Molecular Epidemiological Characteristics Research Articles

Epidemic and drug-resistance patterns of Salmonella choleraesuis in the world

To study clinical infection and molecular epidemiological characteristics of Salmonella. Choleraesuis (S. Choleraesuis) and its drug resistance pattern were analyzed retrospectively based on big data of public health and laboratory surveillance and related literature both at home and abroad. The S. Choleraesuis is confirmed belong to a swine-adapted pathogen which can cause zoonosis among immunocompromised persons due to its highly invasive capacity. Livestock cultivation is probably the means by which S. Choleraesuis acquires drug resistance. Outbreaks or sporadic infections have been found in Thailand, Taiwan and the mainland of China over the past decades. In developed countries, the incidence and resistance rates are at very low levels, but people are susceptible to the disease and it is difficult to isolate S. Choleraesuis from stool samples, which are in consistent with the situation in Asia. It is essential for agricultural sector to take infection source control measures for the control of human and swine infections with S. Choleraesuis and drug resistance spread, and it is necessary to strengthen the capability building of laboratories at all levels to detect S. Choleraesuis. Experience on foodborne outbreaks investigation in developed countries is worth learning.

Staphylococcus aureus carriage in older populations in community residential care homes: Prevalence and molecular characterization of MRSA isolates

IntroductionThe epidemiology of S. aureus depends on conditions in specific populations. Few studies of S. aureus colonization in the older population have been performed in Spain. The aim of this study was to determine the prevalence of methicillin-resistant S. aureus (MRSA) colonization and its molecular epidemiological characteristics in an institutionalized population in community residential care homes in Cadiz, Spain. MethodsA cross-sectional epidemiological study was conducted in three residential care homes for older people. Axilla and nostril samples were tested. Identification of S. aureus and antimicrobial susceptibility testing were by MALDI-TOF and MicroScan panels. MRSA strains were subjected to SCCmec typing, multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). The presence of Panton–Valentine leukocidin (PVL) genes was determined by PCR in all S. aureus strains. ResultsA total of 293 residents were included. Fifty-one residents (17.4%) were colonized with methicillin-sensitive S. aureus (MSSA) and 11 (3.8%) with MRSA. Resistance to at least two aminoglycosides was observed in 25.4% of MSSA and 90.9% and of MRSA isolates, and resistance to levofloxacin in 80.3% of MSSA and 100% of MRSA isolates. SCCmecIV was detected in all isolates and all except one (ST-125) were ST-8. None of the S. aureus isolates were positive for PVL. ConclusionsA low rate of S. aureus carriage was detected and the prevalence of MRSA was very low. ST8-MRSA-IVc was the dominant clone, and only one strain belonged to ST125-MRSA-IVc. We found MRSA transmission within the residential care homes and a very high rate of quinolone resistance in MSSA and MRSA.

Characteristics of Resistance Mechanisms and Molecular Epidemiology of Fluoroquinolone-Nonsusceptible Salmonella enterica Serovar Typhi and Paratyphi A Isolates from a Tertiary Hospital in Dhaka, Bangladesh.

The aim of this study was to characterize the fluoroquinolone (FQ) resistance mechanism of Salmonella enterica serovar Typhi and Paratyphi A in Bangladesh. Salmonella Typhi isolates were classified into sequence type (ST) 1, ST2, and ST2209 and Salmonella Paratyphi A isolates were classified into ST85 and ST129. The most common STs of the FQ-nonsusceptible strain were ST1 (44.4%) and ST129 (66.6%). Thirty-nine percent of Salmonella Typhi isolates were multidrug resistant, and these were all ST1, which is the type prevalent in the Indian subcontinent. Although plasmid-mediated quinolone resistance genes were not detected in any of the tested strains, single and double mutations were identified in the quinolone resistance-determining region (QRDR). The most common QRDR mutation was GyrA_Ser83Phe (66.7% for Salmonella Typhi and 100% for Salmonella Paratyphi A). Treatment with an efflux pump inhibitor resulted in susceptibility of the strains to levofloxacin. All isolates demonstrated 100% susceptibility to ceftriaxone, azithromycin, and carbapenem. Our results suggest that mutations in gyrase A and enhancement of efflux pump activity are responsible for the resistance to FQs; in particular, the AcrAB-TolC efflux pump may be an important resistance factor for levofloxacin. To control the spread of FQ-nonsusceptible Salmonella Typhi, intensive surveillance in endemic areas, including Bangladesh, and effective infection control are necessary.

