医院获得性鲍曼不动杆菌肺炎六例微生物学及临床观察

目的探讨医院获得性鲍曼不动杆菌肺炎患者临床微生物学特点和治疗转归。方法回顾性调查2005年1～8月白求恩国际和平医院经分子生物学方法证实的6例医院获得性产PER-1型超广谱13内酰胺酶（ESBL）鲍曼不动杆菌肺炎患者的临床资料。用脉冲场凝胶电泳检测6株鲍曼不动杆菌的同源性，聚合酶链反应分析相关耐药基因。结果6株鲍曼不动杆菌中5株仅对亚胺培南敏感，4株对美罗培南敏感。脉冲场凝胶电泳将其分为A1型2株，A2～如型各1株，携有β内酰胺酶blaPER-1基因，同时blaTEM-1型基因、耐消毒剂磺胺药物基因（qacEΔ1-sull）和1类整合子酶基因（intll）阳性，其中3株氨基糖苷类修饰酶基因aac（3）-I、aac（6’）-I同时阳性，2株aac（3）-I、ant（3”）-I同时阳性，1株aac（3）-I单独阳性。6例患者均患有严重的基础疾病，使用过呼吸机；检出鲍曼不动杆菌前15d内应用过广谱抗菌药物；经使用碳青霉烯类和（或）头孢哌酮／舒巴坦抗感染治疗，3例临床好转，3例死亡。结论6株产PER-1型ESBL鲍曼不动杆菌具有高度同源性，耐药基因复杂，其所引起的医院获得性肺炎临床预后差。     

Widespread presence of dfrA12 and its association with dfrA12-aadA2 cassette in Salmonella enterica isolates from swine

One hundred and eighty-nine Salmonella isolates from swine were tested for susceptibility to nine antimicrobial agents, presence of dfrA12 and class 1 integrons containing dfrA12-orfF-aadA2 cassette. All isolates were multidrug resistant and exhibited highest resistance prevalence to trimethoprim (93%). Most isolates (89%) were intll-positive and 107 isolates (57%) carried dfrA12, all of which were resistant to trimethoprim. Forty-eight dfrA12-harboring strains (45%) were intl1-positive together with dfrA12-aadA2 gene cassette. Fifteen isolates contained dfrA12 but not intl1 and dfrA12-aadA2 cassette. The results indicated a wide distribution of dfrA12 and its role in dissemination of trimethoprim resistance among Salmonella isolates from fattening pigs.     

Prevalence of extended-spectrum beta-lactamase and class 1 integron integrase gene intl1 in Escherichia coli from Thai patients and healthy adults

Among 120 Escherichia coli isolates from Thai patients, 37 and 9 isolates were extended-spectrum beta-lactamase (ESBL) and suspected ESBL producers respectively while 5 E. coli isolates from 120 Thai healthy adults were suspected ESBL producers. Integrase (intl1) gene was detected in 99% of the clinical and 87% of the non-clinical isolates. Among 37 ESBL producers, percent recovery of bla(TEM), bla(CTX-M), bla(SHV) and bla(VEB) was 78%, 78%, 8% and 8%, respectively. Twenty-five isolates of ESBL producers carried both bla(TEM) and bla(CTX-M), 2 isolates carried 3 genes (bla(TEM), blac(CTX-M), and bla(SHV)) and 3 showed no detectable bla gene. Among the 14 suspected ESBL producers, intl1 and bla(TEM) were detected in 13 isolates. ESBL producers from clinical samples were resistant to most of the tested antimicrobial agents compared to non-ESBL producers and isolates from healthy adults with about half of the latter susceptible to all tested antimicrobial agents. Only one clinical isolate was resistant to imipenem. Susceptibility to trimethoprim/sulfamethoxazole among the clinical isolates in ESBL producer group (27%) and non-producer group (33%) were comparable, whereas the percent susceptibility of the non-clinical isolates was about twice that of the clinical isolates.     

