The current understanding of human gut microbial community is mainly limited to taxonomic features at the genus level. Here, we examined species level by metataxonomics. To achieve this purpose, a high-throughput approach involving operational phylogenetic unit analysis near full-length 16S ribosomal RNA (rRNA) gene sequence was used. A total 1,235 species-level phylotypes (SLPs) were classified in feces 120 Chinese healthy individuals, including 461 previously species, 358 potentially new...

Shiga toxin (Stx) is the key virulent factor in toxin-producing Escherichia coli (STEC). To date, three Stx1 subtypes and seven Stx2 have been described E. coli, which differed receptor preference potency. Here, we identified a novel subtype designated Stx2h strains isolated from wild marmots Qinghai-Tibetan plateau, China. shares 91.9% nucleic acid sequence identity 92.9% amino to nearest subtype. The expression of type strain STEC299 was inducible by mitomycin C, culture supernatant...

Shiga toxin (Stx) is the key virulence factor in producing Escherichia coli (STEC), which can cause diarrhea and hemorrhagic colitis with life-threatening complications. Stx comprises two types, Stx1 Stx2. Several Stx1/Stx2 subtypes have been identified E. coli, are variable sequences, toxicity host specificity. Here, we report identification of a novel Stx2 subtype, designated Stx2k, strains widely detected from diarrheal patients, animals, raw meats China over time. Stx2k exhibits varied...

Abstract Background Shiga toxin-producing Escherichia coli (STEC) is recognized as an important human diarrheal pathogen. Swine plays role a carrier of this In study we determined the prevalence and characteristics STEC from healthy swine collected between May 2011 August 2012 3 cities/provinces in China. Results A total 1003 samples, including 326 fecal, 351 small intestinal contents colon was analyzed. Two hundred fifty five samples were stx -positive by PCR 93 isolates recovered 62...

Abstract Background Hemolytic uremic syndrome (HUS) is a multisystemic disease. In nationwide study, we characterized the incidence, clinical course, and prognosis of HUS caused by Shiga toxin (Stx)–producing Escherichia coli (STEC) strains with emphasis on risk factors, disease severity, long-term outcome. Methods The data pediatric patients from 2000 to 2016 were collected medical records. STEC isolates fecal cultures non-HUS same time period whole genome sequencing analysis. Results...

Abstract Hybrid E. coli pathotypes are representing emerging public health threats with enhanced virulence from different pathotypes. Hybrids of Shiga toxin-producing and enterotoxigenic (STEC/ETEC) have been reported to be associated diarrheal disease hemolytic uremic syndrome (HUS) in humans. Here, we identified characterized four clinical STEC/ETEC hybrids patients or without fever abdominal pain healthy contact Sweden. Rare stx2 subtypes were present hybrids. Stx2 production was...

Abstract The respiratory tract is colonized with low-density microbial communities, which have been shown to impact human health through microbiota–host interactions. However, a lack of fast and cost-effective nucleic acid extraction method for low-microbial biomass samples hinders investigation microbiota. Here, we performed pilot study assess the suitability NAxtra protocol profiling bacterial microbiota in samples. A small number nasopharyngeal aspirate ( n = 8), nasal swab saliva 8) were...

Shiga toxin-producing Escherichia coli (STEC) is an important pathogen that can cause asymptomatic infections, diarrhea, hemorrhagic colitis (HC), and life-threatening hemolytic uremic syndrome (HUS) in humans. toxins (Stxs) are the major virulence factors encoded by prophages, which play a crucial role STEC pathogenesis evolution. In this study, seven Stx phages were obtained from isolates derived four food handlers, two diarrheal patients, one outbreak-related HUS case China. These...

SUMMARY Escherichia albertii is a newly emerging enteric pathogen that has been associated with gastroenteritis in humans. Recently, E. also detected healthy and sick birds, animals, chicken meat water. In the present study, prevalence characteristics of eae -positive, lactose non-fermenting strains retail raw China were evaluated. Thirty isolates such identified from 446 (6·73%) samples, including duck intestines (21·43%, 6/28), (9·52%, 2/21), (8·99%, 17/189), (5·66%, 3/53), mutton (4·55%,...

Shiga toxin-producing Escherichia coli (STEC) causes diarrhea and hemorrhagic colitis with life-threatening complications, such as hemolytic uremic syndrome. The aim of this study was to assess the molecular epidemiologic features non-O157 STEC strains from different resources in China illustrate role animal reservoirs or animal-derived foodstuffs human infections. A collection 301 isolates domestic wild animals (i.e., cattle, goat, pig, yak, pika, antelope), raw meats beef, pork, mutton,...

Escherichia coli is both of a widespread harmless gut commensal and versatile pathogen humans. Domestic animals are well-known reservoir for pathogenic E. coli. However, studies populations from wild that have been separated human activities had very limited. Here we obtained 580 isolates intestinal contents 116 Marmot Marmota himalayana Qinghai-Tibet plateau, China, with five per animal. We selected 125 (hereinafter referred to as strains) the genome sequencing, based on unique pulse field...

Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen. The increasing incidence of non-O157 STEC has posed a great risk to public health. Besides the toxin (Stx), adherence factor, intimin, coded by eae gene plays critical role in pathogenesis. In this study, we investigated prevalence and polymorphisms strains isolated from different sources China. Among 735 strains, was present 70 (9.5%) strains. Eighteen genotypes were identified 62 eae-positive with nucleotide...