Characterization of SCCmec type IV methicillin-resistant Staphylococcus aureus clones increased in Japanese hospitals.

Recently, the prevalence of staphylococcal cassette chromosome mec (SCCmec) type IV isolates, which are the major community-acquired methicillin-resistant Staphylococcus aureus (MRSA), have increased in Japanese hospitals. The aim of this study was to elucidate the detailed molecular epidemiological features of the SCCmec type IV clones in Japanese hospitals. When 2589 MRSA isolated from four hospitals in Tokyo, Japan between 2010 and 2014 were analysed, the proportion of SCCmec type IV overtook that of type II, which was the major type of hospital-acquired MRSA in 2014. Multilocus sequence typing showed that CC1 was the most predominant clone in the SCCmec type IV isolates. The clinical departments that the patients belonged to, pulsed-field gel electrophoresis analysis and antimicrobial susceptibility profiles suggested that the origin of the CC1-SCCmec type IV (CC1-IV) clone was a community setting. Our data show that the CC1-IV clone is becoming a predominant MRSA clone in Japanese hospitals.

Evaluations of newborn screening program performance and enzymatic diagnosis of glucose-6-phosphate dehydrogenase deficiency in Guangzhou

Objective: To reveal the molecular epidemiologic characteristics of glucose-6-phosphate dehydrogenase (G6PD) gene and to evaluate based on the genetic analysis the newborn screening program performance and enzymatic diagnosis of G6PD deficiency in Guangzhou. Methods: G6PD enzyme activities were measured by quantitative fluorescence assay in dry blood spots of 16 319 newborns(8 725 males, 7 594 females) 3-7 days after birth in Guangzhou Newborn Center. They were born in Guangzhou form Oct. 1 to 20, 2016. The cutoff value of G6PD was less than 2.6 U/g Hb in dry blood spots. G6PD deficiency was diagnosed when G6PD<1 700 U/L or G6PD/6PGD<1 in red blood cells. Genetic analysis of G6PD gene was performed on the dry blood spot samples of 823 newborns (including positive 346, negative 477)with various levels of G6PD enzyme activities through fluorescence PCR melting curve analysis(FMCA) to detect 15 kinds of mutations reported to be common among Chinese.G6PD gene Sanger sequency was performed in seven highly suspicious patients with negative results by FMCA. Results: (1) Using the cutoff value of G6PD< 2.6 U/g Hb , a total of 687(4.2%) newborns showed positive screening results, including 560 (6.4%) males and 127(1.7%) females. (2) Among the newborns with positive screening results, 214 males and 122 females were randomly chosen for G6PD gene analysis. The results showed that 197 (92.1%) males were hemizygote and 108(88.6%) females were mutation carriers with one to four alleles. Among the newborns with negative screening results, 41 males with G6PD 2.6-2.8 U/g Hb and 436 females with G6PD 2.6-4.5 U/g Hb were chosen for genetic analysis.Mutations were detected in 5(12.2%)boys, and 226(51.8%) girls were carriers.G6PD gene Sanger sequency of seven highly suspicious patients showed that c.406C>T, c.551C>T, c.835A>T hemizygote were found in 3 male's samples, respectively. (3) The estimated prevalence of harboring mutation was 6.0% in males and 13.5% in females according to rates of mutation in samples with various levels of G6PD enzyme activities. Six common mutations were c.1388G>A、c.1376G>T, c.95A> G, c.871G>A, c.1024C>T, c.392G>T, accounting for 95.5% of detected alleles .(4) based on results of G6PD gene analysis, the newborn scereening of G6PD deficiency with cutoff value G6PD<2.6 U/g Hb yielded a positive predict value(PPV) of 93.5%, a false-positive rate of 0.5%, and a sensitivity of 99.0% for males. A PPV of 88.5%, a false-positive rate of 0.2% . The prevalence of severe type G6PD deficiency in females was about 1.5%. Compared with to genetic analysis, the sensitivity and PPV of G6PD activity assay in red blood cells were 95.5%, 97.2%, respectively. Conclusions: The prevalence of G6PD deficiency in males was 6.0% in Guangzhou. Six mutations c.1388G>A, c.1376G>T, c.95A>G, c.871G>A, c.1024C>T, c.392G>T accounted for 95.5%. The cutoff value of G6PD<2.6 U/g Hb innewborn screening program and the criteria of biochemical diagnosis could accurately identify G6PD deficiency . Combined with biochemical and molecular analysis will improve the accuracy of diagnosis of G6PD deficiency and detect more heterozygous females.

