Halocatena marina sp. nov., a novel filamentous halophilic archaeon isolated from marine tidal flat and emended description of the genus Halocatena.

Three novel filamentous halophilic archaea, strains DFN5T, RDMS1, and QDMS1, were isolated from the coastal saline soil samples of the intertidal zones located in different regions of Jiangsu Province, China. The colonies of these strains were pinkish-white due to the presence of white spores. These three strains are extremely halophilic and grew optimally at 35-37 °C and pH 7.0-7.5. Based on 16S rRNA and rpoB' gene analysis, strains DFN5T, RDMS1, and QDMS1 gathered together in phylogenetic trees and then clustered with the current species of the genus Halocatena showing 96.9-97.4% and 82.2-82.5% similarities, respectively. Both the 16S rRNA gene-based and rpoB' gene-based phylogenies were fully supported by the phylogenomic analysis, and the overall genome-related indexes indicated that strains DFN5T, RDMS1, and QDMS1 should be a novel species of the genus Halocatena. Genome mining revealed that there are considerable differences in the genes related to ß-carotene synthesis among these three strains and the current species of Halocatena. The major polar lipids of strains DFN5T, RDMS1, and QDMS1 are PA, PG, PGP-Me, S-TGD-1, TGD-1, and TGD-2. The minor polar lipids, S-DGD-1, DGD-1, S2-DGD, and S-TeGD may be detected. According to the phenotypic characteristics, phylogenetic analysis, genomic and chemotaxonomic features, strains DFN5T (= CGMCC 1.19401 T = JCM 35422 T), RDMS1 (= CGMCC 1.19411) and QDMS1 (= CGMCC 1.19410) were classified as a novel species of the genus Halocatena with the proposed name, Halocatena marina sp. nov. This is the first report of the description of a novel filamentous haloarchaeon isolated from marine intertidal zones.

Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., Halorussus salinisoli sp. nov.: six extremely halophilic archaea isolated from solar saltern, salt lake and saline soil.

Six novel halophilic archaeal strains of XZYJT10T, XZYJ18T, XZYJT40T, XZYJT49T, YCN54T and LT46T were isolated from a solar saltern in Tibet, a salt lake in Shanxi, and a saline soil in Xinjiang, China. Sequence similarities of 16S rRNA and rpoB' genes among strains XZYJT10T, XZYJ18T, XZYJT40T, XZYJT49T, YCN54T, LT46T and current members of Halorussus were 90.6-97.8% and 87.8-96.4%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization values among these six strains and current Halorussus members were in the range of 76.5-87.5% and 21.0-33.8%, respectively. These values were all below the species boundary threshold values. The phylogenomic tree based on 122 conserved archaeal protein marker genes revealed that the six novel strains formed individual distinct branches and clustered tightly with Halorussus members. Several phenotypic characteristics distinguished the six strains from current Halorussus members. Polar lipid analysis showed that the six novel strains contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and two to three glycolipids. Phenotypic, chemotaxonomic and phylogenetic properties showed that the six strains represented six novel species within the genus Halorussus, for which the names Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., and Halorussus salinisoli sp. nov. are proposed.

Description of Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus halophilus sp. nov. and Halosolutus gelatinilyticus sp. nov., and genome-based taxonomy of genera Natribaculum and Halovarius.

Three extremely halophilic archaeal strains (LT55T, SQT-29-1T and WLHS5T) were isolated from Gobi saline soil and a salt lake, China. These strains were most related to the genera Natribaculum and Halovarius (92.6-95.1 % similarities), and showed low similarities with other genera within the family Natrialbaceae based on 16S rRNA genes. Phylogenomic analysis confirmed that the three strains formed a distinct clade separated from the related genera Halostagnicola and Natronococcus, which indicated that they may represent a novel genus of the family Natrialbaceae. The average nucleotide identity (ANI), in silico DNA-DNA hybridization (isDDH) and average amino acid identity (AAI) values among the three strains were no more than 87, 34 and 85 %, respectively, much lower than the threshold values for species demarcation. The major phospholipids of the three strains were phosphatidic acid (PA), phosphatidylglycerol (PG) and phosphatidylglycerol phosphate methyl ester (PGP-Me). The glycolipid profiles of the three strains were diverse; sulfated mannosyl glucosyl diether (S-DGD-1) and disulfated mannosyl glucosyl diether (S2-DGD) were found in strains LT55T and WLHS5T, while mannosyl glucosyl diether (DGD-1) and S-DGD-1 in strain SQT-29-1T. The combination of phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that strains WLHS5T (=CGMCC 1.13781T = JCM 33558T), SQT-29-1T (=CGMCC 1.16065T = JCM 33554T) and LT55T (=CGMCC 1.15188T = JCM 30838T) represent three novel species of a new genus within the family Natrialbaceae, for which the names, Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus gelatinilyticus sp. nov. and Halosolutus halophilus sp. nov., are proposed. Genome-based classification of genera Natribaculum and Halovarius revealed that Halovarius luteus should be transferred to the genus Natribaculum as Natribaculum luteum comb. nov. and Natribaculum longum as a heterotypic synonym of Natribaculum breve Liu et al. 2015.

