ABSTRACT
Objective:To conduct in-depth study of the distribution and diversity of viruses in poultry is of great importance in monitoring the emergence of interspecies transmission of novel viruses that may cause epidemics with public health significance. Poultry is an economically important source of meat, eggs and feathers which plays an important role as natural reservoirs of many pathogenic viruses. Compared with wild animals, poultry have more frequent interactions and therefore opportunities to transmit their viruses to human.Methods:To study the viromes of different types of poultry in Hainan, China, we used metagenomics for deep viral nucleic acid sequencing of the faecal samples collected from chickens, ducks and pigeons from a live poultry market in Haikou.Result:The poultry viromes were identified by sequence similarity comparisons of viral reads (BLASTxE score, <5) against viral reference database. A total of 15 309 viral reads were obtained, approximately 13 063, 1 370 and 876 viral reads were generated from the chicken, duck, pigeon faecal samples, respectively. The majority of the sequences were homologous to the animal virus of Adenoviridae, Herpeaviridae, Picobirnaviridae, Reoviridae, Retroviridae, Circoviridae, Paramyxoviridae, Astroviridae, Caliciviridae, Coronaviridae, Picornaviridae, and Orthomyxoviridae. The VP4 and VP7 segments of a pigeon rotavirus, similar to fox rotavirus in group A, were sequenced and phylogenetically analyzed. The near full genome of a pigeon circovirus was also analyzed.Conclusion:The major types of poultry in a Haikou harbor many different families of viruses in their feces which may have the potential for interspecies transmissions. Further studies should be conducted to identify the most prevalent and important viruses among a larger number of poultry in Haikou and other areas in Hainan.
ABSTRACT
Objective:Torque teno virus(TTV), are reported in a wide range of mammals. In this study, we sequenced and analyzed the complete genome of a genetic variant of Rodent TTV, RoTTV3-HMU1 (Hainan Medical University). The virus was harbored by a Rattus norvegicus in the residential areas of Hainan Island, China.Methods:Torque Teno virus (TTV) was found widely distributed throughout the world infecting an extensively wide range of mammals .We extracted the viral DNA from a Rattus norvegicus liver which was caught from the residential areas of Hainan Island. Purifying the amplicons in the range of 250-500 bp. Then Five hundred nanograms DNA was subjected to high-throughput sequencing. The contigs were compared with the NCBI nucleiotide database, designed the primers to cover the genome by PCR amplification and amplicons of each PCR which have been cloned and sequenced. Finally the genome was annotated by using NCBI ORF finder and FGENESV0. Phylogenetic analysis was implemented by the neighbor-joining method in the MEGA6 software package.Results:We sequenced the complete genome of a genetic variant of Rodent TTV, RoTTV3- HMU1. The genomic sequence of RoTTV3-HMU1 has been deposited in GenBank under accession number MF688246.1. The complete genome of RoTTV3-HMU1 is 2 570 nucleotides (nt) in length with a G+C content of 46.93%. RoTTV3-HMU1 encoded 3 unidirectional overlapping open reading frames (ORF). Sequence analysis indicated that the genome of RoTTV3-HMU1 virus was most closely related to RN_2_15 (GenBank accession no. KM668486.1). Phylogenetic analysis based on both ORF1 and the total genome sequence placed RoTTV3-HMU1 in to the clad RoTTV3 of the RoTTV.Conclusions:Hainan Island faces mainland across the sea, however, the same genotype of RoTTV was identified in both Hainan Island and the other part of China. The detection of RoTTV3-HMU1 contributed to a better understanding about the origin and evolution of RoTTV.