铜绿假单胞菌耐药基因分析及多位点序列遗传分型

目的 了解2011-2012年深圳市南山区医院病人,各医院、诊所内环境台面涂抹样、医护人员手涂抹样分离的铜绿假单胞菌,抗生素耐药基因分布及基因的遗传多样性。方法 采用聚合酶链反应技术检测铜绿假单胞菌的20种耐药基因:TEM、VEB、CARB、OXA、SHV、PER、GES、GTX、SPM、GIM、IMP、VIM、DHA、oprD、Aac(6')-Ⅰ、Aac(6')-Ⅱ、Aac(3')-Ⅰ、Aac(2″)-Ⅰ、qacE1-sull及Ⅰ类整合子基因。采用多位点序列分子分型方法 进行聚类和克隆分析。结果 检出11种耐药基因:TEM、SHV、IMP、DHA、Aac(6’)-Ⅰ、Aac(6')-Ⅱ、Aac(3')-Ⅰ、Aac(2″)-Ⅰ、qacE1-sull、Ⅰ类整合子及oprD基因,检出率分别为8.1%、6.4%、4.8%、9.7%、4.8%、14.5%、4.8%、56.5%,8.1%,8.1%,oprD基因缺失率为61.2%。52株铜绿假单胞菌检出耐药基因,形成19种耐药基因谱。多位点序列分型方法 将62株铜绿假单胞菌,分为39个ST型,5个克隆群,1个优势克隆群CC244,1个优势独特型ST856。结论 不同类型样本分离菌株携带耐药基因存在差异,部分病人分离株携带多种耐药基因。本研究铜绿假单胞菌具有遗传多样性,存在优势克隆群。     

Class 1 integrons and multidrug resistance among Escherichia coli isolates from human stools

Three hundred and eighteen Escherichia coli isolates from stools of healthy volunteers and outpatients from a major university hospital in southern Thailand were tested for the presence of class 1 integrons using multiplex-PCR and for their susceptibility against 12 antimicrobial agents using standard disc diffusion method. Based on the presence of intl1, 162 isolates harbored class 1 integrons, which were more prevalent in isolates from outpatients compared with those from healthy volunteers. The majority (85%) of the isolates were resistant to at least one antimicrobial agent with the following percent resistance: streptomycin 66%, tetracycline 60%, sulphamethoxazole 59%, ampicillin 52%, trimethoprim/sulphamethoxazole 47%, kanamycin 30%, nalidixic acid 27%, ciprofloxacin 23%, norfloxacin 22%, amoxicillin/ clavulanic acid 16%, gentamicin 8%, and amikacin 2%. The most frequent pattern of multiresistant strains (11%) was sulphamethoxazole- trimethoprim/sulphamethoxazole -ampicillin-tetracycline-streptomycin. Multiple drug resistance was more frequent in integron-positive isolates (89%) than those in integron-negative E. coli (57%). These data indicate that human fecal E. coli is a reservoir of antibiotic-resistant genes that poses a significant risk of the spread of microbial resistance in the community.     

Characterization of class 1 integrons with unusual 3' conserved region from Salmonella enterica isolates

The unusual 3' conserved sequence region of class 1 integrons was characterized in seven Salmonella isolates from swine and poultry. Three types of gene cassette arrays, aadA2-cmlA1-aadA1, sat-psp-aadA2-cm1A1-aadA1 and drfA12-orf-aadA2-cmlA1-aadA1, were found to be linked to a genetic organization qacH-IS440-sul3. All class 1 integrons were located on a conjugative plasmid that could be transferred to Escherichia coli. The results support the notion that the use of an antibiotic can select for resistance not only to that specific agent, but also to other unrelated antimicrobials including those that are no longer approved for use in food animal production.     

Conservation of the cag pathogenicity island is associated with vacA alleles and gastroduodenal disease in South African Helicobacter pylori isolates

BACKGROUND: The development of clinically significant disease in South Africa is associated with the vacuolating cytotoxin gene (vacA) s1 genotype but not with the presence of the cytotoxin associated gene cagA. cagA occurs in >95% of South African isolates and is a variable marker for the entire cag pathogenicity island (PAI). AIM: To characterise the cagPAI in South African isolates and to investigate if structural variants of this multigene locus were associated with variations in vacA status and clinical outcome. PATIENTS AND METHODS: We studied 109 Helicobacter pylori strains (36 from patients with peptic ulceration, 26 with gastric adenocarcinoma, and 47 with no pathology other than gastritis) for differences in selected genes of the cagPAI and alleles of vacA by polymerase chain reaction. RESULTS: All strains were cagA(+). Sixty five (60%) strains had an intact contiguous cagPAI; 78% of peptic ulcer isolates, 73% of gastric adenocarcinoma isolates, but only 40% of gastritis alone isolates (p< 0.01). The entire cagII region was undetectable in 23% of gastritis alone isolates but in only 8% of peptic ulceration isolates (p<0.05). The vacA signal sequence and mid region demonstrated a strong relationship between the virulence associated vacA s1 (p<0.005) and vacA m1 (p=0.05) alleles and an intact cagPAI. CONCLUSION: Although a complete cagPAI was a feature of most infected individuals, deletions in the 5' region of this genetic locus were associated with gastritis alone and with the non-cytotoxic s2/m2 vacA genotype.     