Non-O157 Shiga toxin-producing Escherichia coli (STEC) is an important pathogen that can cause zoonotic diseases. To investigate the antimicrobial resistance of STEC in China, non-O157 isolates, recovered from domestic animals and humans 12 provinces, were analyzed using susceptibility testing whole genome characterization. Out 298 isolates tested, 115 strains showed to at least one 85 multidrug resistance. The highest rate was tetracycline (32.6%), followed by nalidixic acid (25.2%)...

Atypical enteropathogenic Escherichia coli (aEPEC) strains are emerging enteropathogens that have been detected worldwide. A collection of 228 aEPEC (121 from diarrheal patients, 27 healthy carriers, 47 animals and 33 raw meats) were investigated for serotypes, virulence gene profiles phylogenetic relationships. Sixty-six O serogroups identified. For the 20 genes detected, statistically significant differences observed in overall prevalence efa1 (lifA), nleB, nleE, set/ent, paa ehxA among...

Two bacterial strains were isolated from faecal samples of Tibetan antelopes. The isolates Gram-stain-positive, catalase-negative, coccus-shaped organisms that tentatively identified as representing a novel streptococcal species based on their morphological features, biochemical test results and phylogenomic findings. Comparative 16S rRNA gene sequencing studies confirmed the members genus Streptococcus, but they did not correspond to any recognized genus. nearest phylogenetic relative...

The Old World vulture may carry and spread pathogens for emerging infections since they feed on the carcasses of dead animals participate in sky burials humans, some whom have died from communicable diseases. Therefore, we studied precise fecal microbiome with metataxonomics, integrating high-throughput sequencing almost full-length small subunit ribosomal RNA (16S rRNA) gene amplicons tandem operational phylogenetic unit (OPU) analysis strategy. Nine vultures three species were sampled...

Shiga toxin (Stx) is the major virulence factor of toxin-producing Escherichia coli (STEC). Stx evolves rapidly and, as such, new subtypes continue to emerge that challenge efficacy existing disease management and surveillance strategies. A subtype, Stx2k, was recently identified in E. isolated from a wide range sources including diarrheal patients, animals, raw meats, poorly detected by immunoassays. In this study, structure Stx2kE167Q determined at 2.29 Å resolution conservation with Stx2a...

Atypical enteropathogenic Escherichia coli (aEPEC) is considered to be an emerging enteropathogen that more prevalent than typical EPEC in developing and developed countries. The major adherence factor, intimin, outer membrane protein encoded by eae, plays a pivotal role the pathogenesis of aEPEC. This study investigated distribution polymorphisms intimin subtypes 143 aEPEC strains from diarrheal patients, healthy carriers, animals, raw meats China. These belonged 71 different serotypes,...

Gut microbiome plays a significant role in HIV-1 immunopathogenesis and HIV-1-associated complications. Previous studies have mostly been based on 16S rRNA gene sequencing, which is limited taxonomic resolution at the genus level inferred functionality. Herein, we performed deep shotgun metagenomics study with aim to obtain more precise landscape of gut dysbiosis infection. A reduced tendency alpha diversity significantly higher beta were found HIV-1-infected individuals antiretroviral...

Shiga toxin (Stx) is the key virulence factor in Toxin-Producing Escherichia coli (STEC), which can cause diarrhea and hemorrhagic colitis with potential life-threatening complications. There are two major types of Stx: Stx1 Stx2. Several Stx1/Stx2 subtypes have been identified E. coli, varying sequences, toxicity host specificity. Here, we report a novel Stx2 subtype (designated Stx2m) from three clinical strains isolated diarrheal patients asymptomatic carriers Sweden Denmark. The Stx2m...

Shiga toxin (Stx)-producing Escherichia coli (STEC) are recognized as important human pathogens of public health concern. Many animals the sources STEC. In this study we determined occurrence and characteristics STEC in yaks (Bos grunniens) from Qinghai-Tibetan plateau, China. A total 728 yak fecal samples was collected June to August, 2012 screened for presence stx1 stx2 genes by TaqMan real-time PCR after sample enriched modified Tryptone Soya Broth. Of 138 (18.96%) and/or stx2-positive...

The metataxonomic approach combining 16S rRNA gene amplicon sequencing using the PacBio Technology with application of operational phylogenetic unit (OPU) approach, has been used to analyze fecal microbial composition high-altitude and herbivorous Tibetan antelopes. samples antelope were collected in Hoh Xil National Nature Reserve, at an altitude over 4500 m, largest depopulated zone Qinghai-Tibetan Plateau, China, where non-native animals or humans may experience life-threatening acute...

Atypical enteropathogenic Escherichia coli (aEPEC) is regarded as a globally emerging enteropathogen. aEPECs exhibit various level of resistance to range antibiotics, which increasing alarmingly. The present study investigated the antimicrobial aEPEC isolates recovered from diarrheal patients, healthy carriers, animals, and raw meats.Among 267 isolates, 146 (54.7%) were resistant tetracycline, followed by ampicillin (49.4%), streptomycin (46.1%), piperacillin (41.2%). Multidrug (MDR) was...