Halorientalis salina sp. nov., Halorientalis marina sp. nov., Halorientalis litorea sp. nov.: three extremely halophilic archaea isolated from a salt lake and coarse sea salt.

Three halophilic archaeal strains, NEN8T, GDY88T and ZY14T, were isolated from a salt lake in Tibet and coarse sea salt samples from Guangdong and Hebei, China, respectively. These strains formed three separate clades (showing 94.4-95.8% and 87.1-89.4% similarities, respectively) and then clustered with the current Halorientalis members (showing 90.7-97.6% and 87.0-91.2% similarities, respectively), as revealed by phylogenetic analyses based on 16S rRNA and rpoB' genes. The overall genome-related index, average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), average amino acid identity (AAI) and the percentage of conserved proteins (POCP) values, among the three strains and members of the genus Halorientalis were 76.0-88.0%, 21.3-37.2%, 69.0-88.3% and 57.7-78.1%, clearly below the threshold values for species demarcation. Strains NEN8T, GDY88T and ZY14T could be distinguished from current Halorientalis species according to differential phenotypic characteristics. The major polar lipids of the three strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1) and disulfated mannosyl glucosyl diether (S2-DGD). In addition, mannosyl glucosyl diether (DGD-1) was detected in strain NEN8T and phosphatidic acid (PA), posssulfated galactosyl mannosyl glucosyl diether (S-TGD-1) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA) were observed in strain ZY14T. These results revealed that strains NEN8T (= CGMCC 1.17213T = JCM 34155T), GDY88T (= CGMCC 1.18548T = JCM 34481T) and ZY14T (= CGMCC 1.17178T = JCM 34154T) represent three novel species of the genus Halorientalis, for which the names Halorientalis salina sp. nov., Halorientalis marina sp. nov. and Halorientalis litorea sp. nov. are proposed.

Halocatena salina sp. nov., a filamentous halophilic archaeon isolated from Aiding Salt Lake.

A filamentous cell-shaped halophilic archaeon (strain AD-1T) was isolated from Aiding Salt Lake, PR China. Its colonies on HCM7 agar plates were pinkish white, 1-4 mm (diameter), elevated and round. The optimum conditions for growth were observed at 42 °C, 4.3 M NaCl, 0.01 M MgCl2 and pH 7. Strain AD-1T could hydrolyse Tween 60, Tween 80, starch and gelatin. Phylogenetic analysis based on 16S rRNA gene, rpoB' and the concatenated 484 single-copy orthologous proteins revealed that strain AD-1T formed a clade with Halocatena pleomorpha SPP-AMP-1T. The average nucleotide identity and in silico DNA-DNA hybridization values between strain AD-1T and Halocatena pleomorpha SPP-AMP-1T were both below the species delineation thresholds (95~96 and 70 %, respectively). The major phospholipids of strain AD-1T were phosphatidic acid, phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, while the major glycolipids were sulphated galactosyl mannosyl glucosyl diether, galactosyl mannosyl glucosyl diether and glucosyl mannosyl glucosyl diether. The phenotypic, phylogenetic and genome-based analyses suggested that strain AD-1T (=CGMCC 1.13724T=JCM 32960T) represents a novel species, for which the name Halocatena salina sp. nov. is proposed.

HIV and STIs in clients and female sex workers in mining regions of Gejiu City, China.

