Occurrence,integrity and functionality of AcaML1–like viruses infecting extreme acidophiles of the Acidithiobacillus species complex

General knowledge on the diversity and biology of microbial viruses infecting bacterial hosts from extreme acidic environments lags behind most other econiches. In this study, we analyse the AcaML1 virus occurrence in the taxon, its genetic composition and infective behaviour under standard acidic and SOS-inducing conditions to assess its integrity and functionality. Occurrence analysis in sequenced acidithiobacilli showed that AcaML1-like proviruses are confined to the mesothermophiles Acidithiobacillus caldus and Thermithiobacillus tepidarius. Among A. caldus strains and isolates this provirus had a modest prevalence (30%). Comparative genomic analysis revealed a significant conservation with the T. tepidarius AcaML1-like provirus, excepting the tail genes, and a high conservation of the virus across strains of the A. caldus species. Such conservation extends from the modules architecture to the gene level, suggesting that organization and composition of these viruses are preserved for functional reasons. Accordingly, the AcaML1 proviruses were demonstrated to excise from their host genomes under DNA-damaging conditions triggering the SOS-response and to produce DNA-containing VLPs. Despite this fact, under the conditions evaluated (acidic) the VLPs obtained from A. caldus ATCC 51756 could not produce productive infections of a candidate sensitive strain (#6) nor trigger it lysis.     

脉冲场凝胶电泳技术应用于沙门菌鉴定的方法研究

目的利用脉冲场凝胶电泳(PFGE)技术和设备解决沙门菌鉴定困难的难题,探究简便、快速、准确的鉴定方法,确立积极有效检测鉴定手段和监控措施,防止食物中毒及传染病的暴发流行。方法根据测试菌不同,探讨PFGE技术实验条件,沙门菌的PFGE鉴定方法。结果经反复试验证实所建方法灵敏快速、准确可靠、分辨率高,实用性强。在没有图像分析仪的情况下,肉眼即可进行判断,可替代传统的血清学鉴定方法。结论脉冲场凝胶电泳基因分型及同源性鉴定方法分辨率高,应用性强,技术先进。     

耐碳青霉烯类肺炎克雷伯菌分子流行病学研究

目的分析武汉两所医院耐碳青霉烯类肺炎克雷伯菌(CRKP)临床分离株产碳青霉烯酶的情况,以及分子流行病学特征。方法收集武汉两所医院2018年1—10月临床分离的42株非重复CRKP,采用Carba NP试验方法对菌株产碳青霉烯酶情况进行初筛,聚合酶链反应(PCR)检测碳青霉烯酶基因携带情况,采用质粒接合试验分析耐药基因的水平转移情况,应用脉冲场凝胶电泳(PFGE)进行亲缘关系分析。结果 42株CRKP菌株中14株Carba NP试验阳性,其中有10株扩增出NDM-1基因,3株扩增出KPC-2基因。共13株CRKP碳青霉烯基因检测阳性,其中12株质粒接合试验成功。PFGE分析结果显示,携带NDM-1基因的CRKP菌株共分成6型,无明显优势型;携带KPC-2基因的CRKP菌株为同一型别。结论检出产NDM-1和KPC-2的CRKP菌株,质粒接合试验提示质粒介导的水平传播在碳青霉烯酶基因的播散过程中可能起重要作用。     

副溶血性弧菌病原学和分子流行病学流行特征研究进展

副溶血性弧菌是导致我国细菌性食物中毒事件的首要原因.临床分离株和环境分离株的病原学特征有着明显的差异.临床分离株以O3:K6血清型为主,tdh和(或)trh基因携带率较高,一般在80%以上,脉冲场凝胶电泳(PFGE)基因图谱具有明显的优势图谱,并且与血清分型具有一致性.而环境分离株(包括食品)多无优势血清型和优势PFGE图谱,tdh和(或)trh基因携带率远低于临床分离株,多在6%以下.各地临床分离株的耐药性差异较大,但对氨苄西林等早期药物耐药率均较高.环境分离株较临床分离株的耐药性更为严重和复杂.     