Genotypic, phylogenetic and epidemiological characteristics of porcine reproductive and respiratory syndrome virus strains (PRRSV) in Vietnam

Nucleotide sequence of ORF5 encoding the antigenic GP5 for 11 strains collected from different geographic localities in the country during 2008-2011 were obtained. These nucleotide sequences were analyzed for molecular properties (nucleotides and amino acids) to determine genotype, phylogenetic and molecular epidemiological characteristics compared with PRRSV circulating in Vietnam and worldwide. Analysis of nucleotides and deduced amino acids showed that there was very high level of nucleotide identity and amino acid homology (98 – 100%) between the Vietnamese and Chinese PRRSV strains. Phylogenetic analysis based on ORF5 nucleotide sequences revealed two large groups, one derived from the North American lineage of genotype 2, including 11 PRRSV isolates in this study and another of the European lineage of genotype 1. In the genotype 2, further subgroups were found among which there were strains of Asia (Vietnam, China, India), strains of the European/North American origin (Austria, US, Denmark) and a 2012-isolated strain from Canada, in a separate subgroup. Regarding to the epidemiological analysis, our isolates collected during 2008-2011, completely followed the endemic peaks occurred in Viet Nam, such as those in 2007-2008 and in 2010-2011. They all were determined as highly virulent strains due to high homology to the highly virulent strains of China occurred in those periods. We have some conclusions to be made that the outbreaks of highly pathogenic PRRSV in Vietnam were epidemiologically associated with the endemics occurred in China and originated from China.

Recent Increase in the Incidence of TEM-135 β-Lactamase-harboring Neisseria gonorrhoeae in Korea.

BackgroundWe investigated the molecular epidemiological characteristics and antimicrobial susceptibility pattern of penicillinase-producing Neisseria gonorrhoeae (PPNG) isolates to monitor the change in distribution of blaTEM in Korea.MethodsWe collected 804 PPNG isolates from diverse hospitals and clinics mainly located in Seoul, Korea, over a period of 11 years (2005–2015). Isolate susceptibility to seven antimicrobials was determined using the agar dilution test. The molecular epidemiological characteristics of the isolates were determined by Sanger sequencing of blaTEM, N. gonorrhoeae multiantigen sequence typing (NG-MAST) and plasmid typing.ResultsAmong 72 fully sequenced PPNG isolates, sixteen (22.2%) possessed TEM-135. All TEM-135 isolates had a common silent mutation (c.18C>T), which was previously unreported. We observed a pattern of continuous increase in the number of TEM-135 isolates since 2012. The median and 90% minimum inhibitory concentration of azithromycin were substantially lower in the TEM-135 group than in the non-PPNG and TEM-1 groups. All TEM-135 isolates showed different NG-MAST types and predominantly harbored Toronto/Rio (75%) plasmids. A comprehensive comparative analysis of PPNG with TEM-135 according to NG-MAST, plasmid type, and year of isolation revealed a wide distribution.ConclusionsThe proportion of TEM-135 PPNG has continuously increased since 2012, in association with clonal spread. The difference at position 18 of the TEM-135 sequence can be interpreted as the existence of multiple clonal complexes. The possibility that TEM-135 was acquired via foreign plasmids requires careful follow-up and continuous monitoring of TEM-135 to ascertain whether it constitutes a step towards evolutionary change.

