Multilocus sequence typing analysis and second‐generation sequencing analysis of Salmonella Wandsworth

BackgroundSalmonella Wandsworth is a rare serotype of Salmonella. This study analyzed the genotyping, genome structure, and molecular biological functions of Salmonella Wandsworth based on the results of multilocus sequence typing and next‐generation sequencing genome assembly analysis.MethodsSerological typing was performed using the slide‐agglutination method. The micro broth dilution method was used to test antibiotic susceptibility. Multilocus sequence typing (MLST) was used to perform the homology analysis, while the second‐generation sequencing genome analysis was used to analyze the whole genome of the bacteria.ResultsSalmonella Wandsworth is Group Q Salmonella. The MLST of this strain was ST1498. Salmonella Wandsworth was sensitive to antibiotics, such as ceftriaxone, imipenem, chloramphenicol, and colistin, but was resistant to ampicillin, cefalotin, gentamicin, and ciprofloxacin. The second‐generation sequencing results showed that the genome sequence length of the bacteria was 5109457bp. Annotated COG library analysis generated 3,746 corresponding genes. After the comparison with the KEGG library, 1,340 genes, which participate in 19 types of metabolic pathways, were obtained. A total of 249 pathogenic factors and 2 disease islands were predicted. 2 CRISPR sites and 8 Cas sites were predicted. It can be seen from the evolutionary tree that Salmonella Wandsworth MLST1498 and Paratyphi B str.SPB7 are gathered together. We identified one resistance gene, namely, aac(6’)‐Iaa accounting for aminoglycoside resistance.ConclusionSalmonella Wandsworth isolated in this study is Salmonella group Q. Consequently, it is necessary to strengthen the understanding of clinical infections of Salmonella Wandsworth and carry out continuous monitoring and research.     

中国不可分群脑膜炎奈瑟菌的分子分型分析

目的了解我国血清不可分群(non-serogroupable,NG)脑膜炎奈瑟菌分子分型特征。方法选取我国2005-2011年分离的104株血清不可分群脑膜炎奈瑟菌作为研究对象,采用多位点序列分型(MLST)和聚合酶链反应(PCR)基因分群(A、B、C、W、E、X、Y、Z、H、I、L、K、cnl)方法,检测其ST序列群及基因群。结果 104株不可分群脑膜炎奈瑟菌中,基因群分布为荚膜基因缺失菌株(capsule null locus,cnl)(36株)、B群(20株)、C群(14株)、W群(9株)、E群(9株)、X群(3株)和Y群(3株),余下10株未鉴定出基因群;未发现其他基因群菌株。MLST分型将104株NG菌株分为45种ST型,其中14种为新的ST型;17种ST型可归为7个序列群(65株);cnl菌株全属于ST-198序列群,B群和C群菌株以ST-4821为优势序列群,W群以ST-11和ST-174序列群为主。结论我国NG脑膜炎奈瑟菌具有基因多态性,其中ST-198序列群全部为cnl菌株。     

陕西省婴幼儿食品中分离的132株蜡样芽胞杆菌呕吐型基因的检测

目的 了解2012-2016年陕西省市售婴幼儿食品中蜡样芽胞杆菌的呕吐型基因的携带情况及携带呕吐基因菌株的分子分型。方法 采用PCR 方法对2012-2016年陕西省不同地区市售婴幼儿食品中收集到的132株蜡样芽胞杆菌的呕吐型基因进行检测,用多位点序列分型(MLST)方法对携带呕吐型基因的蜡样芽胞杆菌进行分子分型。结果 132株蜡样芽胞杆菌中携带呕吐型基因的共计9株,携带率682%。这9株菌分为4个序列类型(Sequence Type,ST),分别为ST-100(1111%,1/9)、ST-164(1111%,1/9)、ST-246(1111%,1/9)、ST-26(6667%,6/9)。结论 陕西省市售婴幼儿食品中的蜡样芽胞杆菌携带有呕吐型基因,携带率682%,以ST-26为主要流行株,基因型多样,地区间有地区特征性差异。     

多位点序列分型应用于致病性黄疸出血群钩端螺旋体分析

目的 初步探讨MLST(multilocus sequence typing)分型技术在致病性钩端螺旋体中的应用。方法 对我国3个省份的39株致病性钩端螺旋体黄疸出血群菌株提取DNA,采用7个位点进行PCR扩增、序列测定,应用eBURST和BioNumerics (Version5.10)软件进行分析。结果 39株菌株呈现5个ST型别, ST1为中国三省份中主要的基因型,占53.85%(21/39)。eBURST分析显示:39株菌株分为2个 Clonal complexes和1个singleton,其中Group1占66.67%(26/39),Group2占20.51%(8/39),一个singleton占12.82%(5/39);BioNumerics软件聚类分析显示:39株菌株分为3个Group,与eBURST分析中的分群结构一致。MLST基因型别具有明显的地域性特征。结论 MLST方法可初步应用于致病性钩端螺旋体分子流行病学、种群结构、亲缘进化关系等研究。     

