Novel tripeptide RKH derived from Akkermansia muciniphila protects against lethal sepsis.

OBJECTIVE: The pathogenesis of sepsis is complex, and the sepsis-induced systemic proinflammatory phase is one of the key drivers of organ failure and consequent mortality. Akkermansia muciniphila (AKK) is recognised as a functional probiotic strain that exerts beneficial effects on the progression of many diseases; however, whether AKK participates in sepsis pathogenesis is still unclear. Here, we evaluated the potential contribution of AKK to lethal sepsis development. DESIGN: Relative abundance of gut microbial AKK in septic patients was evaluated. Cecal ligation and puncture (CLP) surgery and lipopolysaccharide (LPS) injection were employed to establish sepsis in mice. Non-targeted and targeted metabolomics analysis were used for metabolites analysis. RESULTS: We first found that the relative abundance of gut microbial AKK in septic patients was significantly reduced compared with that in non-septic controls. Live AKK supplementation, as well as supplementation with its culture supernatant, remarkably reduced sepsis-induced mortality in sepsis models. Metabolomics analysis and germ-free mouse validation experiments revealed that live AKK was able to generate a novel tripeptide Arg-Lys-His (RKH). RKH exerted protective effects against sepsis-induced death and organ damage. Furthermore, RKH markedly reduced sepsis-induced inflammatory cell activation and proinflammatory factor overproduction. A mechanistic study revealed that RKH could directly bind to Toll-like receptor 4 (TLR4) and block TLR4 signal transduction in immune cells. Finally, we validated the preventive effects of RKH against sepsis-induced systemic inflammation and organ damage in a piglet model. CONCLUSION: We revealed that a novel tripeptide, RKH, derived from live AKK, may act as a novel endogenous antagonist for TLR4. RKH may serve as a novel potential therapeutic approach to combat lethal sepsis after successfully translating its efficacy into clinical practice.

Association between hyperuricemia and acute kidney injury in critically ill patients with sepsis.

BACKGROUND: Sepsis-related AKI is related to short-term mortality and poor long-term prognoses, such as chronic renal insufficiency, late development of end-stage renal disease, and long-term mortality. In this study, we aimed to investigate the association of hyperuricemia with acute kidney injury (AKI) in patients with sepsis. METHODS: The retrospective cohort study included 634 adult sepsis patients hospitalized in the intensive care unit (ICU) of the First Affiliated Hospital of Guangxi Medical University from March 2014 to June 2020 and the ICU of the Second Affiliated Hospital of Guangxi Medical University from January 2017 to June 2020. Based on the first serum uric acid level within 24 h of admission to the ICU, patients were divided into groups with or without hyperuricemia, and the incidence of AKI within seven days of ICU admission was compared between the two groups. The univariate analysis analyzed the effect of hyperuricemia on sepsis-related AKI, and the multivariable logistic regression model analysis was used. RESULTS: Among the 634 patients with sepsis, 163 (25.7%) developed hyperuricemia, and 324 (51.5%) developed AKI. The incidence of AKI in the groups with and without hyperuricemia was 76.7% and 42.3%, respectively, with statistically significant differences (2 = 57.469, P < 0.001). After adjusting for genders, comorbidities (coronary artery disease), organ failure assessment (SOFA) score on the day of admission, basal renal function, serum lactate, calcitonin, and mean arterial pressure, hyperuricemia was showed to be an independent risk factor for AKI in patients with sepsis (OR = 4.415, 95%CI 2.793 ~ 6.980, P < 0.001). For every 1 mg/dL increase in serum uric acid in patients with sepsis, the risk of AKI increased by 31.7% ( OR = 1.317, 95%CI 1.223 ~ 1.418, P < 0.001). CONCLUSION: AKI is a common complication in septic patients hospitalized in the ICU, and hyperuricemia is an independent risk factor for AKI in septic patients.

Tools for fundamental analysis functions of TCR repertoires: a systematic comparison.

