Deciphering the pivotal role of people with high-frequency occupational animal exposure in antibiotic resistance transmission between humans and animals.

BACKGROUND: The spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) among humans and food-producing animals has been widely reported. However, the transmission routes and associated risk factors remain incompletely understood. METHODS: Here, we used commensal Escherichia coli bacteria strains from faeces of pigs and local citizens [HEG: high exposure group (pig breeders, butchers or restaurant chefs) and LEG: low exposure group (other occupations)] to explore the dynamics of ARB and ARG transmission between animals and humans. RESULTS: Most ARGs (96%) present in pigs were shared with humans. Carriage rates of the shared ARGs suggest two transmission patterns among pigs, the HEG and LEG: one pattern was highest in pigs, gradually decreasing in the HEG and LEG (e.g. floR and cmlA1); the other pattern was increasing from pigs to the HEG but then decreasing in the LEG (e.g. mcr-1.1). Carriage rates of the HEG were higher than in the LEG in both patterns, implicating the HEG as a crucial medium in transmitting ARB and ARGs between food-producing animals and humans. Moreover, frequent inter/intragroup transmission via strains, plasmids and/or mobile elements was evident. Carriage of mcr-1.1 on human-gut-prevalent plasmids possibly promoted its enrichment in the HEG. CONCLUSIONS: The HEG is a crucial factor in transmitting ARB and ARGs between food-producing animals and humans. Rational measures to contain the risks of occupational exposure are urgently needed to keep dissemination of antibiotic resistance in check and safeguard public health.

Genome-wide association study of hemolytic uremic syndrome causing Shiga toxin-producing Escherichia coli from Sweden, 1994-2018.

Shiga toxin-producing Escherichia coli (STEC) infection can cause clinical manifestations ranging from diarrhea to potentially fatal hemolytic uremic syndrome (HUS). This study is aimed at identifying STEC genetic factors associated with the development of HUS in Sweden. A total of 238 STEC genomes from STEC-infected patients with and without HUS between 1994 and 2018 in Sweden were included in this study. Serotypes, Shiga toxin gene (stx) subtypes, and virulence genes were characterized in correlation to clinical symptoms (HUS and non-HUS), and pan-genome wide association study was performed. Sixty-five strains belonged to O157:H7, and 173 belonged to non-O157 serotypes. Our study revealed that strains of O157:H7 serotype especially clade 8 were most commonly found in patients with HUS in Sweden. stx2a and stx2a + stx2c subtypes were significantly associated with HUS. Other virulence factors associated with HUS mainly included intimin (eae) and its receptor (tir), adhesion factors, toxins, and secretion system proteins. Pangenome wide-association study identified numbers of accessory genes significantly overrepresented in HUS-STEC strains, including genes encoding outer membrane proteins, transcriptional regulators, phage-related proteins, and numerous genes related to hypothetical proteins. Whole-genome phylogeny and multiple correspondence analysis of pangenomes could not differentiate HUS-STEC from non-HUS-STEC strains. In O157:H7 cluster, strains from HUS patients clustered closely; however, no significant difference in virulence genes was found in O157 strains from patients with and without HUS. These results suggest that STEC strains from different phylogenetic backgrounds may independently acquire genes determining their pathogenicity and confirm that other non-bacterial factors and/or bacteria-host interaction may affect STEC pathogenesis.

Characterization of the novel temperate Escherichia coli phage phiStx2k.

A novel temperate phage, phiStx2k, was induced from a clinical Escherichia coli isolate producing Shiga toxin (Stx) 2k. The phage particles have an icosahedral head (50 nm in diameter) and a long non-contractile tail (149 nm long). The phage genome consists of 46,647 bp of double-stranded DNA with an average G + C content of 51%. Genome sequence comparisons suggested that phiStx2k represents a new genus in the class Caudoviricetes. phiStx2k was capable of converting non-Stx-producing E. coli strains to Stx producers. These results expand our knowledge on the characteristics of Stx phages and highlight the potential risks of the emergence of Stx-producing strains or novel pathogens via horizontal gene transfer.

Corynebacterium anserum sp. nov., isolated from the faeces of greater white-fronted geese (Anser albifrons) at Poyang Lake, PR China.