Epidemiological analysis of methicillin resistant Staphylococcus aureus in Thailand

The geographical distribution of 65 clinical isolates of methicillin resistant Staphylococcus aureus (MRSA) recovered from 7 hospitals in Thailand was investigated. The presence of mecA gene in MRSA was determined by specific PCR with the use of primers 5'-GTAGTTGTCGGGTTTGGT-3' and 5'-GGTATCATCTTGTACCCA-3'. Chromosomal DNA restriction analysis with SmaI was resolved by pulsed-field gel electrophoresis (PFGE) compared with antibiotype analysis and phage type analysis. All 65 strains carried mecA gene. They all were resistant to penicillin, tetracycline, erythromycin, amoxicillin/clavulanic acid and variably resistant to gentamicin, ofloxacin, trimethoprim-sulfamethoxazole, chloramphenicol, fosfomycin and clindamycin; and all isolates were susceptible to vancomycin. A total of 19 PFGE patterns designated as type A, A1, A2, A3, A4, B, B1, C, D, E, E1, E2, F, F1, F2, G, H, I and J was identified. Type A4 and E were commonly found in every studied areas. Phage typing showed even greater variability that 52 (80%) isolates belonged to 25 different phage types; 13 (20%) isolates were non-typable. The clarity and polymorphism of the PFGE patterns enable us to discriminate between isolates which could not be differentiated by antibiogram or phage type analysis. The findings demonstrate the existence of a common epidemic MRSA clone in Thailand.     

Genetic characterization of the nef gene from human immunodeficiency virus type 1 group M strains representing genetic subtypes A, B, C, E, F, G, and H

Most efforts to characterize sequence variation of HIV isolates has been directed toward the structural envelope gene. Few studies have evaluated the sequence variability of auxiliary genes such as nef. In this study 41 new HIV-1 strains, representing the majority of the described envelope subtypes of HIV-1 (A to H), were genetically characterized in the nef region. Phylogenetic analysis showed that 34 strains could be classified in the same subtype in nef and env, and 7 (19%) of the 41 new viruses were recombinants. For two of the seven strains, recombination occurred upstream of the nef gene, whereas for five of the seven strains recombination occurred within the nef gene with a crossover close to the 5' end of the LTR (long terminal repeat). The low intersubtype distance between subtype B and D in the nef gene confirms previous observations in the pol, env, and gag genes, which suggest a common ancestor for these subtypes. The majority of all the previously described functional domains in the nef gene were relatively conserved among the different subtypes, with only minor differences being observed. The myristoylation signal among the different subtypes, with only minor differences being observed. The myristoylation signal was less conserved for subtype C, with one or more amino acid changes being observed at positions 3, 4, and 5. The highly conserved acidic region (positions 62 to 65), critical for the enhancement of viral synthesis with an increased virus growth rate, was less conserved among the subtype G strains from our study. At least three epitopic regions of the nef gene have been defined and each can be recognized by CTLs under a variety of HLA restrictions; all were also relatively well conserved between the different genetic subtypes. Despite the relatively important genetic variation in nef sequences obtained among the different genetic subtypes, functional domains and CTL epitopes were relatively well conserved. In vitro and/or in vivo studies are necessary to study the relevance of the observed differences.     