The full set of T cell receptors (TCRs) in an individual is known as his or her TCR repertoire. Defining TCR repertoires under physiological conditions and in response to a disease or vaccine may lead to a better understanding of adaptive immunity and thus has great biological and clinical value. In the past decade, several high-throughput sequencing-based tools have been developed to assign TCRs to germline genes and to extract complementarity-determining region 3 (CDR3) sequences using different algorithms. Although these tools claim to be able to perform the full range of fundamental TCR repertoire analyses, there is no clear consensus of which tool is best suited to particular projects. Here, we present a systematic analysis of 12 available TCR repertoire analysis tools using simulated data, with an emphasis on fundamental analysis functions. Our results shed light on the detailed functions of TCR repertoire analysis tools and may therefore help researchers in the field to choose the right tools for their particular experimental design.

Characterization of Peptacetobacter hominis gen. nov., sp. nov., isolated from human faeces, and proposal for the reclassification of Clostridium hiranonis within the genus Peptacetobacter.

A novel, Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, obligately anaerobic bacterium, designated strain ZHW00191T, was isolated from human faeces and characterized by using a polyphasic taxonomic approach. Growth occurred at 25-45 °C (optimum, 37-42 °C), at pH 5.5-10.0 (optimum, pH 6.5-7.0) and with 0-2 % (w/v) NaCl (optimum, 0 %). The end products of glucose fermentation were acetic acid, isobutyric acid and isovaleric acid and a small amount of propionic acid. The dominant cellular fatty acids (>10 %) of strain ZHW00191T were C16 : 0, C18 : 1 ω9с and C18 : 2ω6,9с. Its polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and ten unidentified glycolipids. Respiratory quinones were not detected. The cell-wall peptidoglycan contained meso-2,6-diaminopimelic acid, and the whole-cell sugars were ribose and glucose. The genomic DNA G+C content was 32.8 mol%. Analysis of the 16S rRNA gene sequence indicated that ZHW00191T was most closely related to Clostridium hiranonis TO-931T (95.3 % similarity). Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses with closely related reference strains indicated that reassociation values were both well below the thresholds of 95-96% and 70 % for species delineation, respectively. Based on phenotypic, chemotaxonomic and genetic studies, a novel genus, Peptacetobacter gen. nov., is proposed. The novel isolate ZHW00191T (=JCM 33482T=GDMCC 1.1530T) is proposed as the type strain of the type species Peptacetobacter hominis gen. nov., sp. nov. of the proposed new genus. Furthermore, it is proposed that Clostridium hiranonis be transferred to this novel genus, as Peptacetobacter hiranonis comb. nov.

Cervical artery dissection-an easily neglected cause of stroke: a case report.

BACKGROUND: In recent years, the incidence of stroke has gradually increased in young people. There are many reasons causing stroke, including atherosclerosis, artery embolization, and cervical artery dissection and so on. However, cervical artery dissection is a major cause of stroke in young people. We present a case of ischemic stroke caused by dissection, whose distal vascular occlusion due to detachment of the thrombosis in the right internal carotid artery. CASE PRESENTATION: A 33-year-old male patient was admitted to the hospital because of stroke. Imaging examination showed that there was no visualization of the right middle cerebral artery and there were a large number of mural thrombus in the C1 segment of the right internal carotid artery. After emergency surgery, the patient had vascular recanalization and the symptoms were significantly improved. Magnetic resonance imaging showed a high signal in the C1 segment of the right internal carotid artery, the abnormal signal disappeared after antiplatelet therapy. CONCLUSIONS: When a patient has symptoms of stroke, we need to explore the root cause of stroke. Especially in young people, cervical artery dissection is an important reason that can't be ignored. Through review and analysis of this case, we hope to improve the understanding of radiologists and clinicians about the cervical artery dissection, reduce the rate of misdiagnosis, and improve patients' prognosis.

