Extensive Genetic Diversity and Epidemiological Patterns of Factor H-Binding Protein Variants among Neisseria meningitidis in China.

Factor H-binding protein (fHbp) is a virulence factor expressed by Neisseria meningitidis (N. meningitidis), the primary causative agent of invasive meningococcal disease (IMD) in humans. fHbp is utilized as the main component in vaccines to provide protection against IMD caused by serogroup B N. meningitidis. In order to comprehensively investigate the genetic diversity and epidemiological patterns of fHbp variants within isolates of Chinese N. meningitidis, we utilized the NEIS0349 locus, which encompasses the complete coding sequences of fHbp. This enabled us to identify allelic variants of fHbp with enhanced resolution. A total of 109 fHbp variants were identified in 1013 Chinese N. meningitidis isolates. We reconstructed a phylogenetic tree and analyzed the epidemiological characteristics of each variant. Considering both temporal and geographical distribution patterns, only four fHbp variants (v2.16, v2.18, v2.404, and v2.21) exhibited persistent nationwide prevalence during the previous decade (2011-2021). These variants were highly prevalent in both serogroup B strains from patients and healthy individuals, suggesting their potential as suitable vaccine candidates for nationwide implementation against IMD caused by serogroup B strains. Our study emphasizes the significance of conducting continuous surveillance of meningococcal strains to monitor the genetic diversity of fHbp for the purpose of vaccine development.

Genetic characteristics and potential pathogenic agents in Campylobacter upsaliensis based on genomic analysis.

Campylobacter upsaliensis was the most common Campylobacter species in pets' gastrointestinal tracts and has been isolated from patients with bacteremia, hemolytic-uremic syndrome, spontaneous abortion, and Guillain-Barré syndrome. However, the genetic characteristics and the full extent of its significance as a human pathogen remain to be fully understood. This study involved an investigation for genomic analysis of 154 strains from different sources and additional antimicrobial resistance profiles of 26 strains for this species. The genomes contained 1,558-1,971 CDS and the genome sizes were estimated to vary from 1.53 Mb to 1.86 Mb, with an average GC content of 34.71%. The entire analyzed genomes could be divided into three clades (A, B, and C) based on ANI and phylogenomic analysis. Significantly, nearly all strains in Clade B were isolated from patient samples, and the virulence-related sequences FlgD, GmhA, and CdtC might serve as determining factors for the classification of Clade B. Half of the tested isolates had MIC values over 64 µg mL-1 for nalidixic acid, gentamicin, and streptomycin. Isolates from pets in China carried more resistant elements in the genomes. This study both provided a comprehensive profile of C. upsaliensis for its genomic features and suggested some pathogenic agents for human infection with this species.

Identification of pneumococcal serotypes with individual recognition of vaccine types by a highly multiplexed real-time PCR-based MeltArray approach.

BACKGROUND: Pneumococcus serotyping is important for monitoring serotype epidemiology, vaccine-induced serotypes replacement and emerging pathogenic serotypes. However, the lack of high-resolution serotyping tools has hindered its widespread implementation. METHODS: We devised a single-step, multiplex real-time polymerase chain reaction (PCR)-based MeltArray approach termed PneumoSero that can identify 92 serotypes with individual recognition of 54 serotypes, including all 24 currently available vaccine types. The limit of detection (LOD) and the ability to coexisting serotypes were studied, followed by analytical evaluation using 92 reference pneumococcal strains and 125 non-pneumococcal strains, and clinical evaluation using 471 pneumococcus isolates and 46 pneumococcus-positive clinical samples. RESULTS: The LODs varied with serotypes from 50 to 100 copies per reaction and 10 % of the minor serotypes were detectable in samples containing two mixed serotypes. Analytical evaluation presented 100 % accuracy in both 92 reference pneumococcal strains and 125 non-pneumococcal strains. Clinical evaluation of 471 pneumococcus isolates displayed full concordance with Sanger sequencing results. The 46 clinical specimens yielded 45 typeable results and one untypeable result. Of the 45 typeable samples, 41 were of a single serotype and four were of mixed serotypes, all of which were confirmed by Sanger sequencing or separate PCR assays. CONCLUSION: We conclude that the PneumoSero assay can be implemented as a routine tool for pneumococcal serotyping in standard microbiology laboratories and even in clinical settings.