多药耐药大肠埃希菌老年患者分离株抗菌制剂11种外排泵基因研究

目的了解多药耐药大肠埃希菌中外排泵基因的存在情况。方法微量稀释法检测耐药菌株的药敏结果,采用聚合酶链反应（PCR）扩增法,检测11种抗菌制剂外排泵基因：emrB、emrD、emrE、mdfA、sugE、mdtI、tehA、oqxA、qacE△1、qacEs、mr-2等11种抗菌制剂外排泵基因,扩增产物纯化后基因测序。结果大肠埃希菌对阿米卡星耐药率为60%,对复方新诺明耐药率为95%,对第三代头孢菌素耐药率为100%（均为产ESBLs菌株）,外排泵基因检出率分别为emrB 95.0%、emrD 75.0%e、mrE 50.0%、mdfA 80.0%、sugE 70.0%、mdtI 80.0%、qacE△1 80.0%、tehA 80.0%、oqxA 15.0%,qacE、smr-2基因均未检测到,最少者检出1种基因,最多1株检出9种基因。结论本组分离的大肠埃希菌对β-内酰胺类、氨基糖苷类、喹诺酮类、磺胺类、氯霉素等抗菌药物呈多重耐药,可能与细菌携带多种抗菌制剂（包括灭菌剂、消毒剂、抗菌药物等）外排泵基因相关。     

Identifying and elucidating the resistance of Staphylococcus aureus isolated from hospital environment to conventional disinfectants

BackgroundStaphylococcus aureus is a nosocomial pathogen, detection and elucidation of its resistance mechanisms to conventional disinfectants may aid in limiting its spread on environmental surfaces in health care settings. In the current study, disinfectant susceptibility of S. aureus strains isolated from the hospital environment as well as possible associations between the presence of disinfectant-resistance genes and reduced susceptibility to disinfectants was investigated.MethodsA total of 245 samples were collected from the hospital environmental surfaces. The minimum inhibitory (MIC) and bactericidal concentrations (MBC) of disinfectants against S. aureus isolates were determined using the micro-broth dilution method. The qac genes (qacA, qacE, and qacΔE1) were detected by PCR and confirmed by sanger sequencing.ResultsA total of 47 S. aureus strains were isolated, with more than 85% of them showing methicillin resistance. The qacA, qacE, and qac?E1 genes were found in 23.4%, 29.7%, and 4.2% isolates respectively. All the isolates with qac genes had higher MIC and MBC values to selected disinfectants.ConclusionsSignificant methicillin resistant S. aureus (MRSA) contamination in the hospital environment was detected. Furthermore, higher qac gene frequencies were found in MRSA isolates that also correlated with higher MIC/MBC values to different disinfectants. The study proposes that hospitals should develop policies to determine disinfectant MICs against the common environmental isolates to contain the spread of resistant strains.     

Surprisingly little polymorphism in the merozoite-surface-protein-2 (MSP-2) gene of Indian Plasmodium falciparum

The polymorphism in the merozoite-surface-protein-2 (MSP-2) gene of six Indian Plasmodium falciparum isolates was studied by PCR amplification, cloning and sequencing. One of the isolates showed a deletion of 63 bp and all showed point mutations, although some of these mutations were silent. All the isolates also exhibited 5' and 3' conserved regions, with the two 32-mer amino-acid repeats characteristic of the FC27 family, and none belonged to the IC-1/3D7 family. Although the MSP-2 genes of these isolates represent new allelic sequences, they belong to the FC27 family and show remarkably little variation.     

临床痢疾志贺菌整合子检测及耐药基因盒序列分析

目的 检测印度东部1988、1995和2002年部分临床分离痢疾志贺菌中细菌耐药关系密切的1、2、3类整合酶基因及整合子携带的耐药基因盒的分布,分析整合子系统对志贺菌耐药的影响.方法 纸片扩散法检测实验菌株对药物的敏感性;应用PCR方法对16株临床耐药菌株进行1、2、3类整合酶基因(intI)筛选,对阳性样本可变区基因盒序列进行鉴定分析.结果 所有16株菌均耐4种及4种以上药物,包括β-内酰胺类、氨基糖苷类、四环素类、磺胺类、氯霉素类和喹诺酮类.13株菌检出1类整合酶基因,全部菌株含2类整合酶基因,即发现同时存在两种整合子结构菌株,未检测到3类整合酶基因.1类整合酶插入基因盒以blaara30-aadAl基因家族为主,分别对β-内酰胺类抗生素、链霉素、壮观霉素耐药;2类整合酶插人基因盒以dfrAl-satl组合为主,分别对甲氧苄氨嘧啶、链丝菌素耐药,同时在4株菌中发现dfrAl-satl-aadAl基因盒组合.结论 2类整合子普遍存在于临床志贺菌中.整合子与志贺菌的多重耐药具有密切相关性.     