Risk Factors for Carbapenem-Resistant Pseudomonas aeruginosa, Zhejiang Province, China.

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a public health concern worldwide, but comprehensive analysis of risk factors for CRPA remains limited in China. We conducted a retrospective observational study of carbapenem resistance in 71,880 P. aeruginosa isolates collected in Zhejiang Province during 2015-2017. We analyzed risk factors for CRPA, including the type of clinical specimen; the year, season, and region in which it was collected; patient information, including age, whether they were an outpatient or inpatient, and whether inpatients were in the intensive care unit or general ward; and the level of hospital submitting isolates. We found CRPA was more prevalent among isolates from patients >60 years of age and in inpatients, especially in intensive care units. In addition, specimen types and seasons in which they were collected were associated with higher rates of CRPA. Our findings can help hospitals reduce the spread of P. aeruginosa and optimize antimicrobial drug use.

Disordered intestinal microbes are associated with the activity of Systemic Lupus Erythematosus.

Intestinal dysbiosis is implicated in Systemic Lupus Erythematosus (SLE). However, the evidence of gut microbiome changes in SLE is limited, and the association of changed gut microbiome with the activity of SLE, as well as its functional relevance with SLE still remains unknown. Here, we sequenced 16S rRNA amplicon on fecal samples from 40 SLE patients (19 active patients, 21 remissive patients), 20 disease controls (Rheumatoid Arthritis (RA) patients), and 22 healthy controls (HCs), and investigated the association of functional categories with taxonomic composition by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). We demonstrated SLE patients, particularly the active patients, had significant dysbiosis in gut microbiota with reduced bacterial diversity and biased community constitutions. Amongst the disordered microbiota, the genera Streptococcus, Campylobacter, Veillonella, the species anginosus and dispar, were positively correlated with lupus activity, while the genus Bifidobacterium was negatively associated with the disease activity. PICRUSt analysis showed metabolic pathways were different between SLE and HCs, and also between active and remissive SLE patients. Moreover, we revealed that a random forest model could distinguish SLE from RA and HCs (area under the curve (AUC) = 0.792), and another random forest model could well predict the activity of SLE patients (AUC = 0.811). In summary, SLE patients, especially the active patients, show an apparent dysbiosis in gut microbiota and its related metabolic pathways. Amongst the disordered microflora, four genera and two species are associated with lupus activity. Furthermore, the random forest models are able to diagnose SLE and predict disease activity.

Spinal cord infarction presenting as Brown-Séquard syndrome from spontaneous vertebral artery dissection: a case report and literature review.

BACKGROUND: Spinal cord infarction (SCI) is rarely caused by vertebral artery dissection (VAD), which is an important cause of posterior circulation stroke in young and middle-aged patients. We report the case of a middle-aged patient without obvious risk factors for atherosclerosis who had SCI from right VAD. CASE PRESENTATION: An otherwise healthy 40-year-old man presented with acute right-sided body weakness. Six days earlier, he had experienced posterior neck pain without obvious inducement. Neurologic examination revealed a right Brown-Séquard syndrome. Magnetic resonance imaging (MRI) of the head was normal. Further, cervical spine MRI showed spinal cord infarction (SCI) on the right at the C1-C3 level. Three-dimensional high-resolution MRI (3D HR-MRI) volumetric isotropic turbo spin echo acquisition (VISTA) scan showed evidence of vertebral artery dissection (VAD). The patient was significantly relieved of symptoms and demonstrated negative imaging findings after therapy with anticoagulation (AC) and antiplatelets (AP) for 3 months. CONCLUSIONS: The possibility of vertebral artery dissection (VAD) should be considered in the case of young and middle-aged patients without obvious risk factors for atherosclerosis. Furthermore the VISTA black blood sequence plays an important role in the pathological diagnosis of vertebral artery stenosis. Early correct diagnosis and active therapy are crucial to the prognosis.

Central nervous system vasculopathy caused by Fabry disease: a case report.