Two Gram-stain-positive, facultatively aerobic, non-motile and rod- to coccoid-shaped bacterial strains, 23H37-10T and 4HC-13, were isolated from the faeces of greater white-fronted geese (Anser albifrons) at Poyang Lake, Jiangxi Province, PR China. Optimal growth was observed at 35-37 °C, pH 7.0-8.0 and with 0.5-1.5 % (w/v) NaCl. The 16S rRNA gene sequences of strains 23H37-10T and 4HC-13 were identical. Phylogenetic and phylogenomic analyses indicated that strains 23H37-10T and 4HC-13 formed an independent cluster within the genus Corynebacterium and showed 98.8, 97.4, 97.4 and 97.2 % 16S rRNA gene sequence similarity to Corynebacterium urogenitale LMM 1652T, Corynebacterium urealyticum DSM 7109T, Corynebacterium falsenii DSM 44353T and Corynebacterium jeikeium NCTC 11913T, respectively. Cells contained C18 :1 ω9c, C18 : 0 and C16 : 0 as the major cellular fatty acids and MK-9 (H2) as the predominant respiratory quinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidyl inositol mannosides, two unidentified phospholipids, four unidentified glycolipids and one unidentified lipid. Strain 23H37-10T contained mycolic acids, with meso-diaminopimelic acid and arabinose as the major whole-cell hydrolysates. The genome G+C content of strains 23H37-10T and 4HC-13 was 55.2 mol%. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains 23H37-10T and 4HC-13 were 94.4 and 99.6 %, respectively. Strains 23H37-10T and 4HC-13 had dDDH and ANI values of less than 70 and 96 % with all available genomes of the genus Corynebacterium, respectively. The differential genotypic inferences, together with phenotypic and biochemical characteristics, suggested that strains 23H37-10T and 4HC-13 represent a novel species within the genus Corynebacterium, for which the name Corynebacterium anserum sp. nov. is proposed. The type strain is 23H37-10T (=GDMCC 1.1737T=KACC 21672T).

Nanchangia anserum gen. nov., sp. nov., isolated from feces of greater white-fronted geese (Anser albifrons).

Two rod-shaped and Gram-stain-positive bacteria (strains C64T and C62) were isolated in 2020 from faeces of greater white-fronted geese (Anser albifrons) from Poyang Lake, PR China. Their optimal growth conditions were at 37 °C, pH 7.0 and with 0.5 % (w/v) NaCl. The two isolates showed a highest 16S rRNA gene sequence similarity to Bowdeniella nasicola DSM 19116T (92.1 %). Phylogenetic/phylogenomic analyses indicated that strains C64T and C62 clustered independently in the vicinity of the genera Varibaculum, Winkia and Mobiluncus within the family Actinomycetaceae, but could not be classified clearly as members of any of these known genera. The average amino acid identity values between our isolates and available genomes of members of the family Actinomycetaceae were around the genus threshold value (45-65 %). The major cellular fatty acids of the strains were C18 : 1ω9c and C16 : 0. The predominant polar lipids were phosphatidylinositol, phosphatidylglycerol, phosphatidylcholine, diacylglycerol, triacylglycerol and cardiolipin. The amino acid composition of peptidoglycan contained alanine, glutamic acid and glycine. The major respiratory menaquinones were MK-8(H4) and MK-9(H4). The whole cell sugars included galactose, arabinose and glucose. On the basis of the results of the 16S rRNA gene sequences comparison, whole-genome phylogenomic analysis, phenotypic and chemotaxonomic characteristics, we propose that strains C64T and C62 represent a novel species belonging to a novel genus within the family Actinomycetaceae, for which the name Nanchangia anserum gen. nov., sp. nov. is proposed. The type strain is Nanchangia anserum C64T (=CGMCC 1.18410T=GDMCC 1.1969T=KCTC 49511T=KACC 22143T).

Escherichia coli strains producing a novel Shiga toxin 2 subtype circulate in China.