Genomic diversity and taxonomic marker for Arcobacter species.

Arcobacter was recognized as an emerging enteropathogen and controversies regarding its classification persisted. This study aimed to reevaluate the taxonomy of Arcobacter utilizing the 16S rRNA gene, 23S rRNA gene, single-copy orthologous genes, as well as genomic indices such as Average Nucleotide Identity (ANI) and in silico DNA-DNA hybridization (isDDH). The taxonomy of this genus was reevaluated in this study using multiple indices with a dataset of 371 genomes comprising 34 known species and 14 potentially new species. Good discrimination could be achieved only in some species but not for the species with higher sequence similarity using the comparisons of the 16S rRNA gene and 23S rRNA gene sequences. A high-accuracy phylogenomic approach for Arcobacter was established using 84 single-copy orthologous genes obtained through various bioinformatics methods. One marker gene (gene711), which was found to possess the same distinguishing ability as ANI, isDDH, and single-copy orthologous methods, was identified as a reliable locus for inferring the phylogeny of the genus. The effective species classification was achieved by employing gene711 with a sequence similarity exceeding 96%, even for species like A. cloacae, A. lanthieri, and A. skirrowii, which exhibited ambiguous classification using ANI and isDDH. Additionally, excellent subspecies categorizing among A. cryaerophilus could be distinguished using gene711. In conclusion, this framework strategy had the potential advantage of developing rapid species identification, particularly for highly variable species, providing a novel insight into the behavior and characteristics of Arcobacter.

Helicobacter zhangjianzhongii sp. nov., isolated from dog feces.

In 2019, two distinct bacterial isolates were independently isolated from the fecal samples of separate dogs in Beijing, China. These cells exhibit microaerobic, are Gram-negative, motile, and possess a characteristic spiral shape with bipolar single flagellum. They display positive results for the oxidase test while being negative for both catalase and urease. These organisms measure approximately 0.2-0.3 µm in width and 4.5-6 µm in length. The colonies are wet, flat, grey, circular, and smooth with sizes ranging from 1 to 2 mm in diameter after 2 days of growth. However, strains may exhibit variations in size and morphology following extended incubation. Phylogenetic analyses based on the 16S rRNA gene and core genome indicated that these two isolates belong to the genus Helicobacter and formed a robust clade that was remains distinctly separate from currently recognized species. These two isolates shared low dDDH relatedness and ANI values with their closest species Helicobacter canis CCUG 32756T, with these values falling below the commonly cutoff values for strains of the same species. The genomic DNA G + C contents of strain XJK30-2 were 44.93 mol%. Comparing the phenotypic and phylogenetic features between these two isolates and their closely related species, XJK30-2 represents a novel species within the genus Helicobacter, for which the name Helicobacter zhangjianzhongii sp. nov. (Type strain XJK30-2T = GDMCC 1.3695T) is proposed.

Phenotypic and Genomic Characteristics of Campylobacter gastrosuis sp. nov. Isolated from the Stomachs of Pigs in Beijing.

Campylobacter is among the four main causes of gastroenteritis worldwide. Most reported Campylobacter infections are caused by C. jejuni and C. coli. However, other emerging Campylobacter pathogens have been recognized as important pathogens in humans and animals. A novel bacterial strain, PS10T, was isolated from the gastric mucous of pigs in 2022 in Beijing, China. The cell was Gram-negative, microaerobic, motile, and negative for catalase, oxidase, and urease. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene and core genome indicated that this isolate belongs to the genus Campylobacter. There were low dDDH relatedness and ANI values shared within this strain and its closest species C. mucosalis below the cut-off values generally recognized for isolates of the same species. The draft genome size of PS10T is 2,240,910 bp in length with a percentage of DNA G+C contents of 37.72%. Comparing the phenotypic and phylogenetic features among this isolate and its related organisms, strain PS10T represents a novel species within the genus Campylobacter, for which the name Campylobacter gastrosuis sp. nov. (Type strain PS10T = GDMCC 1.3686T = JCM 35849T) is proposed.