BACKGROUND: Fabry disease is rare, and the diagnosis is often delayed. Here, we describe a case of Fabry disease resulting in vasculopathy of the central nervous system. Magnetic resonance (MR) black-blood sequence (three-dimensional T1 volumetric isotropic turbo spin echo acquisition), with the unique advantage of imaging the vascular wall, facilitated a clear identification of the vasculopathy. CASE PRESENTATION: A 27-year-old man visited our hospital for the treatment of " double vision 6d." After a series of examinations, the patient was diagnosed with Fabry disease, which caused vasculopathy of the central nervous system. Subsequently, the patient was treated with corticosteroids and his symptoms were attenuated. Two months after the initial treatment, the initial lesion in the vascular vessel disappeared, however, a new lesion appeared. Similarly, four months after the initial treatment, although the previous lesion disappeared, a new lesion appeared. CONCLUSIONS: This case highlights that clinicians should use MR black-blood sequence scan in a timely manner in case of young patients with migratory lesions of brain. In case of detection of a vascular lesion in combination with other systemic lesions, the possibility of Fabry disease should be considered.

Eagle Syndrome as a Cause of Cerebral Venous Sinus Thrombosis.

A 15-year-old teenager presented with a 2-month history of headache. Neurological examination was normal except for papilledema. Further lumbar puncture indicated intracranial hypertension (330 mm H2O). Brain magnetic resonance imaging (MRI) was normal but phase contrast-magnetic resonance venography (PC-MRV) (Figure 1(A)) suggested possible left transverse-sigmoid sinus thrombosis; subsequent contrast-enhanced 3D fat-saturated T1 volumetric isotropic turbo spin echo acquisition (VISTA) MRI (Figure 1(B)) confirmed the pathology. Hyper-coagulable panel results (including six steroid sex hormones, antithrombin III, protein C, protein S, lupus anticoagulant, and anticardiolipin antibodies) were all within normal range. In further examination, computed tomography (CT) venography images (Figure 1(C) and (D)) showed that the left jugular vein was compressed by the styloid process, consistent with Eagle syndrome.1 The patient who refused the recommended surgical treatment, however, chose anticoagulant therapy consisting of low-molecular weight heparin subcutaneous injection in addition to new oral anticoagulant. At 18-month follow-up, the patient reported no symptoms remained.

Study on the Clinical, Imaging, and Pathological Characteristics of 18 Cases with Primary Central Nervous System Vasculitis.

BACKGROUND: To summarize the characteristics of primary central nervous system vasculitis from clinical, imaging, and pathological aspects by retrospective study. METHODS: From March 2015 to December 2017, the data of the inpatients of primary central nervous system vasculitis in first Hospital of Jilin University were collected, and their clinical manifestation, imaging, and pathological characteristics were analyzed by using a descriptive method. RESULTS: There were 18 patients, 10 males (55.56%) and 8 females (44.44%) separately. The age ranges from 16 years old to 49 years old, with the median age of 32 years old. There were 8 cases (44.44%) of epileptic seizure, 6 cases (33.33%) of abnormal behavior and cognition, 10 cases (55.56%) with sensorimotor abnormalities, 4 cases (22.22%) with dizziness, 4 cases (22.22%) with headache, 2 cases (11.11%) with facial pain, 2 cases (11.11%) with blurred vision, and 2 cases (11.11%) with unstable walking. Eight patients (44.44%) were identified with cerebral spinal fluid abnormalities. There were 12 cases (66.67%) with bilateral lesions and 6 cases (33.33%) with unilateral lesions, including the frontal lobe (18 cases, 100%), the parietal lobe (10 cases, 55.56%), the temporal and occipital lobe (8 cases, 44.44%). There were 12 cases (66.67%) combined with subcortical white matter involvement, 6 cases (33.33%) combined with meningeal involvement, 2 cases (11.11%) complicated with basal ganglia involvement and 2 cases (11.11%) complicated with spinal cord involvement. Most of the lesions were with unclear border (16 cases, 88.89%), 2 cases (11.11%) were with clear border. Cortical atrophy was identified in 6 cases (33.33%). There were 12 cases (66.67%) with the enhancement of the lesions and meningeal. The 3D Vessel Wall magnetic resonance imaging (VW-MRI) showed uniform thickness in all patients (18/18) with contrast enhancement of the vessel wall of the vasculitis artery. CONCLUSIONS: The clinical manifestation and imaging in primary central nervous system vasculitis are diverse. The 3D VW-MRI could achieve quantification assessment of vasculitis and provide more utility for primary angiitis of the central nervous system.