Shiga toxin (Stx) is the key virulence factor in Shiga toxin producing Escherichia coli (STEC), which can cause diarrhea and hemorrhagic colitis with life-threatening complications. Stx comprises two toxin types, Stx1 and Stx2. Several Stx1/Stx2 subtypes have been identified in E. coli, which are variable in sequences, toxicity and host specificity. Here, we report the identification of a novel Stx2 subtype, designated Stx2k, in E. coli strains widely detected from diarrheal patients, animals, and raw meats in China over time. Stx2k exhibits varied cytotoxicity in vitro among individual strains. The Stx2k converting prophages displayed considerable heterogeneity in terms of insertion site, genetic content and structure. Whole genome analysis revealed that the stx2k-containing strains were genetically heterogeneous with diverse serotypes, sequence types, and virulence gene profiles. The nine stx2k-containing strains formed two major phylogenetic clusters closely with strains belonging to STEC, enterotoxigenic E. coli (ETEC), and STEC/ETEC hybrid. One stx2k-containing strain harbored one plasmid-encoded heat-stable enterotoxin sta gene and two identical copies of chromosome-encoded stb gene, exhibiting STEC/ETEC hybrid pathotype. Our finding enlarges the pool of Stx2 subtypes and highlights the extraordinary genomic plasticity of STEC strains. Given the wide distribution of the Stx2k-producing strains in diverse sources and their pathogenic potential, Stx2k should be taken into account in epidemiological surveillance of STEC infections and clinical diagnosis.

Luteimonas chenhongjianii, a novel species isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae).

Two Gram-stain-negative, strictly aerobic, bright-yellow-pigmented and rod-shaped bacteria (strains 100069 and 100111T) with a single polar flagellum were isolated from the rectal contents of plateau pika (Ochotona curzoniae). Based on the results of nearly full-length 16S rRNA gene sequence and phylogenetic analyses, strains 100069 and 100111T belong to the genus Luteimonas, and are closest to Luteimonas rhizosphaerae 4-12T (98.02 % similarity), Luteimonas aestuarii B9T (97.8 %) and Luteimonas terrae THG-MD21T (97.74 %). The DNA G+C contents of these two isolates were 68.30 mol% and 68.29 mol%, respectively. The highest average nucleotide identity (ANI) value between strain 100111T and its closely related species was 83.34 %, well below the threshold of 95-96 %. The major cellular fatty acids were iso-C11 : 0, iso-C15 : 0 and iso-C17 : 1 ω9. Polar lipid content was dominated by diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. Ubiquinone-8 (Q-8) was the predominant respiratory quinone. These two isolates grew optimally at 35-37 °C, pH 7.0-8.0 and with 1.0 % (w/v) NaCl. The results of ANI analysis and other characteristics obtained from our polyphasic study showed that strains 100069 and 100111T represent a novel species in genus Luteimonas, for which the name Luteimonas chenhongjianii sp. nov. (type strain 100111T=DSM 104077T=CGMCC 1.16429T) is proposed.

Genome-by-genome approach for fast bacterial genealogical relationship evaluation.

Motivation: Large-scale whole-genome sequencing dataset-based studies are becoming increasingly common in pathogen surveillance and outbreak investigations. A highly discriminative and time-efficient bioinformatics tool is needed to transform large amounts of sequencing data into usable biological information. To replace the intuitive, yet inefficient, way of gene-by-gene allele calling algorithm, a new algorithm using genome-by-genome approach was developed. Results: Tests showed that the program equipped with the new algorithm achieved significant improvements in allele calling efficiency compared to a conventional gene-by-gene approach. The new program, Fast-GeP, rendered a fast and easy way to infer high-resolution genealogical relationships between bacterial isolates using whole-genome sequencing data. Availability and implementation: FAST-GeP is freely available from: https://github.com/jizhang-nz/fast-GeP. Supplementary information: Supplementary data are available at Bioinformatics online.

High prevalence of non-O157 Shiga toxin-producing Escherichia coli in beef cattle detected by combining four selective agars.