ABSTRACT
Objective:Microsporidia have been rapidly emerging as pathogens in both immunocompromised and immunocompetent humans. Enterocytozoon bieneusi (E. bieneusi) is the most common microsporidial species found in human. E. bieneusi has also been found in a wide range of animals and is considered to be a potentially important zoonotic pathogen. The epidemiological and genetic characterization of E. bieneusi among long-tailed macaques [Macaca fascicularis (M. fascicularis) is not fully understood. Here, we conducted the first molecular epidemiological investigation of E. bieneusi among M. fascicularis in Hainan Province, the southernmost part of China.Methods:A total of 193 fecal specimens of M. fascicularis were collected from a breeding base housing non-human primates for experimental use in Hainan Province, China. E. bieneusi was identified and genotyped by nested PCR analysis of the internal transcribed spacer (ITS) region of the rRNA gene. Phylogenetic analysis was performed by constructing a neighboring-joining tree of the ITS gene sequences using MEGA6.Results:A total of 59 (30.6%) of the M. fascicularis were PCR-positive for E. bieneusi. All 59 samples were sequenced successfully and 16 ITS genotypes were identified. These included nine known genotypes: Type IV (n=19), D (n=11), CM1 (n=8), PigEBITS7 (n=4), Pongo2 (n=4), Peru 8 (n=3), Peru11 (n=1), WL21 (n=1) and CM2 (n=1). Additionally, seven novel genotypes named as HNM-I to HNM-VII (one each) were identified. Importantly, genotypes D, Type IV, Peru8, PigEBITS7, and Peru11, which were the predominant (38/59, 64.4%) genotypes identified among M. fascicularis in this study, are also well-known human-pathogenic genotypes. All the genotypes of E. bieneusi identified in this study, including the seven novel ones, belonged to zoonotic group 1.Conclusions:This is the first report of the identification of E. bieneusi in M. fascicularis in Hainan Province, China. The findings of numerous known human-pathogenic types and seven novel genotypes (HNM-I to HNM-VII) of E. bieneusi all belong to zoonotic group 1 indicate the possibility of transmission of this important pathogenic parasite between M. fascicularis and humans.
ABSTRACT
<p><b>BACKGROUND</b>Identification of hospitalized carbapenem-resistant Enterobacteriaceae (CRE)-positive patient is important in preventing nosocomial transmission. The objective of this study was to illustrate the implementation of proactive infection control measures in preventing nosocomial transmission of CRE in a healthcare region of over 3200 beds in Hong Kong between October 1, 2010 and December 31, 2011.</p><p><b>METHODS</b>The program included active surveillance culture in patients with history of medical tourism with hospitalization and surgical operation outside Hong Kong within 12 months before admission, and "added test" as an opportunistic CRE screening in all fecal specimens submitted to the laboratory. Outbreak investigation and contact tracing were conducted for CRE-positive patients. Serial quantitative culture was performed on CRE-positive patients and the duration of fecal carriage of CRE was analyzed.</p><p><b>RESULTS</b>During the study period, a total of 6533 patients were screened for CRE, of which 76 patients were positive (10 from active surveillance culture, 65 from "added test", and 1 secondary case from contact tracing of 223 patients with no nosocomial outbreak), resulting in an overall rate of CRE fecal carriage of 1.2%. The median time of fecal carriage of CRE was 43 days (range, 13-119 days). Beta-lactam-beta-lactamase-inhibitors, cephalosporins, and fluoroquinolones were associated significantly with high fecal bacterial load when used 90 days before CRE detection, while use of cephalosporins, carbapenems, and fluoroquinolones after CRE detection are significantly associated with longer duration of carriage. The duration of fecal carriage of CRE also correlates significantly with the initial fecal bacterial load (Pearson correlation: 0.53; P = 0.02).</p><p><b>CONCLUSION</b>Proactive infection control measures by enhanced surveillance program identify CRE-positive patients and data obtained are useful for the planning of and resource allocation for CRE control.</p>
Subject(s)
Humans , Anti-Bacterial Agents , Therapeutic Uses , Carbapenems , Therapeutic Uses , Cephalosporins , Therapeutic Uses , Drug Resistance, Bacterial , Enterobacteriaceae , Enterobacteriaceae Infections , Fluoroquinolones , Therapeutic Uses , Infection Control , MethodsABSTRACT
<p><b>BACKGROUND</b>Proactive infection control management is crucial in preventing the introduction of multiple drug resistant organisms in the healthcare setting. In Hong Kong, where vancomycin-resistant enterococci (VRE) endemicity is not yet established, contact tracing and screening, together with other infection control measures are essential in limiting intra- and inter-hospital transmission. The objective of this study was to illustrate the control measures used to eradicate a VRE outbreak in a hospital network in Hong Kong.</p><p><b>METHODS</b>We described an outbreak of VRE in a healthcare region in Hong Kong, involving a University affiliated hospital and a convalescent hospital of 1600 and 550 beds respectively. Computer-assisted analysis was utilized to facilitate contact tracing, followed by VRE screening using chromogenic agar. Multi-locus sequence typing (MLST) was performed to assess the clonality of the VRE strains isolated. A case-control study was conducted to identify the risk factors for nosocomial acquisition of VRE.