幽门螺杆菌中国株cagA全长基因克隆及其分子特征分析

目的克隆幽门螺杆菌中国株MEL-Hp 27cagA全长基因,并进行分子特征分析。方法参考Hp26695基因组序列,分别针对cagA基因编码区保守序列和位于cagA基因上、下游的基因序列设计两对PCR引物,交叉分段扩增包括cagA基因编码区、5′、3′非编码区在内的全长基因序列,并对cagA基因调控序列、编码序列及源自中国的CagA分子EPIYA基序分布特点进行分析。结果Hp27cagA基因编码区长3510bp,编码1169个氨基酸。5′端非编码区长649bp,-10区、-35区分别位于起始密码子ATG上游89bp和154bp处,3′端非编码区长476bp。Hp27cagA基因编码区核苷酸序列与东亚菌株同源性为96%,与西方菌株的同源性仅为86%左右。Hp27CagA分子存在典型的EPIYA基序,属于ABD型,与国际参考株NCTC11637的AB-CCC型不同。比较源自中国的HpCagA序列的EPIYA基序分布特点,未发现中国Hp分离株之间存在CagAEPIYA基序与疾病结局(胃癌、慢性胃炎和十二指肠溃疡)的聚类关系。结论成功克隆幽门螺杆菌全长ca-gA基因;cagA基因编码区及非编码区序列存在东西方差异;未发现中国Hp分离株之间存在CagA EPIYA基序与疾病结局的聚类关系。     

呼吸重症监护病房多重耐药鲍曼不动杆菌耐药基因研究

目的 观察我院呼吸重症监护病房(RICU)临床分离多重耐药鲍曼不动杆菌β-内酰胺酶基因和消毒剂耐药基因qacE△1-sul1存在状况.方法 收集RICU分离多重耐药鲍曼不动杆菌16株,采用PCR方法检测8种β-内酰胺酶基因(TEM、SHV、PER、DHA、IMP、VIM、OXA-23、OXA-24)和消毒剂耐药基因(qacE△1-sul1)共9种基因.采用多基因聚类分析方法进行多重耐药菌株亲缘性分析.结果 16株多重耐药鲍曼不动杆菌中blaOXA-23阳性5株(31.25%),blaTEM阳性2株(12.50%),blaDHA 2株(12.50%),blaOXA-24 1株(6.25%),blaPER 1株(6.25%).blaSHV、blaIMP、blaVIM均未检出,消毒剂耐药基因检测qacE△1-sull阳性16株(100.00%).多基因聚类分析发现存在克隆传播现象.结论 我院RICU多重耐药鲍曼不动杆菌携带多种β-内酰胺酶基因,消毒剂耐药基因携带率高,聚类分析显示存在克隆传播现象,应引起临床重视.     

Sequence analysis of the 5'' noncoding region of hepatitis C virus.

We have determined the nucleotide sequence of the 5' noncoding (NC) region of the hepatitis C virus (HCV) genome in 44 isolates from around the world. We have identified several HCV isolates with significantly greater sequence heterogeneity than reported previously within the 5' NC region. The most distantly related isolates were only 90.1% identical. Nucleotide insertions were seen in three isolates. Analysis of the nucleotide sequence from 44 HCV isolates in this study combined with that of 37 isolates reported in the literature reveals that the 5' NC region of HCV consists of highly conserved domains interspersed with variable domains. The consensus sequence was identical to the prototype HCV sequence. Nucleotide variations were found in 45 (16%) of the 282 nucleotide positions analyzed and were primarily located in three domains of significant heterogeneity (positions -239 to -222, -167 to -118, and -100 to -72). Conversely, there were three highly conserved domains consisting of 18, 22, and 63 completely invariant nucleotides (positions -263 to -246, -199 to -178, and -65 to -3, respectively). Two nucleotide domains within the 5' NC region, conserved among all HCV isolates studied to date, shared statistically significant similarity with pestivirus 5' NC sequences, providing further evidence for a close evolutionary relationship between these two groups of viruses. Additional analysis revealed the presence of short open reading frames in all HCV isolates. Our sequence analysis of the 5' NC region of the HCV genome provides additional information about conserved elements within this region and suggests a possible functional role for the region in viral replication or gene expression. These data also have implications for selection of optimal primer sequences for the detection of HCV RNA by the PCR assay.     