OBJECTIVE: To investigate HIV/sexually transmitted infections (STIs) among female sex workers (FSWs) and clients in a mining region of China. GOAL: To estimate HIV/STI prevalence and to identify HIV risk factors among FSWs and miner clients. STUDY DESIGN: A cross-sectional study of 96 FSWs and 339 miner clients. RESULTS: In FSWs, prevalence of HIV was 8.3%, herpes simplex virus-2 70.8%, syphilis 12.5%, Neisseria gonorrhoeae 36.8%, Chlamydia trachomatis 46.3%, Trichomonas vaginalis 22.1%, and 90.6% were infected with any STI. Illegal drug use was associated with HIV [adjusted odds ratio (OR) = 45.1, 95% confidence interval, 6.4-317.9] in FSWs, and 45.8% reported no condom use with the last client. In miner clients, HIV prevalence was 1.8%, herpes simplex virus-2 14.9%, syphilis 2.4%, N. gonorrhoeae 2.1%, C. trachomatis 6.5%, and 23.2% were infected with any STI. Never using condoms with FSWs and regular partners were reported in 61.2% and 84.1%, respectively. Independent risk factors for HIV in miner clients were illegal drug use (OR 190.2), symptoms of urethral discharge or frequent urination (OR 32.9), early sexual debut (OR 7.1), and visiting 4 or more FSWs in the last 12 months (OR 11.5). CONCLUSIONS: HIV/STI prevalence is high among FSWs and moderate among clients in mining regions of Gejiu City. Drug use is the most important factor placing FSWs and miner clients at risk for HIV in Gejiu City; risky sexual characteristics such as early sexual debut, frequent visits to FSWs, and STI symptoms are also important factors for miner clients. FSWs and miner clients may constitute bridging groups for HIV to low-risk populations.

[Comprehensive evaluation on the potential risk for HIV infection in 12 villages with a history of former paid blood donation].

OBJECTIVE: To learn the potential risk for human immunodeficiency virus (HIV) infection in 12 villages with a history of former paid blood donation, and to provide different measures for HIV/AIDS prevention and control. METHODS: Seven indexes were selected, including HIV sero-prevalence rates, hepatitis C virus (HCV) sero-prevalence rates, HIV/AIDS KAB (knowledge, attitude and belief), proportion of paid blood/plasma donation, risks on related behavioral information on sex and HIV/AIDS infections. Rank Sum Ratio (RSR) was performed to synthetically evaluate the potential risk of HIV infection in those 12 selected villages. RESULTS: According to the results of evaluation by 18 experts, weight coefficient of HIV sero-prevalence rate was the highest (0.28), and HIV/AIDS KAB the lowest (0.09) among the seven indexes. The results of comprehensive evaluation with RSR showed that the villages coded 01 and 02 belonged to higher level of potential risk of HIV infection, villages 09, 12, 05, 10 and 03 were at medium level while villages 04, 06, 08, 07 and 11 were at low level. CONCLUSION: The level of potential risk for HIV infection was different in 12 villages with a history of former paid blood donation. Different measures of HIV/AIDS prevision and control should be performed according to the potential risk level for HIV infection of the 12 villages.

[Study on the association between vaginal douching and sexually transmitted diseases among female sex workers in a county of Yunnan province].

OBJECTIVE: To explore the epidemic characteristics of vaginal douching, human immunodeficiency virus (HIV) and other sexually transmitted diseases(STD) among female sex workers (FSWs) in Yunnan province. METHODS: FSWs were recruited to be investigated on their demographic data, drug abuse and sexual behavior, HIV/AIDS knowledge and procreation health status. Venous blood were collected to test for HIV, herpes simplex virus 2 (HSV-2) and syphilis while urine specimen was for morphine, cervical secretion for Gonorrhoea and Chlamydia trachomatis, and vaginal secretion for Trichomonas. RESULTS: A total number of 833 blood specimen were collected, in which 84 specimen were confirmed to be HIV positive with a prevalence rate of 10.1%. The prevalence rates of syphilis and HSV-2 were 8.2% and 68.4% respectively. 832 vaginal and cervical secretion specimen were collected with the prevalence rates of Gonorrhoea, Chlamydia trachomatis and Trichomonas were 11.5%, 28.2% and 11.9% respectively. In multivariate logistic analysis, the factors associated with vaginal douching were: being Han nationality, locations of sex work at middle/high level, ever heard of HIV/AIDS, emerged hypogastric pain last year, the number of sex work location > or =4. CONCLUSION: Vaginal douching was shown a risk factor for HIV and some STD.

[Epidemiologic study on STD/HIV infections among tin mining workers in Gejiu, Yunnan province].