Vaccine-driven serotype-rearrangement is seen with latency in clinical isolates: Comparison of carried and clinical pneumococcal isolates from the same time period in Hungary

Young children – the main asymptomatic carriers of pneumococcus – are often the source of pneumococcal infections. PCV13 replaced PCV7 in 2010 in Hungary and it became a mandatory vaccine in 2014. In this work we surveyed the effect of vaccination in three groups: in healthy children under 7?years; in children of the same age but infected with pneumococcus (P1); in older patients (P2) who were very likely not vaccinated.Nasal swabs were taken from 522 healthy children to screen pneumococcal carriage between March 2015 and May 2016. In the same time period, 146 clinical isolates were collected, mainly from mucosal infections. Serotypes, antibiotic susceptibility and clonality of the isolates was determined and compared.The carriage rate was 39.1%. Regarding carriage, the serotype distribution showed the total disappearance of serotypes 3 and 6A compared to former Hungarian studies. The prevalence of PCV13 serotypes was only 5.8% represented by three serotypes (19F, 19A, 9V). Of note, serotype 19A (a very resistant and invasive type) also decreased significantly. In the patient groups, PCV13 prevalence was higher: 17.5% (P1) and 32.6% (P2). Although serotype 3 was present in P1 (7.9%), the leading serotype was 23B (22.2%), a non-vaccine type (NVT). P2 showed the most diverse serotype distribution, but serotype 3 was predominant here (15.7%). Pneumococcal isolates from the patients were more resistant towards the tested antibiotics compared to those from carriers.PCV13 seems to be highly successful in reducing the prevalence of vaccine serotypes. The serotype-rearrangement can be seen also among clinical isolates, albeit somewhat later in time. Fortunately, the replacing serotypes are less invasive and less resistant, but, most worrisome, serotype 19F can be found again with increased frequency among carriage isolates and mucosal infections. Further surveillance is needed to carefully monitor such successful, antibiotic resistant “refugees”.     

Whole genome mapping of the first reported case of KPC-2–positive Klebsiella pneumoniae ST258 in Nebraska

Three ertapenem-resistant Klebsiella pneumoniae carrying bla_KPC-2 were isolated from a single patient in Nebraska over a span of 5 months. A comparative analysis of the genetic relatedness of these isolates was investigated using pulsed-field gel electrophoresis, multilocus sequence typing, and whole genome mapping.     

Clonal dissemination of a single Shigella sonnei strain among Iranian children during Fall 2012 in Tehran,I.R. Iran

Shigella species are a common cause of bacterial diarrhea worldwide and the disease is characterized by seasonality. Shigella has been encountered by widespread resistance to commonly used antibiotics which is a serious concern. The aim of this study was to analyze the epidemiological relatedness of Shigella strains isolated from children during one year period by PFGE method and to investigate antimicrobial resistance determinants and cassettes among Shigella species. The occurrence of Shigella spp. in the present study was 1.32% during the study period and the majority of cases (56 (80%)) were occurred during autumn while Shigella sonnei was the most prevalent species identified. Multi-drug resistance phenotype was seen in 98.5% of total isolates with SXT^r/TE^r/TMP^r resistance pattern. Among the 70 Shigella spp. analyzed in this study, 16 isolates were positive for class I integron (int1⁺) with two types of gene cassette arrays (dfrA17/aadA5 and dfrA7).The class 2 integron was more frequently detected among the isolates (85.71%) with dfrA1/sat1/aadA1 (10%) and dfrA1/sat1 (75.71%) gene cassettes. The tetA and tetB determinants were observed in 75.7% and 21.42% of Shigella isolates and tet(A) was the foremost in S. sonnei and Shigella flexneri population. In this study 5 tetracycline resistant isolates had no tetracycline resistance gene (A–D) and no association was recognized between the value of MIC against tetracycline and the tet genes content of isolates. Fifty three of total Shigella isolates (75.7%) showed an identical PFGE patterns. Seven PFGE clusters observed in our study were composed of members with one to three band variations, which is indicative of closely related isolates. The major cluster (cluster C) constituted 75.7% of total isolates, all of which (except eight isolates) consonantly showed identical class 2 integron of 1500 bp which strongly suggests the dissemination of a single S. sonnei clone among the pediatric population in 2012 autumn in Tehran, Iran, in comparison with the equal data from the comparable time period from recent years.     