Prevalence and serogroup changes of Neisseria meningitidis in South Korea, 2010\u20132016

Determination of the major serogroups is an important step for establishing a vaccine programme and management strategy targeting Neisseria meningitidis. From April 2010 to November 2016, a total of 25 N. meningitidis isolates were collected in South Korea, in collaboration with the Korean Society of Clinical Microbiology. Among isolates, 19 isolates were recovered from blood and/or cerebrospinal fluid (CSF) in 46 patients who suffered from invasive meningococcal disease (IMD), and six isolates were found in sputum or the throat. The most common serogroup was serogroup B (overall, 36%, n = 9/25; IMD, 37%, n = 7/19), which was isolated in every year of the research period except for 2011. There were five serogroup W isolates recovered from patients in military service. W was no longer isolated after initiation of a vaccine programme for military trainees, but serogroup B caused meningitis in an army recruit training centre in 2015. In MLST analysis, 14 sequence types were found, and all isolates belonging to W showed the same molecular epidemiologic characteristics (W:P1.5-1, 2-2:F3-9:ST-8912). All isolates showed susceptibility to ceftriaxone, meropenem, ciprofloxacin, minocycline, and rifampin; however, the susceptibility rates to penicillin and ampicillin for isolates with W and C capsules were 22% and 30%, respectively.

Prevalence of mutations in genes associated with isoniazid resistance in Mycobacterium tuberculosis isolates from re-treated smear-positive pulmonary tuberculosis patients: A meta-analysis.

The prevalence of isoniazid (INH) monoresistance is high in India. In this study, molecular epidemiological characteristics associated with INH resistance mutations in Mycobacterium tuberculosis in codon katG315 and in the promoter region of the inhA gene were investigated. Sputum specimens of smear-positive tuberculosis (TB) patients were subjected to GenoType MTBDRplus assay to identify katG and inhA mutations in M. tuberculosis. In addition to the current study, 17 publications assessed 14100 genotypically resistant M. tuberculosis isolates for mutations in katG inclusive of codon 315. In total, 1821 (11.8%) of 15438 INH-resistant strains had detectable mutations: 71.0% in katG315 and 29.0% in the inhA promoter region. The prevalence of IHN monoresistance was 89.1% in the economically-active age group, 0.4% in the paediatric age group and 10.5% in those aged >60years; the rate in males and females was 12.0% and 10.8%, respectively. Meta-analysis derived a pooled katGS315T resistant TB prevalence of 67.3% (95% CI 59.3-75.4%) with Q=732.19, I2=98.35% and P=0.000 for treated TB cases. INH resistance was spread widely and transmission of INH-resistant isolates, especially with katG315T mutation, was confirmed. Therefore, it is important to diagnose katG315T mutants among INH-resistant strains as it may be a risk factor for subsequent development of multidrug-resistant TB (MDR-TB). Prompt detection of patients with INH-resistant strains would expedite modification of treatment regimens, and appropriate infection control measures could be taken in time to diminish the risk of further development and transmission of MDR-TB.

Molecular epidemiology and virulence characteristics of Staphylococcus aureus nasal colonization in medical laboratory staff: comparison between microbiological and non-microbiological laboratories

BackgroundMedical laboratory staff are a high-risk population for colonization of Staphylococcus aureus (S. aureus) due to direct and dense contact with the pathogens; however, there is limited information about this colonization. This study sought to determine the prevalence and molecular characteristics of nasal colonization by S. aureus in medical laboratory staff in Guangzhou, southern China, and to compare the differences between microbiological laboratory (MLS) and non-microbiological laboratory (NMLS) staff.MethodsS. aureus colonization was assessed by nasal swab cultures from 434 subjects, including 130 MLSs and 304 NMLSs from 33 hospitals in Guangzhou. All S. aureus isolates underwent the antimicrobial susceptibility test, virulence gene detection and molecular typing.ResultsThe overall prevalence of S. aureus carriage was 20.1% (87/434), which was higher in MLSs than in NMLSs (26.2% vs. 17.4%, P < 0.05), while the prevalence of Methicillin-resistant S. aureus (MRSA) was similar. Living with hospital staff was associated with S. aureus carriage. The majority of the isolates harboured various virulence genes, and those in MLSs appeared less resistant to antibiotics and more virulent than their counterparts. A total of 37 different spa types were detected; among these, t338, t437, t189 and t701 were the most frequently encountered types. T338 was the main spa type contributing to nasal colonization Methicillin-sensitive S. aureus (MSSA) (13.0%), and t437-SCCmec IV was predominant in MRSA isolates (40%).ConclusionsThese findings provide insight into the risk factors, molecular epidemiology and virulence gene profiles of S. aureus nasal carriage among the medical laboratory staff in Guangzhou.