A new subtype of 3′ region of cagA gene in Helicobacter pyloristrains isolated from Zhejiang Province in China

AIM: To isolate the subtypes of 3′ region of cagA gene in Helicobacter pylori (H pylon) strains from Zhejiang Province in China and to investigate their relations to H pylori-associated gastroduodenal diseases. METHODS: One hundred and thirty-seven H pylori clinical strains were isolated from the gastric mucosa specimens of 74 patients with chronic gastritis, 61 with peptic ulceration, and 2 with gastric cancer. Bacterial genomic DNA was extracted and 3′ region of cagA gene was amplified by polymerase chain reaction (PCR). Subtypes of 3′ region of cagA gene were determined by the size of PCR amplified segments. The sequences of the subtypes were analyzed by PCR-based sequencing. RESULTS: Of the 137 H pyloriisolates from Zhejiang Province, 132 (96.4%) yielded PCR products that could be classified into three groups of subtypes, named as subtypes Ⅰ, Ⅱ, and Ⅲ according to their sizes. The sizes of subtypes Ⅰ, Ⅱ, and Ⅲ were 648-650bp, 705-707bp, and 815bp, respectively. Among the 132 cagA-positive H pylori strains, 123(93.2%) belonged to the group of subtype Ⅰ, 6 (4.5%) presented subtype Ⅱ, 1(0.8%) was subtype Ⅲ, and 2(1.5%) presented subtypes Ⅰ and Ⅲ both. The primary structure of subtype Ⅰ was composed of 3 repeats of R1, 1 repeat of R2 and 1 repeat of R3. Subtype Ⅱ possessing 4 repeats of R1, 2 repeats of R2 and 1 repeat of R3 was a newly found type of 3′ region of cagA gene which had not been reported before. The primary structure of subtype Ⅲ consisted of 4 repeats of R1, Ⅰ repeat of R2 and 2 repeats of R3. Comparison of the sequences of subtype Ⅰ strains with the corresponding sequences deposited in GenBank, showed a similarity of 95.0% (94.0-96.1%) for nucleotide sequences and 95.9% (94.9-97.4%) for deduced amino acid sequences. Comparison of the sequences of subtype Ⅲ strains with the corresponding sequences deposited in GenBank, showed a similarity of 93.9% (90.8-96.9%) for nucleotide sequences and 93.2% (90.2-96.2%) for deduced amino acid sequences. Among subtype Ⅱ strains, the nucleotide and deduced amino acid sequences showed a similarity of 95.2% (94.1-96.5%) and 96.4% (93.8-97.9%),respectively. There were no statistical differences in the distribution of subtypes of 3′ region of cagA gene among different H pylori-associated gastroduodenal diseases (x^2=11.544, P&gt;0.05). CONCLUSION: There are three subtypes (Ⅰ,Ⅱ, and Ⅲ) of 3′ region of cagA gene in Hpylori strains isolated from Zhejiang Province, and subtype Ⅰ is predominant. Subtype Ⅱ is a newly found subtype of 3′ region of cagA gene. The result of this study does not support the view that the subtypes of 3′ region of cagA gene in H pylori isolated from Zhejiang Province are correlated with the clinical outcomes of H pylori infection.     

At least 12 genotypes of hepatitis C virus predicted by sequence analysis of the putative E1 gene of isolates collected worldwide.