福建省非典型肠致病性大肠埃希菌的分子特征研究

摘要：目的　研究福建省非典型肠致病性大肠埃希菌（ａＥＰＥＣ）菌株的毒力基因特征和菌株间的遗传相似
度;结合菌株的背景资料分析不同的分子特征对ａＥＰＥＣ 流行的影响。方法　运用ＰＣＲ 技术进行系列的相
关毒力基因扩增;同时运用脉冲场凝胶电泳分子分型技术,对福建省２０１０－２０１２年分离的ａＥＰＥＣ 菌株进
行脉冲场凝胶电泳（ＰＦＧＥ）分子分型。结果　分离３０株实验菌株毒力基因的检测呈阳性的分别为：犫１１２１
５３．３％ （１６）,狔犻犪犃３６．７％ （１１）,狊犲狋／犲狀狋、狀犾犲犅、狀犾犲犈均为３０％ （９）,犾狆犳犃犚１４１２３．３％ （７）,犲犳犪／犾犻犳犃
２０％ （６）,犲犺狓犃３．３３％ （１）;其余毒力基因均未检出;９３．３％ （２８）菌株不同程度地携带有相关的毒力因
子。２９株菌按照１００％的相似度分为１５个ＰＦＧＥ 型别（Ｐ１ Ｐ１５）;其中存在４组不同的ＰＦＧＥ 簇（Ｉ Ⅳ）,
相同ＰＦＧＥ 簇的病例在发病的时间和地区上有聚集性,同时相同簇内菌株的毒力基因谱也表现相同。结论
　犫１１２１、狔犻犪犃和ＥＨＥＣ 毒力岛ＯＩ １２２ 相关基因（犲犳犪１／犾犻犳犃,狀犾犲犅,狀犾犲犈,狊犲狋／犲狀狋） 在福建省ａＥＰＥＣ 菌
株中携带率较高。非典型肠致病性大肠埃希菌的毒力谱表现为多样性, 基因组也呈现遗传多态性;同时
ＰＦＧＥ 分析发现福建省存在由ａＥＰＥＣ 新发病原菌引起的聚集性病例。
关键词：非典型肠致病性大肠埃希菌;毒力基因;ＰＦＧＥ
中图分类号：Ｒ３７８　　文献标识码：Ａ　　文章编号：１００９ ６６３９ （２０１４）０３ ０２１６ ０５
犕狅犾犲犮狌犾犪狉犮犺犪狉犪犮狋犲狉犻狊狋犻犮狊狅犳犪狋狔狆犻犮犪犾犲狀狋犲狉狅狆犪狋犺狅犵犲狀犻犮     

Penicillin-resistant,ampicillin-susceptible Enterococcus faecalis of hospital origin: pbp4 gene polymorphism and genetic diversity

Despite the spread of penicillin-resistant, ampicillin-susceptible Enterococcus faecalis (PRASEF) isolates in diverse countries, the mechanisms leading to this unusual resistance phenotype have not yet been investigated. The aim of this study was to evaluate whether polymorphism in the pbp4 gene is associated with penicillin resistance in PRASEF isolates and to determine their genetic diversity. E. faecalis isolates were recovered from different clinical specimens of hospitalized patients from February 2006 to June 2010. The β-lactam minimal inhibitory concentrations (MICs) were determined by E-test®. The PCR-amplified pbp4 gene was sequenced with an automated sequencer. The genetic diversities of the isolates were established by PFGE (pulsed-field gel electrophoresis) and MLST (multilocus sequencing typing). Seventeen non-producing β-lactamase PRASEF and 10 penicillin-susceptible, ampicillin-susceptible E. faecalis (PSASEF) strains were analyzed. A single-amino-acid substitution (Asp-573 → Glu) in the penicillin-binding domain was significantly found in all PRASEF isolates by sequencing of the pbp4 gene but not in the penicillin-susceptible isolates. In contrast to the PSASEF isolates, a majority of the PRASEFs had similar PFGE profiles. Six representative PRASEF isolates were resolved by MLST into ST9 and ST524 and belong to the globally dispersed clonal complex 9 (CC9). In conclusion, it appears quite likely that the amino acid alteration (Asp-573 → Glu) found in the PBP4 of the Brazilian PRASEF isolates may account for their reduced susceptibility to penicillin, although other resistance mechanisms remain to be investigated.     

Prevalence,identification by a DNA microarray-based assay of human and food isolates Listeria spp. from Tunisia

Objectives

We aimed at evaluating the prevalence of Listeria species isolated from food samples and characterizing food and human cases isolates.

Material and methods

Between 2005 and 2007, one hundred food samples collected in the markets of Tunis were analysed in our study. Five strains of Listeria monocytogenes responsible for human listeriosis isolated in hospital of Tunis were included. Multiplex PCR serogrouping and pulsed field gel electrophoresis (PFGE) applying the enzyme AscI and ApaI were used for the characterization of isolates of L. monocytogenes. We have developed a rapid microarray-based assay to a reliable discrimination of species within the Listeria genus.

Results

The prevalence of Listeria spp. in food samples was estimated at 14% by using classical biochemical identification. Two samples were assigned to L. monocytogenes and 12 to L. innocua. DNA microarray allowed unambiguous identification of Listeria species. Our results obtained by microarray-based assay were in accordance with the biochemical identification. The two food L. monocytogenes isolates were assigned to the PCR serogroup IIa (serovar 1/2a). Whereas human L. monocytogenes isolates were of PCR serogroup IVb, (serovars 4b). These isolates present a high similarity in PFGE. Food L. monocytogenes isolates were classified into two different pulsotypes. These pulsotypes were different from that of the five strains responsible for the human cases.

Conclusion

We confirmed the presence of Listeria spp. in variety of food samples in Tunis. Increased food and clinical surveillance must be taken into consideration in Tunisia to identify putative infections sources.