OBJECTIVE: To estimate human immunodeficiency virus (HIV)/sexually transmitted diseases (STDs) related knowledge, the prevalence and risk factors for HIV/STDs among tin miners in Gejiu, Yunnan Province. METHODS: A cross-sectional study was conducted in tin miners working at 5 mining regions from March to June 2006 in Gejiu City, Yunnan Province. A total of 1796 miners were enrolled in the study, and a standardized questionnaire was administered probing socio-demographic factors, knowledge of HIV/STDs and sexual behavior. 7 ml-volume venous blood and 15 ml urine specimens were collected for HIV/STDs testing. RESULTS: Twelve participants [0.7%] (12/1760) were identified HIV positive. While, the positive proportions for syphilis, herpes simplex virus type-2 (HSV-2), Neisseria gonorrhea and Chlamydia trachoma were 1.8% (31/1760), 9.6% (169/1760), 0.8% (14/1773), 4.8% (85/1773), respectively. The total prevalence of STDs was 14.9% (264/1776). Factors associated with HIV infection were illegal drug use (adjusted OR = 17.8; 95% CI: 4.0 - 78.8), frequencies of visiting female sex workers in the past twelve months (adjusted OR = 8.7; 95% CI: 1.9 - 39.0), tattoos (adjusted OR = 6.6; 95% CI: 1.8 - 24.0), surgical operation experiences (adjusted OR = 6.0; 95% CI: 1.6 - 22.5) and toothbrush sharing (adjusted OR = 5.6; 95% CI: 1.0 - 31.3). Factors associated with STDs infection were race (adjusted OR = 2.0; 95% CI: 1.5 - 2.7), age (adjusted OR = 1.7; 95% CI: 1.0 - 2.9), illegal drug use (adjusted OR = 2.3; 95% CI: 1.0 - 5.2), living with spouses (adjusted OR = 1.4; 95% CI: 1.1 - 1.9) and visiting female sex workers (adjusted OR = 1.9; 95% CI: 1.4 - 2.6). Only 4.1% (49/1201) of respondents aware the correct transmission routes of HIV. 21.6% (339/1569) of the miners who had previous sexual experience self-reported visiting female sex workers. CONCLUSION: HIV and other STDs are highly prevalent amongst miners in this region. In addition, the awareness of HIV/STDs is low and multiple routes of HIV transmission, such as heterosexual intercourse and IDU, were also observed in these study subject. HIV/STDs interventions should therefore be reinforced among the miners in this region.

[A cross-sectional survey on human immunodeficiency virus infection in a former commercial blood donating community, Shanxi Province].

OBJECTIVE: To determine the sero-prevalence of and the risk factors for human immunodeficiency virus infection among residents in a former commercial blood donating community, Shanxi Province. METHODS: A community-based cross-sectional survey was conducted among all residents aged 18 - 64 years in 4 villages in a rural county of Shanxi Province. A standardized structured questionnaire was administered to collect socio-demographic, medical and risk behavioral information. Venous blood was collected for HIV antibody testing. Generalized estimating equation with logistic regression was used to analyze the risk factors for HIV infection. Population attributable fraction was used to evaluate the role of public health in the risk factors for the incidence of HIV. RESULTS: A total of 3062 villagers participated in the study and provided their blood samples for HIV antibody testing. 29.5% of the participants had a history of selling blood and/or plasma. Among the subgroup of former blood donors (FBDs), 71.9% sold whole blood only, 4.1% sold plasma only and 24.0% sold both. Forty HIV infected persons were identified in the four villages. HIV prevalence was 1.3%, overall, 4.1% in FBDs and 0.1% in non-FBDs in the community. Amongst the subgroup of FBDs, HIV prevalence was 1.5% for whole blood only, 21.6% for plasma only and 8.8% for both. Univariate analysis showed that village of residence, education, marital status, gender, plasma/blood donation were statistically associated with HIV seropositivity in the villagers. Other variables, such as gender, age, occupation, number of sexual partners, drug use, histories of tooth extraction, acupuncture, surgical operation and medical injection were not found to be statistically associated with HIV seropositivity. Multivariate analysis found that selling whole blood only (adjusted OR = 13.25, 95% CI: 3.02 - 58.25) and selling plasma or both (adjusted OR = 87.85, 95% CI: 22.22 - 347.27) were significantly associated with HIV seropositivity, and the additive population attributable fraction (PAF) was 89.8%. Villagers in village 03 were more likely to be HIV positive than those in village 04 (adjusted OR = 12.26, 95% CI: 1.46 - 103.00). CONCLUSION: At present, HIV epidemic in the former commercial blood donating community has a low prevalence in Shanxi Province and the majority of HIV infections should be related to the blood and plasma donation. This study reveals the existence of HIV second-generation transmission from the infected blood donors to the general population. However, HIV had not been evidently extended from the blood/plasma donors to general population.

Epidemiologic study on human immunodeficiency virus infection among children in a former paid plasma donating community in China.