Dissemination of Panton-Valentine leukocidin–positive methicillin-resistant Staphylococcus aureus USA300 clone in multiple hospitals in Tokyo, Japan

ObjectivesPanton-Valentine leukocidin (PVL) gene (lukS/F-PV)-positive community-acquired methicillin-resistant Staphylococcus aureus (MRSA), particularly the USA300 clone, is a health concern worldwide. Recently, community-acquired MRSA clones have been found to spread and persist in hospital settings. We aimed to investigate the prevalence and molecular epidemiologic features of lukS/F-PV–positive MRSA in Japanese hospitals. MethodsA total of 3433 MRSA isolated from nine hospitals in 2011–2015 were assessed. Molecular epidemiologic analysis performed by staphylococcal cassette chromosome mec typing, PVL typing, arginine catabolic mobile element typing, detection of virulence determinants, multilocus sequence typing, pulsed-field gel electrophoresis and antimicrobial susceptibility testing. ResultsThe detection rate of lukS/F-PV was increased annually from 0.6% (5/817) in 2011 to 3.1% (17/544) in 2015. Molecular epidemiologic analysis for 64 lukS/F-PV–positive MRSA isolates revealed that 42 isolates (65.6%) were the USA300 clone. Resistance rates of levofloxacin and gentamicin among lukS/F-PV–positive isolates increased annually as a result of increased prevalence of the multidrug-resistant USA300 clone. ConclusionsThis is the first report on dissemination of the USA300 clone and PVL-positive MRSA in multiple Japanese hospitals. Our data strongly suggest that the USA300 clone may become epidemic in Japanese hospitals.

Microbial infection pattern, pathogenic features and resistance mechanism of carbapenem-resistant Gram negative bacilli during long-term hospitalization

BackgroundCarbapenem-resistant Gram-negative bacilli (GNB) have become an important cause of nosocomial infections of hospitalized patients. MethodsTo investigate the microbial infection patterns and molecular epidemiology characteristics of the carbapenem-resistant GNB isolates from a long-term hospitalized patient, antimicrobial susceptibility testing, phenotypic screening test for carbapenemase production, PCR screening and DNA sequencing of carbapenemase genes, repetitive extragenic palindromic sequence-based PCR (REP-PCR), multilocus sequencing typing (MLST) and genetic environment analysis were performed. ResultsTwelve strains with carbapenemase genes were detected from 63 carbapenem-resistant isolates, including two blaIMP-25-carrying Pseudomonas aeruginosa, one blaNDM-1-carrying Citrobacter freundii, three blaNDM-1-carrying Klebsiella pneumoniae and six blaKPC-2-carrying K. pneumoniae. Only the blaNDM-1 genes were successfully transferred from three K. pneumoniae strains to Escherichia coli C600 by conjugation. Genetic environment of blaIMP-25, blaNDM-1 and blaKPC-2 genes in our study were consistent with previous reports. Molecular typing of K. pneumoniae performed by MLST revealed that most of the isolates belonged to ST11. blaNDM-1-carrying K. pneumoniae sequencing type 1416 was first reported in our study. ConclusionsCarbapenem-resistant GNB are common pathogens during long-term hospitalization, and ST11 blaKPC-2-carrying K. pneumoniae is the dominant bacterium in our study. Colonization and horizontal transmission of resistance by plasmids of carbapenem-resistant GNB have increased the risks of persistent infection and mortality of long-term hospitalized patients.

