 from synovial fluid, respectively. The antibiotic resistance profiles varied between different Nocardia species. All Nocardia isolates were susceptible to linezolid, followed by imipenem and amikacin (both 92.5% susceptibility rate). N. terpenica, rarely documented elsewhere, showed a different antimicrobial susceptibility profile. In summary, herein, the clinical and antibiotic resistance features of Nocardia species reported would be helpful for understanding the diversity of Nocardia species circulating in China and for decision making in the context of empiric therapy.

Purpose. Group B Streptococcus (GBS) is one of the major pathogens in severe materno-neonatal infections. We aimed to describe the clinical and molecular characteristics of GBS isolates causing infections in 45 maternal and 50 neonatal subjects, collected from eight healthcare centres in mainland China over the period 2010– 2017. Methodology. The phenotypic and genotypic features of the GBS isolates, including capsular polysaccharide (cps) serotypes, pilus island (PI) genes and antibiotic resistance profiles and genes, were characterized by both conventional and molecular methods. The clonal relationship between these strains was investigated using multilocus sequence typing (MLST). Results. Of the 95 isolates, the predominant serotypes were III (51, 53.7 %), V (13, 13.7 %) and Ib (13, 13.7 %). All GBS strains carried at least one pilus island, with 32.6 % carrying PI-2b and 67.4 % PI-2a, singly or in combination. The most frequently-detected pilus island pattern was the combination of PI-1 and PI-2a, accounting for 56.8 % (54 isolates), followed by PI-1 combined with PI-2b (28, 29.5 %), PI-2a (10, 10.5 %) and PI-2b (3, 3.2 %). The strains were classified into 17 individual sequence types, and further clustered into six clonal complexes (CCs). A high prevalence of CC17/PI-1 and PI-2b (17, 34.0 %) was detected in 50 GBS isolates causing neonatal infections. No strain was resistant to penicillin, ampicillin, ceftriaxone or vancomycin, whereas 78.9, 76.8 and 81.5 % were resistant to erythromycin, clindamycin and tetracycline, respectively. Conclusion. Our study highlights the high genotypic diversity of GBS strains causing materno-neonatal infections, and the CC17/PI-1 and PI-2b sublineages should be noted in neonatal infections.

Group B streptococcus (GBS) is an increasing pathogen threat to newborns and adults with immunodepressive diseases. Here, a total of 193 GBS, including 51 invasive and 142 noninvasive isolates, were collected from the patients with infections in 7 tertiary hospitals from 5 cities in China during the year 2008 to 2015. The strains of GBS were characterized by classical and molecular techniques for capsular polysaccharide serotyping, genes for pilus island (PI) and α-like protein (alp), and antibiotic resistance profiling. Of 193 isolates, the predominant serotypes were III (45.6%) and Ia (18.7%). All strains carried at least 1 PI gene. The combination of PI-2b and PI-1 was present in 46.1% isolates, followed by PI-2a alone (80, 41.5%) and PI-2b alone (23, 11.9%). The most prevalent alp gene was rib (87, 45.1%), followed by α-C (47, 24.4%), ε (33, 17.1%), alp2/3 (7, 3.6%) and alp4 (2, 1.0%), respectively. The clonal relationships between strains were investigated using multilocus sequence typing. The strains were distinguished into 26 individual sequence typing, and further clustered into 6 clonal complexes. A significant association was noted between the distributions of alp genes, serotyping and PI profiles, such as serotype III-rib-PI+PI-2a, Ib-α-C, and Ia-ε-PI-2a. No penicillin-resistant strains were detected, and 74.1%, 64.2%, and 68.9% were resistant to erythromycin, clindamycin, and tetracycline, respectively. The infective GBS isolates in China demonstrated epidemical features.

Staphylococcus aureus, a commensal and a pathogenic bacterium, causes a wide variety of diseases in humans and animals with a high impact on public health and the livestock industry. The risk of zoonotic transmission to humans highlights the need to understand the molecular ecology of S. aureus in foods. In this study, we obtained 25 S. aureus isolates from 39 crayfish samples in Hubei, China. PCR was applied for detection of presence of virulence and methicillin resistance genes in the pathogen genome. The result revealed that all of the 25 S. aureus isolates harbored at least four virulence genes, and 64 % of them were positive for five or more virulence genes. The most predominant virulence genes were coa, α-HL and β-HL genes (100 %), followed by sea (68 %), fnbA (60 %), tsst-1 (36 %), while none of the examined isolates presented positive for mecA gene conferring methicillin resistance. Subsequently, all of the isolates were assessed for phenotypic biofilm formation with the microtiter plate assay. The results showed 92 % isolates could produce biofilm with different forming capacity. Multilocus sequence typing divided the isolates into five sequence types (STs), three of which (ST1920, ST188 and ST398) were the same with the isolates from livestock and clinic in China. This study provides preliminary insights into the genetic diversity and virulence gene profiles of S. aureus from crayfish, suggesting that S. aureus isolates from crayfish is a potential hazard for consumers and deserves further attention.

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.

Plant diseases, insects, and insect vectored viruses can do extensive damages to host plants and result in severe yield losses. It is reported that overall about 15% of the U.S. crop production is lost annually to infectious crop diseases despite the fact that American agricultural producers are using cutting-edge disease control technology and pesticide products, and adapting newly bred disease-resistant crop cultivars and hybrids. This Nebraska Crop Surveillance Network project has accomplished three objectives. First, it uses advanced computer, database and network technology to automate experimental field data collection, processing and centralization storage processes, thus relieving research staff from tedious and redundant work while also reducing the likelihood of human error during the data collection and transcription processes. Second, it tracks soybean disease infection patterns under different management, environmental and soil conditions during the growing season in Nebraska. Third, it produces an online graphical visualization system based on the near realtime data collected from the experimental field to simulate, monitor and predict soybean disease infection patterns. These graphical representations of patterns are intended to help convey disease infection related concepts and disease control decision-making information to agriculturalists. The online tracking system is designed to help Nebraska farmers to make the right decisions on their daily agricultural practices, such as choosing the right planting date and applying the right pesticide to minimize plant damage and maximize yield potential. We use a Zope Web server, a MySQL relational database, and a graphic rendering product, ZGDChart to build this data visualization system which completely automates data gathering and storage processes and enables users to observe a graphical representation of plant disease infection patterns during the growing season in Nebraska under different management and environmental conditions.