Rapid Increase in Prevalence of Carbapenem-Resistant Enterobacteriaceae (CRE) and Emergence of Colistin Resistance Gene mcr-1 in CRE in a Hospital in Henan, China.

The global spread of carbapenem-resistant Enterobacteriaceae (CRE) is one of the most severe threats to human health in a clinical setting. The recent emergence of plasmid-mediated colistin resistance gene mcr-1 among CRE strains greatly compromises the use of colistin as a last resort for the treatment of infections caused by CRE. This study aimed to understand the current epidemiological trends and characteristics of CRE from a large hospital in Henan, the most populous province in China. From 2014 to 2016, a total of 7,249 Enterobacteriaceae isolates were collected from clinical samples, among which 18.1% (1,311/7,249) were carbapenem resistant. Carbapenem-resistant Klebsiella pneumoniae and carbapenem-resistant Escherichia coli were the two most common CRE species, with Klebsiella pneumoniae carbapenemases (KPC) and New Delhi metallo-ß-lactamases (NDM), respectively, responsible for the carbapenem resistance of the two species. Notably, >57.0% (n = 589) of the K. pneumoniae isolates from the intensive care unit were carbapenem resistant. Furthermore, blaNDM-5 and mcr-1 were found to coexist in one E. coli isolate, which exhibited resistance to almost all tested antibiotics. Overall, we observed a significant increase in the prevalence of CRE isolates during the study period and suggest that carbapenems may no longer be considered to be an effective treatment for infections caused by K. pneumoniae in the studied hospital.

Occurrence of Plasmid- and Chromosome-Carried mcr-1 in Waterborne Enterobacteriaceae in China.

The aim of this study was to investigate the prevalence of the polymyxin resistance gene mcr-1 in Enterobacteriaceae from environmental water sources in Hangzhou, China. Colistin-resistant bacteria were isolated from environmental water samples using an enrichment broth culture method, were screened for mcr-1, and then were analyzed for the location and transferability of mcr-1 Isolates positive for mcr-1 were further examined to determine their susceptibility profiles and were screened for the presence of additional resistance genes. Twenty-three mcr-1-positive isolates (16 Escherichia coli, two Citrobacter freundii, two Klebsiella oxytoca, two Citrobacter braakii, and one Enterobacter cloacae) were isolated from 7/9 sampling locations; of those, eight mcr-1-positive isolates also contained ß-lactamase-resistance genes, eight contained qnrS, and 10 contained oqx No mcr-2-positive isolates were identified. The majority of isolates demonstrated a low to moderate level of colistin resistance. Transconjugation was successfully conducted from 14 of the 23 mcr-1-positive isolates, and mcr-1 was identified on plasmids ranging from 60 to 220 kb in these isolates. Conjugation and hybridization experiments revealed that mcr-1 was chromosome-borne in only three isolates. Pulsed-field gel electrophoresis showed that the majority of E. coli isolates belonged to different clonal lineages. Multilocus sequence typing analysis revealed that sequence type 10 (ST10) was the most prevalent, followed by ST181 and ST206. This study demonstrates the utility of enrichment broth culture for identifying environmental mcr-1-positive isolates. Furthermore, it highlights the importance of responsible agriculture and clinical use of polymyxins to prevent further widespread dissemination of polymyxin-resistant pathogens.