Prevalence and Genotype Analysis of Newborn α-Thalassemia in Wuhan Area of China

To investigate the genotypes of newborn α-thalassemia and to analyze its characteristics of molecular epidemiology in Wuhan area. The newborn α-thalassemia gene in 1376 cases with positive confirmed in the primary screening in Wuhan area was detected by PCR, flow cytometry and FISH. The α-thalassemia in 436 newborns and α- β-composite thalassemia in 10 newborns were confirmed by detection in Wuhan area. The majority of thalassemia cases [up to 92.20% (402/436)] were found to be minor and static type thalassemia including 237 cases of -SEAαα (54.36%), 135 cases of -α3.7 / αα (30.96%) and 30 case of -α4.2/αα (6.88%), however, the intermediate type -α3.7/-SEA was found in 1 newborn. The -SEA/detetion, -α3.7/detetion and -α4.2/detetion were major in the detetion, the frequency was 54.12%, 32.29% and 7.13%, respectively; while the αCS mutation, αQS mutation and αWS mutation were less in the mutation, their frequency was 3.7%, 2.45% and 0.22% respectively. The minor and static type newborn thalassemia is most common, the incidence of detetion type -SEA/αα, -α3.7/αα and α4.2/αα is more high in Wuhan area of china.

Genetic polymorphisms identify in species/biovars of Brucella isolated in China between 1953 and 2013 by MLST

BackgroundBrucellosis incidence in China is divided into three stages: high incidence (1950s–1960s), decline (1970s–1980s), and re-emergence (1990s–2010s). At the re-emergence stage, Brucellosis incidence grew exponentially and spread to all 32 provinces. We describe the magnitude and the etiological distribution changes in mainland China by genotyping data and emphasize its recent reemergence. We also provide the genetic diversity and molecular epidemiological characteristics of Brucella.ResultsFrom a total of 206 Brucella isolates, 19 MLST genotypes (STs) were identified and 13 new STs(ST71–83)were found. MLST grouped the population into three clusters. B. melitensis, B. abortus and B. suis were grouped into cluster 1, 2 and 3 respectively. The predominant genotype in the first cluster by MLST, remained unchanged during the three stages. However, the proportion of genotypes in the three stages had changed. More isolates were clustered in ST8 at the re-emergence stage. STs71–74, which were not found in the two former stages, appeared at the re-emergence stage.ConclusionsThe changing molecular epidemiology of brucellosis improve our understanding of apparent geographic expansion from the historically affected north of China to southern provinces in recent reemergence.

MLVA and LPS Characteristics of Brucella canis Isolated from Humans and Dogs in Zhejiang, China.

Brucella canis is a pathogenic bacterium that causes brucellosis in dogs, and its zoonotic potential has been increasing in recent years. B. canis is a rare source of human brucellosis in China, where Brucella melitensis has been the major pathogen associated with human brucellosis outbreaks. In late 2011, a case of a B. canis infection was detected in a human patient in Zhejiang Province, China. To compare the genotypes between strains of B. canis isolated from the patient and from dogs, a multiple-locus variable-number tandem-repeat analysis (MLVA-16) was performed. In addition, the lipopolysaccharide-synthesis-related genes were analyzed with the B. canis reference strain RM6/66. 32 B. canis strains were divided into 26 genotypes using MLVA-16 [Hunter-Gaston Diversity Index (HGDI) = 0.976]. The HGDI indexes for various loci ranged between 0.000 and 0.865. All four Hangzhou isolates were indistinguishable using panel 1 (genotype 3) and panel 2A (genotype 28). However, these strains were distinctly different from other isolates from Beijing, Jiangsu, Liaoning, and Inner Mongolia at Bruce 09. The emergence of a human B. canis infection was limited to an area. Comparative analysis indicated B. canis from canines and humans have no differences in lipopolysaccharide-synthesis locus. The comprehensive approaches have been used to analyze human and canine B. canis isolates, including molecular epidemiological and LPS genetic characteristics. Further detailed analysis of the whole genomic sequencing will contribute to understanding of the pathogenicity of B. canis in humans.