</p><p><b>RESULTS</b>Between November 26 and December 17, 2011, 11 patients (1 exogenous case and 10 secondary cases) in two hospitals with VRE colonization were detected during our outbreak investigation and screening for 361 contact patients, resulting in a clinical attack rate of 2.8% (10/361). There were 8 males and 3 females with a median age of 78 years (range, 40 - 87 years). MLST confirmed sequence type ST414 in all isolates. Case-control analysis demonstrated that VRE positive cases had a significantly longer cumulative length of stay (P < 0.001), a higher proportion with chronic cerebral and cardiopulmonary conditions (P = 0.001), underlying malignancies (P < 0.001), and presence of urinary catheter (P < 0.001), wound or ulcer (P < 0.001), and a greater proportion of these patients were receiving β-lactam/β-lactamase inhibitors (P = 0.009), carbapenem group (P < 0.001), fluoroquinolones (P = 0.003), or vancomycin (P = 0.001) when compared with the controls.</p><p><b>CONCLUSION</b>Extensive contact tracing and screening with a "search-and-confine" strategy was a successful tool for outbreak control in our healthcare region.</p>
Subject(s)
Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Enterococcus faecium , Virulence , Gram-Positive Bacterial Infections , Epidemiology , Hong Kong , Epidemiology , Vancomycin ResistanceABSTRACT
<p><b>BACKGROUND</b>The environmental sources associated with community-acquired or nosocomial legionellosis were not always detectable in the mainland of China and Hong Kong, China. The objective of this study was to illustrate the control measures implemented for nosocomial and community outbreaks of legionellosis, and to understand the environmental distribution of legionella in the water system in Hong Kong, China.</p><p><b>METHODS</b>We investigated the environmental sources of two cases of legionellosis acquired in the hospital and the community by extensive outbreak investigation and sampling of the potable water system using culture and genetic testing at the respective premises.</p><p><b>RESULTS</b>The diagnosis of nosocomial legionellosis was suspected in a patient presenting with nosocomial pneumonia not responsive to multiple beta-lactam antibiotics with subsequent confirmation by Legionella pneumophila serogroup 1 antigenuria. High counts of Legionella pneumophila were detected in the potable water supply of the 70-year-old hospital building. Another patient on continuous ambulatory peritoneal dialysis presenting with acute community-acquired pneumonia and severe diarrhoea was positive for Legionella pneumophila serogroup 1 by polymerase chain reaction (PCR) testing on both sputum and nasopharyngeal aspirate despite negative antigenuria. Paradoxically the source of the second case was traced to the water system of a newly commissioned office building complex. No further cases were detected after shock hyperchlorination with or without superheating of the water systems. Subsequent legionella counts were drastically reduced. Point-of-care infection control by off-boiled or sterile water for mouth care and installation of water filter for showers in the hospital wards for immunocompromised patients was instituted. Territory wide investigation of the community potable water supply showed that 22.1% of the household water supply was positive at a mean legionella count of 108.56 CFU/ml (range 0.10 to 639.30 CFU/ml).</p><p><b>CONCLUSIONS</b>Potable water systems are open systems which are inevitably colonized by bacterial biofilms containing Legionella species. High bacterial counts related to human cases may occur with stagnation of flow in both old or newly commissioned buildings. Vigilance against legionellosis is important in healthcare settings with dense population of highly susceptible hosts.</p>
Subject(s)
Aged , Aged, 80 and over , Female , Humans , Male , Biofilms , Community-Acquired Infections , Diagnosis , Epidemiology , Hong Kong , Epidemiology , Legionellosis , Diagnosis , Epidemiology , Water MicrobiologyABSTRACT
<p><b>OBJECTIVE</b>The present study aimed to clone and express three fragments of genomic RNA derived from SARS associated coronavirus (SARS-CoV) S1 domain and to study its immunogenicity.</p><p><b>METHODS</b>The S1 domain gene was amplified by PCR with specific primers and was inserted into the prokaryotic expression vector pQE-30. Three fragments (40-751, 746-1344 and 746-2001 bp) derived from S1 domain produced after the recombinant plasmid (pQE-30/S1) was digested by restriction endonucleases. The three fragments were cloned into pQE-30 and expressed in M15 strains of Escherichia coli. The expression products, designated S1a, S1b and S1c respectively, were purified by Ni affinity chromatography. The immunogenicity was analyzed by Western Blot and ELISA using serologically confirmed sera from SARS patients and the sera from healthy donors was used as control at the same assay.</p><p><b>RESULTS</b>Three recombinant plasmids (pQE-30/S1a, pQE-30/S1b, pQE-30/S1c) were constructed.Fusion proteins with relative molecular mass of 26,700, 22,500 and 46,000 dalton were successfully expressed with amounts of 35%, 35% and 30% of total cell protein and purified by Ni affinity chromatography, respectively. Western Blot and ELISA analysis showed that the S1c protein could be specifically recognized by the sera from SARS patients.</p><p><b>CONCLUSION</b>The recombinant S1c protein was a good immunogen and has the potential to be used as a vaccine against SARS-CoV infection.</p>