Dissemination of the same cfr-carrying plasmid among methicillin-resistant Staphylococcus aureus and coagulase-negative staphylococcal isolates in China.

Six cfr-harboring methicillin-resistant Staphylococcus aureus (MRSA) isolates, which belonged to the same clone of sequence type 5 (ST5)-staphylococcal cassette chromosome mec element II (SCCmec II)-spa t311, were investigated in this study. Complete sequencing of a cfr-carrying plasmid, pLRSA417, revealed an 8,487-bp fragment containing a Tn4001-like transposon, cfr, orf1, and ISEnfa4. This segment, first identified in an animal plasmid, pSS-01, was observed in several plasmids from clinical coagulase-negative staphylococci in China, suggesting that the cfr gene, which might originate from livestock, was located in the same mobile element and disseminated among different clinical staphylococcal species.

Emergence of KPC-2-producing Pseudomonas aeruginosa sequence type 463 isolates in Hangzhou, China.

Thirty-nine Klebsiella pneumoniae carbapenemase (KPC)-producing Pseudomonas aeruginosa isolates, all exhibiting high-level resistance to carbapenems and other ß-lactam antibiotics, were isolated in Hangzhou, China. Molecular epidemiology analysis indicated the presence of two dominant clones, namely, clones A and B, both of which belong to sequence type 463 (ST463). A genetic environment analysis demonstrated that both clones harbor an ISKpn8 transposase, bla(KPC-2), and an ISKpn6-like transposase. These findings depict the features of clonal expansion and transmission of KPC-2-producing P. aeruginosa strains in Hangzhou, China.

Homogeneity of the vaginal microbiome at the cervix, posterior fornix, and vaginal canal in pregnant Chinese women.

The vaginal microbiome is an emerging concern in prenatal health. Because the sampling process of vaginal microbiota may pose potential risks for pregnant women, the choice of sampling site should be carefully considered. However, whether the microbial diversity is different across various sampling sites has been controversial. In the present study, three repeated swabs were collected at the cervix (C), posterior fornix (P), and vaginal canal (V) from 34 Chinese women during different pregnancy stages, and vaginal species were determined using the Illumina sequencing of 16S rRNA tag sequences. The identified microbiomes were classified into four community state types (CSTs): CST I (dominated by L. crispatus), CST II (dominated by L. gasseri), CST III (dominated by L. iners), and CST IV-A (characterized by a low abundance of Lactobacillus, but with proportions of various species previously shown to be associated with bacterial vaginosis). All individuals had consistent CST at the three sampling sites regardless of pregnancy stage and CST group. In addition, there was little heterogeneity across community structures within each individual, as determined by LEfSe, indicating high vaginal microbiome homogeneity at the three sampling sites. The present study also revealed different beta diversity during pregnancy stages. The vaginal microbiome variation among women during trimester T1 (9 ± 2.6 weeks) is larger than that of non-pregnant women and women from other trimesters, as demonstrated by the UniFrac distance (P < 0.05). In particular, the present study is the first one that demonstrates the notably difference of vaginal microbiome of postpartum women compare to women in gestation. These results will be useful for future studies of the vaginal microbiota during pregnancy.

Emergence of Escherichia coli sequence type 131 isolates producing KPC-2 carbapenemase in China.