Epidemiology reveals Zhaotong City as the hub of human immunodeficiency virus type 1 transmission from the Yunnan province to other regions in China.

The Yunnan province in China has a high incidence of human immunodeficiency virus-1 (HIV-1) infection. Zhaotong City is located in the Yunnan province, a neglected 'important region'. In this study, we evaluated the unique molecular epidemiological characteristics of HIV-1 infection in Zhaotong City. We collected 305 serum samples from HIV-infected patients in Zhaotong City between May 2015 and April 2016. A total of 122 samples were selected for HIV-1 gag-pol gene amplification, of which 88 were successfully amplified and sequenced for phylogenetic and phylogeographic analysis. Circulating recombinant forms 07_BC (CRF07_BC, 23 cases, 26.14 %) and CRF08_BC (49 cases, 55.68 %) were the predominant subtypes; the high proportions of these two subtypes differed from those elsewhere in the Yunnan province. The other subtypes were CRF01_AE (11 cases, 12.5 %), B (one case, 1.14 %) and unique recombinant forms (four cases, 4.55 %). Phylogeographic analysis of the CRF07_BC and CRF08_BC subtype strains revealed that Zhaotong was one of the regions in which CRF07_BC and CRF08_BC entered initially. The CRF08_BC strain originated from this region closer to the 'root' position of the phylogenetic tree. Thus, Zhaotong City may have been an important channel in the transmission route of HIV-1 from Yunnan to other parts of the country. Based on this unique distribution of HIV-1 subtypes in Zhaotong City, the epidemic outbreak in this area may have played an important role in the spread of CRF07_BC and CRF08_BC subtypes.

Molecular epidemiological characterization of Brucella isolates from sheep and yaks in northwest China.

Animal brucellosis is a re-emerging disease in China with high prevalence in the northwest region. A total of 66 isolates of Brucella were recovered from sheep and yaks in the Inner Mongolia, Xinjiang, Qinghai and Gansu provinces of northwest China in 2015 and 2016. Using classical biotyping and the Brucella AMOS PCR assay, all isolates were identified as Brucella melitensis biovar 3 (n=58), B.melitensis biovar 1 (n=1), Brucella abortus (n=5), or Brucella suis biovar 3 (n=2), and B.melitensis biovar 3 was found to be mainly responsible for sheep brucellosis in northwest China. Multilocus variable-number tandem-repeat analysis (MLVA) was used to identify the epidemiological relationships among the isolates and to assess their genetic diversity. Multilocus variable-number tandem-repeat analysis-16 identified 46 genotypes in these populations, including 37 unique and nine shared genotypes. Multilocus variable-number tandem-repeat analysis-11 showed that 71% of the isolates (47 of 66) were genotype 116 (1-5-3-13-2-2-3-2-4-41-8), a characteristic subgroup of the East Mediterranean group, showing that isolates from different geographical areas exhibit similar epidemiological characteristics in different regions and may be epidemiologically linked. Multilocus variable-number tandem-repeat analysis-11 also revealed that an isolate from Inner Mongolia had a novel genotype, 369 (1-5-3-13-2-2-3-2-7-41-8). Multilocus variable-number tandem-repeat analysis-16 genotyping of northwest China Brucella isolates allows a better understanding of the epidemiology of animal brucellosis in this region. This study is the first analysis of B.melitensis in Gansu province, and the results confirmed that in this province, isolates of this species are disorderly and unsystematic.

Clonal spread and azole-resistant mechanisms of non-susceptible Candida albicans isolates from vulvovaginal candidiasis patients in three Shanghai maternity hospitals.