BACKGROUND: Illegal plasma collecting activities in mid 1990s caused a large number of human immunodeficiency virus (HIV) infections in rural areas of central-eastern China. Although most of these activities have been stopped, there were few reports on secondary transmission from infected former plasma donors to their spouses and from infected mothers to their children. This study was to determine the extent of HIV infections among young children in a rural community with a large proportion of plasma donors. METHODS: A survey was conducted among children aged under 7 years in a former plasma donating community in September 2000: finger blood was collected for HIV antibody testing. Another survey was repeated among children aged under 8 years and their families in the same community in April 2001: urine samples were collected for HIV testing. HIV positive children and samples of HIV negative children, whose mothers were positive based on 2001 survey, were followed up until September 2002 to investigate HIV seroconversion, disease progression and HIV strain analysis. Questionnaires were administered to collect information on children's delivery, breast feeding, medical history and their parents' commercial blood donation history and HIV status. RESULTS: Among 169 children surveyed in 2000, 10 (5.9%) were HIV positive. Of 224 children, 11 were positive in 2001. The overall prevalence rate in the two surveys was 5.0% (17/337) when counting 56 repeated children only once. Of children born to HIV positive mothers, 28.9% were infected. A seroconversion rate of 2.5 per 100 child-years was observed by following up 28 HIV negative children. No statistically significant associations were found between children's HIV infection and their histories of blood transfusion, surgery, immunization injection or medical injections. All infections were HIV-1 subtype B' strain, the average dispersion rate is 7.4%. DNA sequence analysis showed a close relationship between the seroconverted children and their infected mothers. CONCLUSIONS: HIV vertical transmissions in the rural former plasma donating community was significant. Intervention measures should be taken to prevent further transmission. It was estimated that the HIV spread in this community occurred in 1994 or even earlier. Many infected people are developing AIDS now: treatment and care are urgently needed for these sick people.

[A cross-sectional survey on hepatitis C virus infection among residents aged 18-59 years in a former commercial blood donating community, Shanxi Province].

OBJECTIVE: To determine sero-prevalence of and risk factors for hepatitis C virus infection (HCV) among residents aged 18-59 years in a former commercial blood donating community, Shanxi province. METHODS: A community-based cross-sectional survey was conducted among 660 randomly selected residents aged 18-59 years from 12 villages in a rural county of Shanxi province. Structured questionnaire was administered to collect socio-demographic,medical and risk behavioral information. 7 ml-volume venous blood was collected for HCV antibody testing. RESULTS: The overall HCV sero-prevalence rates were 8.2% and 27.7% among former commercial blood donors in the community. Data from multivariate logistic regression analysis showed that people ever selling blood (adjusted OR = 14.28, 95% CI: 6.83-29.87) and receiving blood transfusion (adjusted OR = 8.66,95% CI: 2.31-32.47) were the primary risk factors for HCV infection. Subgroup analysis in blood donors explored that ever selling plasma (adjusted OR = 8.56,95% CI: 2.87-25.54) was the risk factor for HCV infection. Villagers who stopped selling blood in 1994 and thereafter were less likely to be HCV positive than those stopping selling blood before 1994 (adjusted OR = 0.32,95% CI: 0.11-0.93). Female donors had a lower risk than male ones (adjusted OR = 0.28, 95% CI: 0.10-0.83). CONCLUSION: A HCV epidemic was once existing in rural community residents in the province that former commercial blood/plasma donation was the main reason for HCV epidemic in the community. It is urgent to make efficient measures to prevent HCV secondary transmission and provide patients with care and treatment to this community.

[An epidemiological study on sexual transmission of human immunodeficiency virus among pre-marital group in Yining city, Xinjiang].

OBJECTIVE: To study the human immunodeficiency virus (HIV) status through heterosexual transmission in Yining city and to provide information on effective intervention measures. METHODS: Cohort of HIV sero-discordant couples identified from 1997 to 2000 was formed. Proportional risk model was used to analyze the time of HIV sero-conversion and the related factors. All the recruiters were under informed consent. RESULTS: Through following on 22 sero-discordant couples, we found that the incidence density (ID) of HIV sero-conversion was 32.49/100 person-year (PY) with 33.74/100 PY for women. In the proportional hazard model, the course of sero-conversion was only 2.43 years and the frequency of sexual contact was statistically significant (>or= 3 times/week vs. < 3 time/week: RR = 1.984, 95% CI: 1.045 - 3.767), indicating this factor was related to the hazard of HIV sero-conversion. However, the viral load of HIV infections has no such effect on HIV sero-conversion of their spouses. In addition, the ratio of CD4(+)/CD8(+) was lower in spouses of HIV sero-conversion than that in spouses of HIV non-sero conversion (t test: t = 4.77, P < 0.01). CONCLUSION: In order to control HIV transmission among general population, we suggested that HIV/AIDS counseling and testing be developed for pre-marital people in the region with high HIV prevalence.