Twenty-two KPC-2-producing Escherichia coli isolates were obtained from three hospitals in Hangzhou, China, from 2007 to 2011. One isolate, with OmpC porin deficiency, exhibited high-level carbapenem resistance. Pulsed-field gel electrophoresis showed that few isolates were indistinguishable or closely related. Multilocus sequence typing indicated that sequence type 131 (ST131) was the predominant type (9 isolates, 40.9%), followed by ST648 (5 isolates), ST405 (2 isolates), ST38 (2 isolates), and 4 single STs, ST69, ST2003, ST2179, and ST744. Phylogenetic analysis indicated that 9 group B2 isolates belonged to ST131, and 5 of 11 group D isolates belonged to ST648. Only one group B1 isolate and one group A isolate were identified. A representative plasmid (pE1) was partially sequenced, and a 7,788-bp DNA fragment encoding Tn3 transposase, Tn3 resolvase, ISKpn8 transposase, KPC-2, and ISKpn6-like transposase was obtained. The blaKPC-2-surrounding sequence was amplified by a series of primers. The PCR results showed that 13 isolates were consistent with the genetic environment in pE1. It is the first report of rapid emergence of KPC-2-producing E. coli ST131 in China. The blaKPC-2 gene of most isolates was located on a similar genetic structure.

Molecular typing of CTX-M-producing escherichia coli isolates from environmental water, swine feces, specimens from healthy humans, and human patients.

CTX-M-producing Escherichia coli is the predominant type of extended-spectrum ß-lactamase (ESBL)-producing E. coli worldwide. In this study, molecular typing was conducted for 139 CTX-M-producing E. coli isolates, phenotypically positive for ESBLs, isolated from environmental water, swine, healthy humans, and hospitalized patients in Hangzhou, China. The antibiotic resistance profiles of the isolates for the cephalosporins and fluoroquinolones were determined. The isolates showed 100% resistance to cefotaxime and ceftriaxone while maintaining relatively high susceptibility to cefoxitin, cefepime, and ceftazidime. A total of 61.9% (86/139) of the isolates, regardless of origin, showed high resistance to fluoroquinolones. PCRs and DNA sequencing indicated that blaCTX-M-14 was the most prevalent CTX-M-9 group gene and that blaCTX-M-15 and blaCTX-M-55 were the dominant CTX-M-1 group genes. Isolates from all sources with CTX-M types belonging to the CTX-M-1 or CTX-M-9 group were most frequently associated with epidemics. Molecular homology analysis of the isolates, conducted by phylogenetic grouping, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST), demonstrated that the dominant clones belonged to B2-ST131, D-ST648, D-ST38, or A-CC10. These four sequence types (STs) were discovered in E. coli isolates both from humans and from environmental water, suggesting frequent and continuous intercompartment transmission between humans and the aquatic environment. Seven novel sequence types were identified in the current study. In conclusion, this study is the first to report the molecular homology analysis of CTX-M-producing E. coli isolates collected from water, swine, and healthy and hospitalized humans, suggesting that pathogens in the environment might originate both from humans and from animals.

Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons.

BACKGROUND: Deep sequencing of the variable region of 16S rRNA genes has become the predominant tool for studying microbial ecology. As sequencing datasets have accumulated, meta-analysis of sequences obtained with different variable 16S rRNA gene targets and by different sequencing methods has become an intriguing prospect that remains to be evaluated experimentally. RESULTS: We amplified a group of fecal samples using both V4F-V6R and V6F-V6R primer sets, excised the same V6 fragment from the two sets of Illumina sequencing data, and compared the resulting data in terms of the α-diversity, ß-diversity, and community structure. Principal component analysis (PCA) comparing the microbial community structures of different datasets, including those with simulated sequencing errors, was very reliable. Procrustes analysis showed a high degree of concordance between the different datasets for both abundance-weighted and binary Jaccard distances (P < 0.05), and a meta-analysis of individual datasets resulted in similar conclusions. The Shannon's diversity index was consistent as well, with comparable values obtained for the different datasets and for the meta-analysis of different datasets. In contrast, richness estimators (OTU and Chao) varied significantly, and the meta-analysis of richness estimators was also biased. The community structures of the two datasets were obviously different and led to significant changes in the biomarkers identified by the LEfSe statistical tool. CONCLUSIONS: Our results suggest that beta-diversity analysis and Shannon's diversity are relatively reliable for meta-analysis, while community structures and biomarkers are less consistent. These results should be useful for future meta-analyses of microbiomes from different data sources.