BACKGROUND: Shiga toxin-producing Escherichia coli (STEC) are emerging foodborne pathogens that are public health concern. Cattle have been identified as the major STEC reservoir. In the present study, we investigated the prevalence and characteristics of STEC strains in beef cattle from a commercial farm in Sichuan province, China. RESULTS: Among 120 beef cattle fecal samples, stx genes were positive in 90% of samples, as assessed using TaqMan real-time PCR, and 87 (72.5%) samples were confirmed to yield at least one STEC isolate by culture using four selective agars, MacConkey, CHROMagar™ ECC, modified Rainbow® Agar O157, and CHROMagar™ STEC, from which 31, 32, 91, and 73 STEC strains were recovered, respectively. A total of 126 STEC isolates were selected and further characterized. Seventeen different O:H serotypes were identified, all of which belonged to the non-O157 serotypes. One stx1 subtype (stx1a) and three stx2 subtypes (stx2a, stx2c, and stx2d) were present among these isolates. The intimin encoding gene eae, and other adherence-associated genes (iha, saa, and paa) were present in 37, 125, 74, and 30 STEC isolates, respectively. Twenty-three isolates carried the virulence gene subA, and only one harbored both cnf1 and cnf2 genes. Three plasmid-origin virulence genes (ehxA, espP, and katP) were present in 111, 111, and 7 isolates, respectively. The 126 STEC isolates were divided into 49 pulsed-field gel electrophoresis (PFGE) patterns. CONCLUSIONS: Our study showed that the joint use of the selective MacConkey and modified Rainbow® Agar O157 agars increased the recovery frequency of non-O157 STEC strains in animal feces, which could be applied to other samples and in regular STEC surveillance. Moreover, the results revealed high genetic diversity of non-O157 STEC strains in beef cattle, some of which might have the potential to cause human diseases.

Neisseria weixii sp. nov., isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae).

Three independent isolates (10022T, 10 009 and 10011) of a novel catalase-positive, Gram-stain-negative coccus in the genus Neisseria were obtained from the rectal contents of plateau pika on the Qinghai-Tibet Plateau, PR China. Based on 16S rRNA gene sequence analysis, our newly identified organisms were most closely related to Neisseria iguanae, Neisseria flavescens and Neisseria perflava with similarities ranging from 98.02 to 98.45 %, followed by seven other species in the genus Neisseria. Phylogenetic analysis based on 16S rRNA and rplF genes showed that our three novel isolates group with members of the genus Neisseria. Results of the average nucleotide identity (ANI) analysis confirmed that our isolates are of the same species, and the ANI values between type strain 10022T and other Neisseria species are 74.12-85.06 %, lower than the threshold range of 95-96 %. The major cellular fatty acids for our novel species are C16 : 0 and C16:1ω7c/C16:1ω6c, which along with their phenotypic characteristics can distinguish our isolates from other Neisseria species. On the basis of polyphasic analyses, our isolates are proposed to represent a novel species in genus Neisseria, with the name Neisseria weixii sp. nov. The type strain is 10022T (=DSM 103441T=CGMCC 1.15732T).

Neisseria chenwenguii sp. nov. isolated from the rectal contents of a plateau pika (Ochotona curzoniae).

Two Gram-stain negative, catalase positive, coccus shaped bacteria, designated 10023T and 10010, were isolated from the rectal contents of a plateau pika (Ochotona curzoniae) in Qinghai-Tibet Plateau, China. Based on 16S rRNA gene sequence analysis, phylogenetic trees showed that these two isolates (10023T, 10010) group with members of the genus Neisseria. Additionally, these two isolates exhibited high 16S rRNA gene sequence similarity with Neisseria zalophi CSL 7565T (96.98%), Neisseria wadsworthii WC 05-9715T (96.92%) and Neisseria canis ATCC 14687T (96.79%). Further phylogenetic analysis based on the rplF gene showed that these two novel strains can be easily discriminated from phylogenetically closely related species. Optimal growth was found to occur on BHI agar with 5% defibrinated sheep blood at 37 °C and growth was also observed on nutrient agar, Columbia blood agar and chocolate agar plates; however, growth was not observed on MacConkey agar after 7 days. The major cellular fatty acids of these strains were identified as C16:0 and C16:1ω7c/C16:1ω6c. The complete genome size of the type strain 10023T is 2,496,444 bp, with DNA G+C content of 54.0 mol %. The average nucleotide identity values were 73.5-79.3% between isolate 10023T and reference Neisseria spp. Based on polyphasic analysis, these isolates (10023T and 10010) are considered to represent a novel species in the genus Neisseria, for which the name Neisseria chenwenguii sp. nov. is proposed. The type strain is 10023T (= DSM 103440T = CGMCC 1.15736T).