In a previous study we sequenced the 5' noncoding (NC) region of 44 isolates of hepatitis C virus (HCV) and identified heterogeneous domains that provided evidence for additional genetic groups of HCV not previously recognized. In this study we have determined the complete nucleotide sequence of the putative envelope 1 (E1) gene in 51 HCV isolates from around the world and found that they could be grouped into at least 12 distinct genotypes. The E1 gene sequence of 8 of these genotypes has not been reported previously. Although the genetic relatedness of HCV isolates determined by the previous analysis of the 5' NC region predicted the relationships observed in the E1 gene, analysis of the 5' NC sequence alone did not accurately predict all HCV genotypes. The nucleotide and amino acid sequence identities of the E1 gene among HCV isolates of the same genotype were in the range of 88.0-99.1% and 89.1-98.4%, respectively, whereas those of HCV isolates of different genotypes were in the range of 53.5-78.6% and 49.0-82.8%, respectively. The latter differences are similar to those found when comparing the envelope gene sequences of the various serotypes of the related flaviviruses as well as other RNA viruses. We found that some genotypes of HCV were widely distributed around the world, whereas others were identified only in discreet geographical regions. Four genotypes were identified exclusively in Africa and comprised the majority of HCV isolates on that continent. The E1 gene was exactly 576 nucleotides in length in all 51 HCV isolates with no in-frame stop codons. Analysis of the predicted E1 protein identified several conserved domains that may be important for maintaining its biological function: (i) eight invariant cysteine residues, (ii) three potential N-linked glycosylation sites, (iii) a domain of nine amino acids (GHRMAWDMM), and (iv) an amino acid doublet (GV) near the putative cleavage site at the C terminus of the protein. In conclusion, the discovery of at least 12 genotypes of HCV has important implications for HCV diagnosis and vaccine development.     

Molecular diversity of class 1 integrons in human isolates of Aeromonas spp. from southern Taiwan

This work studies antimicrobial resistance and class 1 integrons of Aeromonas spp. in human isolates from southern Taiwan. PCR amplification and DNA sequence analyses were performed to characterize the gene cassette regions of the class 1 integron in 204 isolates of Aeromonas hydrophila, 36 isolates of A. sobria, 23 isolates of A. veronii, and 4 isolates of A. caviae. By using Southern hybridization with an intI1 probe to determine the presence of class 1 integrons in the 9 isolates of Aeromonas spp. harboring plasmid DNA, only 2 isolates, one A. veronii AV69 harboring 176-kb plasmid DNA, and one A. hydrophila AH207 harboring 149-kb plasmid DNA were identified. A conjugation experiment was carried out with 2 isolates of A. veronii AV69 and A. hydrophila AH207. Only one transconjugant of Escherichia coli AH207, containing 149-kb plasmids obtained from A. hydrophila AH207, was identified. ERIC-PCR analysis was performed to analyze the genetic relatedness in all isolates of Aeromonas spp. that carry class 1 integrons. The results of cluster analysis in this experiment revealed that none of these isolates were clonal, which may indicate that they were not related to the outbreak. Among the 267 isolates tested, class 1 integrons were detected in 37 isolates (13.9%) of Aeromonas spp. from humans. No class 2 or class 3 integrons were detected in this study. Gene cassette structures were identified in 30 (81.0%) of 37 isolates of Aeromonas spp. containing class 1 integrons. The gene cassette of dfrA12-orfF-aadA2 was the most prevalent in the gene cassette array (16.0%), followed by arr3-aacA4 (13.3%) and dfr2d-catB3-aadA1 (10.0%). Four novel arrays of gene cassettes were also identified, namely, dfr2d-catB3-aadA1, aadA1-aac(6')-II, aadA4a, and aac(6')-II-blaOXA-21-catB3. This is the first report of Aeromonas spp. isolates from humans.     

Characterization of the South African HIV type 1 subtype C complete 5' long terminal repeat, nef, and regulatory genes

Human immunodeficiency virus type 1 (HIV-1) subtype C has become the major etiological agent in the global and especially African epidemic. To gain better understanding of the genetic diversity and rapid transmission of HIV-1 subtype C, we have characterized the complete 5' long terminal repeat (LTR) region along with the regulatory genes tat and rev as well as the accessory gene nef of 14 South African HIV-1 subtype C isolates. Phylogenetic analysis revealed a subtype C 5' LTR cluster, as well as subclustering of our nef sequences with various subtype C strains separate from the India and China subclusters. At least 3 NF-kappaB sites were present in the 5' LTR of most isolates and 13 isolates had the subtype C-specific Rev truncation. Some length variation in exon 2 and the absence of a critical cysteine were found in Tat. Residue variation in the myristoylation signal and motifs involved in CD4 and MHC-I downregulation was recorded in our nef gene sequences.