The dominant methicillin‐resistant Staphylococcus aureus clone from hospitals in Cape Town has an unusual genotype: ST612

There is currently limited information available on the molecular epidemiology of methicillin‐resistant Staphylococcus aureus (MRSA) in South Africa. A molecular characterization of 100 MRSA from five hospitals in Cape Town was carried out in this study. The strains were separated into six clusters by pulsed‐field gel electrophoresis, indicating transmission of MRSA between local hospitals. None of the strains carried the Panton‐Valentine Leukocidin gene. SCCmec typing, multilocus sequence typing and spa typing were used to further characterize the MRSA. Three clones corresponded to frequently described pandemic clones: ST239‐MRSA‐III, ST36‐MRSA‐II and ST5‐MRSA‐I. ST239‐MRSA‐III and ST36‐MRSA‐II were minor clones and collectively accounted for 16% of the isolates. ST5‐MRSA‐I was the second‐most prevalent clone and accounted for 37% of the isolates. The dominant local clone was the infrequently described ST612‐MRSA‐IV (44% of isolates), which has only been described in South Africa and Australia.     

Analysis of multilocus sequence typing schemes for 35 different bacteria revealed that gene loci of 10 bacteria could be replaced to improve cost-effectiveness

Although multilocus sequence typing (MLST) has been widely used for bacterial typing, the contribution of the gene loci to the discriminatory power of each MLST scheme is unknown. We analyzed the discriminatory powers of 36 MLST schemes using all combinations of the 7 loci and contributions of each locus to the schemes. In 10 schemes, sequencing 6 loci can achieve the discriminatory powers of 7 loci. For the other 26 schemes, the median marginal increase in discriminatory power when 7 instead of 6 loci were used is 0.0004. Sequencing the 7 loci of 50 strains each of Pseudomonas aeruginosa and Acinetobacter baumannii revealed that the discriminatory power for P. aeruginosa was 0.9861 when either 6 (without trp) or 7 loci were used and that for A. baumannii was 0.9363 when 5, 6, or 7 loci were used. Genes that have no additional or minimal contribution to the overall discriminatory powers should be replaced.     

Comparison of genotypes of Streptococcus pneumoniae serotypes 6A and 6B before and after the introduction of PCV7 vaccination in Korea

We investigated changes of serotypes in Streptococcus pneumoniae and the characteristics of serotypes 6A and 6B in Korean hospitals after the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7). PCV7 serotypes decreased significantly from 66.8% in 1996-2001 to 41.3% in 2008-2009 (P<0.001). However, serotype 6B did not decrease during these 2 periods (5.7% to 6.4%). Non-PCV7 serotypes that increased significantly were 3 (3.6% to 9.1%), 6A (3.1% to 8.5%), 13/28 (0 to 3.7%), 15 (2.2% to 6.7%), 16.36.37 (0 to 1.2%), 19A (1.2% to 9.7%), and 23A (0 to 1.5%). Multilocus sequence typing indicated that 9 STs were identified among 36 isolates of serotype 6A and 19 among 35 isolates of serotype 6B. No STs were found both in the 2 serotypes. The increase in serotype 6A was associated mainly with ST81, a Spain-23F clone genotype. The association of serotype 6A and ST81 is unique to Korea. Clones of serotype 6B isolates changed between the 2 periods. ST282, the main clone of serotype 6B in the PCV7 period, was found only in Korea. Our study demonstrates changing characteristics of pneumococcal serotypes 6A and 6B isolates in Korea and suggests selective evolution of certain clones in the era of PCV7 vaccination.     

Species distribution of Burkholderia cepacia complex isolates in cystic fibrosis and non-cystic fibrosis patients in New Zealand

Burkholderia cepacia complex (Bcc) isolates from 39 CF patients and 25 non-CF patients in New Zealand were speciated and characterised using the multilocus sequence typing (MLST) scheme for Bcc. B. multivorans predominated in CF patients (31/39, 79.5%) and in non-CF patients (7/25, 28%). Sequence types (ST) with an international distribution were identified (27/64, 42.2%) among the New Zealand Bcc isolates. MLST revealed a high level of diversity among Bcc isolates in CF patients indicating a lack of person-to-person transmission. Non-CF patients showed less diversity in MLST types, however, individuals with shared STs were geographically and chronologically separated. The use of MLST analysis allows continued surveillance of isolates with the potential to identify outbreaks. The identification of internationally distributed strains may provide an indicator of the relative transmissibility and infectivity of these strains and warrants further investigation.     

Enterotoxigenic Escherichia coli Multilocus Sequence Types in Guatemala and Mexico

The genetic backgrounds of 24 enterotoxigenic Escherichia coli (ETEC) strains from Mexico and Guatemala expressing heat-stable toxin (ST) and coli surface antigen 6 (CS6) were analyzed. US travelers to these countries and resident children in Guatemala were infected by ETEC strains of sequence type 398, expressing STp and carrying genetically identical CS6 sequences.