Complete genome sequence of a novel virulent phage ST31 infecting Escherichia coli H21.

More and more virulent phages that are fundamental materials for phage therapy have been isolated, characterized and categorized on GenBank. Phage ST31 infecting Escherichia coli H21 was isolated from wastewater and sequenced using an Illumina Hiseq system. Opening reading frames were identified using PHASTER and predicted using BLASTp analysis. Genomic analyses revealed that this was a virulent phage containing a circular double-stranded DNA and that the complete genome consisted of 39,693 nucleotides with an average GC content of 49.98 %. This study may provide possible alternative materials for phage therapy.

Enterococcus wangshanyuanii sp. nov., isolated from faeces of yaks (Bos grunniens).

The taxonomic position of four phenotypically closely related strains isolated from faecal samples of yaks (Bos grunniens) collected from the Qinghai-Tibetan plateau, China, was determined by a polyphasic approach. The strains were non-spore-forming, non-motile Gram-stain-positive, ovoid cocci, occurring predominantly in pairs and short chains or in irregular clusters. The 16S rRNA gene of strain MN05T was related phylogenetically to those of Enterococcushaemoperoxidus, Enterococcusrotai, Enterococcusquebecensis, Enterococcusplantarum, Enterococcuscrotali, Enterococcusmoraviensis, Enterococcussilesiacus, Enterococcuscaccae, Enterococcustermitis, Enterococcusureasiticus and Enterococcusureilyticus, all belonging to the Enterococcusfaecalis species group. The sequence similarities of three selected genes of MN05T to those of the type strains of phylogenetically related species were measured, with values within the range of 99.2-99.5 % (16S rRNA gene), 90.0-97.3 % (rpoA) and 80.0-85.3 % (pheS), respectively. The genome of MN05T (3 842 361 bp) contained 4299 genes with a DNA G+C content of 37.5 mol%. A whole-genome phylogenetic tree based on 808 core genes confirmed that MN05T belongs to a distinct lineage, well separated from all recognized species of the Enterococcusfaecalis species group. DNA-DNA hybridization in silico showed that MN05T displayed less than 70 % DNA-DNA relatedness with the other 13 species of the Enterococcusfaecalis species group. Moreover, their phenotypic features distinguished the four strains from the other species of the Enterococcusfaecalis species group. Based upon these data obtained from the polyphasic characterization performed in the present study, a novel species of the genus Enterococcus, Enterococcus wangshanyuanii sp. nov., is proposed, with the type strain MN05T (=DSM 104047T=CGMCC 1.15942T).

Streptococcuspantholopis sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii).

Two bacterial strains were isolated from faecal samples of Tibetan antelopes. The isolates were Gram-stain-positive, catalase-negative, coccus-shaped organisms that were 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 that the organisms were members of the genus Streptococcus, but they did not correspond to any recognized species of the genus. The nearest phylogenetic relative of the unknown coccus was Streptococcus ursoris NUM 1615T (93.4 % 16S rRNA gene sequence similarity). Analysis of groEL and rpoB gene sequences of the novel isolates showed interspecies divergence of 27.0 and 22.2 %, respectively, from the type strain of its closest 16S rRNA gene phylogenetic relative, S. ursoris. The complete genome of strain TA 26T has been sequenced. Digital DNA-DNA hybridization studies between strain TA 26T and other species of the genus Streptococcus deposited in the GenBank database showed less than 70 % DNA-DNA relatedness, supporting a novel species status of the strain. On the basis of their genotypic and phenotypic differences from recognized Streptococcus species, the two isolates represent a novel species of the genus Streptococcus, for which the nameStreptococcus pantholopis sp. nov. (type strain TA 26T=CGMCC 1.15667T=DSM 102135T) is proposed.

Effect of enterohaemorrhagic Escherichia coli O157:H7-specific enterohaemolysin on interleukin-1ß production differs between human and mouse macrophages due to the different sensitivity of NLRP3 activation.

Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 infection in humans can cause acute haemorrhagic colitis and severe haemolytic uraemic syndrome. The role of enterohaemolysin (Ehx) in the pathogenesis of O157:H7-mediated disease in humans remains undefined. Recent studies have revealed the importance of the inflammatory response in O157:H7 pathogenesis in humans. We previously reported that Ehx markedly induced interleukin-1ß (IL-1ß) production in human macrophages. Here, we investigated the disparity in Ehx-induced IL-1ß production between human and mouse macrophages and explored the underlying mechanism regarding the activation of NOD-like receptor family, pyrin domain containing 3 (NLRP3) inflammasomes. In contrast to the effects on human differentiated THP-1 cells and peripheral blood mononuclear cells, Ehx exerted no effect on IL-1ß production in mouse macrophages and splenocytes because of a disparity in pro-IL-1ß cleavage into mature IL-1ß upon caspase-1 activation. Additionally, Ehx significantly contributed to O157:H7-induced ATP release from THP-1 cells, which was not detected in mouse macrophages. Confocal microscopy demonstrated that Ehx was a key inducer of cathepsin B release in THP-1 cells but not in mouse IC-21 cells upon O157:H7 challenge. Inhibitor experiments indicated that O157:H7-induced IL-1ß production was largely dependent upon caspase-1 activation and partially dependent upon ATP signalling and cathepsin B release, which were both involved in NLRP3 activation. Moreover, inhibition of K(+) efflux drastically diminished O157:H7-induced IL-1ß production and cytotoxicity. The findings in this study may shed light on whether and how the Ehx contributes to the development of haemolytic uraemic syndrome in human O157:H7 infection.

Helicobacter himalayensis sp. nov. isolated from gastric mucosa of Marmota himalayana.

A Gram-stain-negative, microaerophilic strain, 80(YS1)T, with a spiral-shaped morphology and 1-2 sheathed flagella at each end of the cells was isolated from the gastric mucosa of Marmota himalayana, the animal reservoir of Yersinia pestis in China, on the Qinghai-Tibet Plateau. The strain grew at 30, 35 and 42 °C, but not at 25 °C. Growth was in the form of a thinly spreading film on brain heart infusion agar containing 8 % sheep blood under microaerobic conditions. The strain did not hydrolyse urea or hippurate, and did not grow on media containing 1 % glycine. It reduced nitrate to nitrite, and was catalase- and alkaline-phosphatase-positive, susceptible to nalidixic acid and resistant to cefalotin. It was positive for genus-specific PCR for the genus Helicobacter, but could not be classified to any recognized species according biochemical tests results. Therefore, a phylogenetic study based on 16S rRNA, 23S rRNA, 60 kDa heat-shock protein (hsp60) and gyrase subunit B (gyrB) genes was conducted. The 16S rRNA gene sequence (1468 bp) analysis showed that strain 80(YS1)T was most closely related to Helicobacter marmotae (96.7 % similarity). The 23S rRNA gene sequence (2879 bp) analysis showed that the strain was most closely related to Helicobacter canis (96 % similarity). The complete gyrB gene sequence (2325 bp) analysis showed that it was related phylogenetically to Helicobacter cinaedi (79.4 % similarity) and H. marmotae (79.1 % similarity). Analysis of the partial sequence of the hsp60 gene of strain 80(YS1)T showed closest similarity to the sequences of Helicobacter equorum (82 %) and H. cinaedi (81 %), respectively. However, there was no hsp60 sequence of H. marmotae available for analysis. The data of morphological, biochemical and phylogenetic characteristics all supported that this strain represents a novel species. The name Helicobacter himalayensis sp. nov. is proposed for this novel species with the type strain 80(YS1)T ( = CGMCC 1.12864T = DSM 28742T).

Genome-wide analysis of synonymous codon usage in Huaiyangshan virus and other bunyaviruses.