In our multicenter study, 43 fluconazole non-susceptible and 45 fluconazole-susceptible isolates were collected from vulvovaginal candidiasis (VVC) patients from three Shanghai maternity hospitals to analyze their molecular epidemiological features and fluconazole resistant mechanisms. Cross-resistance to fluconazole, itraconazole and voriconazole was observed in 53.5% of the nonsusceptible isolates. Though we acquired 12 clonal complexes (CCs) of diploid sequence types (DSTs) in clinical isolates by a multilocus sequence typing method, fluconazole nonsusceptible isolates all belonged to CC69 with a predominant genotype of DST 79. Increased expressions of efflux pump genes (CDR1, CDR2, and MDR1) were observed only in minor fluconazole non-susceptible isolates by real-time quantitative polymerase chain reaction (PCR). However, ERG11 genes of fluconazole SDD and resistant isolates had significantly higher expression levels than fluconazole-susceptible isolates. Moreover, 13 distinct amino acid substitutions in Erg11p were found in clinical isolates. Three of the substitutions were novel amino acid substitutions (T123I, P98S, and Y286D), which were not in the susceptible isolates. Only two heterozygous amino acid substitutions (A18P/A and R365G/R) in Erg3p were found in two isolates with cross-resistance to fluconazole, itraconazole, and voriconazole. Taken together, we observed the clonal spread of CC69 in fluconazole non-susceptible isolates of Candida albicans from VVC patients with the dominant genotype DST79. ERG11 gene mutations and overexpression predominantly contributed to fluconazole resistance instead of the more common increased expressions of efflux pump genes (CDR1, CDR2, and MDR1).

Molecular and clinical characterization of human respiratory syncytial virus in South Korea between 2009 and 2014.

Respiratory syncytial virus (RSV) can cause serious respiratory infections, second only to influenza virus. In order to know RSV's genetic changes we examined 4028 respiratory specimens from local hospital outpatients in Gyeonggi Province, South Korea over six consecutive years by real-time one-step RT-PCR; 183 patients were positive for RSV infection. To investigate the specific distribution of RSV genotypes, we performed partial sequencing of the glycoprotein gene. Of the 131 RSV-A specimens sequenced, 61 (43·3%) belonged to the ON1 genotype, 66 (46·8%) were NA1 genotype, 3 (2·1%) were GA5 genotype, and 1 (0·7%) belonged to the GA1 genotype. Of the 31 RSV-B specimens sequenced, 29 were BA9 genotype (87·9%) and 2 were BA10 genotype (6·1%). The most common clinical symptoms were fever, cough, nasal discharge, and phlegm; multiple logistic regression analysis showed that RSV-positive infection on pediatric patients was strongly associated with cough (OR = 2·8, 95% CI 1·6-5·1) and wheezing (OR = 2·8, 95% CI 1·7-4·4). The ON1 genotype was significantly associated with phlegm (OR = 11·8, 95% CI 3·8-46·7), while the NA1 genotype was associated with the pediatric patients' gender (males, OR = 2·4, 95% CI 1·1-5·4) and presence of chills (OR = 5·1, 95% CI 1·1-27·2). RSV subgroup B was showed association with nasal obstruction (OR = 4·6, 95% CI 1·2-20·0). The majority of respiratory virus coinfections with RSV were human rhinovirus (47·2%). This study contributes to our understanding of the molecular epidemiological characteristics of RSV, which promotes the potential for improving RSV vaccines.

Molecular epidemiology of carbapenem resistant Klebsiella pneumoniae in a hospital in Beijing

Objective: To reveal the molecular epidemiological characteristics of Carbapenem-Resistant Klebsiella pneumoniae (CRKP) isolated from a three level teaching hospital in Beijing. Methods: Pulsed field gel electrophoresis (PFGE) was carried out to subtyping 375 CRKP isolated in that hospital between May 2010 and October 2015. Fifteen strains were chose based on the PFGE patterns to be analyzed by multi-locus sequence typing (MLST) and detection of carbapenem-resistance genes. One strain (A1502) was selected for whole genome sequencing and analyzing. Results: The 375 CRKP were divided into 140 PFGE types, among which five types contained more than five strains. The dominant types were distributed in different time periods and wards. Among the 15 strains tested by MLST and carbapenem-resistance genes detection, 13 were ST11 strains carrying KPC-2 gene. By genome-based typing, A1502 was clustered together with strains from other hospitals of Beijing but far from the strains from Shanghai and Hangzhou. Conclusion: The CRKP epidemic clone (ST11 clone carrying KPC-2) has been spreading within single hospital and across different hospitals in Beijing.