Huaiyangshan virus (HYSV) is a newly discovered bunyavirus, which is transmitted by ticks and causes hemorrhagic fever-like illness in human. The interplay of codon usage among viruses and their hosts is expected to affect viral survival, evasion from host's immune system and evolution. However, little is known about the codon usage in HYSV genome. In the present study, we analyzed synonymous codon usage in 120 available full-length HYSV sequences and performed a comparative analysis of synonymous codon usage patterns in HYSV and 42 other bunyaviruses. The relative synonymous codon usage (RSCU) analysis showed that the preferred synonymous codons were G/C-ended. A comparative analysis of RSCU between HYSV and its hosts reflected that codon usage patterns of HYSV were mostly coincident with that of its hosts. Our data suggested that although mutational bias dominated codon usage, patterns of codon usage in HYSV were also under the influence of nature selection. Phylogenetic analysis based on RSCU values across different HYSV strains and 42 other bunyaviruses suggested that codon usage pattern in HYSV was the most similar with that of Uukuniemi virus among these bunyaviruses and that viruses belonged to Phlebovirus showed a diversity of codon usage patterns.

[Multilocus sequence typing analysis of enteropathogenic escherichia coli isolates in 8 provinces of China, 2006-2014].

OBJECTIVE: To investigate the molecular typing feature of enteropathogenic Escherichia coli (EPEC) strains isolated from different reservoirs in eight provinces of China from 2006 to 2014. METHODS: According to the time, place, reservoir, and PFGE pattern of the EPEC strains isolated from stools of humans with diarrhea, animal feces, and foods in eight provinces of China between 2006 and 2014, 149 EPEC strains were selected and characterized by multilocus sequence typing (MLST) using seven housekeeping genes provided by E.coli MLST database. Strain analysis demonstrated 56 different sequence types (STs). SeqMan II, MEGA 5.05, and eBURST V3 were applied to analyze the genetic relationships of domestic and forein existing 392 strains (243 EPEC strains included in the E.coli MLST database and 149 EPEC strains comprised in the present study). RESULTS: Among the 56 different STs, the prevalent ST was ST-40, which included 19 (19/149, 12.8%) isolates. Nineteen new STs were identified. Eleven new alleles were detected in six house-keeping genes (adk, fumC, gyrB, icd, mdh, and purA). Six STs were simultaneously detected among EPEC strains isolated from patients with diarrhea and animals. And these EPEC strains were all aEPEC strains. Two STs were simultaneously identified among EPEC strains isolated from patients with diarrhea and foods. Also, these EPEC strains were all aEPEC strains. 33 out of 173 STs were divided into five major clone complexes by eBURST, STC-29, STC-10, STC-20, STC-28, and STC-517. The remaining EPEC strains included in the other 140 STs were part of the other clone complexes or just were singletons. CONCLUSION: A high degree of phylogenetic heterogeneity was observed among the EPEC strains isolated in eight provinces of China. The EPEC strains with same STs of human isolates isolated from animal feces and foods were all aEPEC strains.

Extensive diversity of Rickettsiales bacteria in two species of ticks from China and the evolution of the Rickettsiales.

BACKGROUND: Bacteria of the order Rickettsiales (Alphaproteobacteria) are obligate intracellular parasites that infect species from virtually every major eukaryotic lineage. Several rickettsial genera harbor species that are significant emerging and re-emerging pathogens of humans. As species of Rickettsiales are associated with an extremely diverse host range, a better understanding of the historical associations between these bacteria and their hosts will provide important information on their evolutionary trajectories and, particularly, their potential emergence as pathogens. RESULTS: Nine species of Rickettsiales (two in the genus Rickettsia, three in the genus Anaplasma, and four in the genus Ehrlichia) were identified in two species of hard ticks (Dermacentor nuttalli and Hyalomma asiaticum) from two geographic regions in Xinjiang through genetic analyses of 16S rRNA, gltA, and groEL gene sequences. Notably, two lineages of Ehrlichia and one lineage of Anaplasma were distinct from any known Rickettsiales, suggesting the presence of potentially novel species in ticks in Xinjiang. Our phylogenetic analyses revealed some topological differences between the phylogenies of the bacteria and their vectors, which led us to marginally reject a model of exclusive bacteria-vector co-divergence. CONCLUSIONS: Ticks are an important natural reservoir of many diverse species of Rickettsiales. In this work, we identified a single tick species that harbors multiple species of Rickettsiales, and uncovered extensive genetic diversity of these bacteria in two tick species from Xinjiang. Both bacteria-vector co-divergence and cross-species transmission appear to have played important roles in Rickettsiales evolution.