Prevalence, genomic characterization and antimicrobial resistance of Campylobacter spp. isolates in pets in Shenzhen, China.

The prevalence of Campylobacter spp.in pets is a potential concern for human health. However, little is known about the pet-related Campylobacter spp. in China. A total of 325 fecal samples were collected from dogs, cats, and pet foxes. Campylobacter spp. were isolated by culture, and MALDI-TOF MS was used to identify 110 Campylobacter spp. isolates in total. C. upsaliensis (30.2%, 98/325), C. helveticus (2.5%, 8/325), and C. jejuni (1.2%, 4/325) were the three found species. In dogs and cats, the prevalence of Campylobacter spp. was 35.0% and 30.1%, respectively. A panel of 11 antimicrobials was used to evaluate the antimicrobial susceptibility by the agar dilution method. Among C. upsaliensis isolates, ciprofloxacin had the highest rate of resistance (94.9%), followed by nalidixic acid (77.6%) and streptomycin (60.2%). Multidrug resistance (MDR) was found in 55.1% (54/98) of the C. upsaliensis isolates. Moreover, 100 isolates, including 88 C. upsaliensis, 8 C. helveticus, and 4 C. jejuni, had their whole genomes sequenced. By blasting the sequence against the VFDB database, virulence factors were identified. In total, 100% of C. upsaliensis isolates carried the cadF, porA, pebA, cdtA, cdtB, and cdtC genes. The flaA gene was present in only 13.6% (12/88) of the isolates, while the flaB gene was absent. By analyzing the sequence against the CARD database, we found that 89.8% (79/88) of C. upsaliensis isolates had antibiotic target alteration in the gyrA gene conferring resistance to fluoroquinolone, 36.4% (32/88) had the aminoglycoside resistance gene, and 19.3% (17/88) had the tetracycline resistance gene. The phylogenetic analysis using the K-mer tree method obtained two major clades among the C. upsaliensis isolates. All eight isolates in subclade 1 possessed the gyrA gene mutation, the aminoglycoside and tetracycline resistance genes, and were phenotypically resistant to six classes of antimicrobials. It has been established that pets are a significant source of Campylobacter spp. strains and a reservoir for them. This study is the first to have documented the presence of Campylobacter spp. in pets in Shenzhen, China. In this study, C. upsaliensis of subclade 1 required additional attention due to its broad MDR phenotype and relatively high flaA gene prevalence.

Isolation and Genomic Characteristics of Cat-Borne Campylobacter felis sp. nov. and Sheep-Borne Campylobacter ovis sp. nov.

Nine novel bacterial strains were isolated from the feces of cats and sheep in 2019 and 2020 in Beijing, China. Cells were 1-3 µm long and ≤0.5 µm wide, Gram-stain negative, microaerobic, motile, oxidase positive, and urease negative. Phylogenetic analyses based on 16S rRNA gene sequences indicated that these nine isolates belong to the genus Campylobacter but formed two robust clades that were clearly separate from the currently recognized species and, respectively, isolated from the cat and sheep. Both these strains shared low 16S rRNA gene sequence similarity, dDDH relatedness, and ANI values with their closest species C. upsaliensis CCUG 14913T and C. lanienae NCTC 13004T, and against each other, which are below the cut-off values generally recognized for isolates of the same species. The genomic DNA G + C contents of type strains XJK22-1T and SYS25-1T were 34.99 mol% and 32.43 mol%, respectively. Electron microscopy showed that these cells were spiral shaped, with bipolar single flagella. Based on results from genotypic, phenotypic, phylogenetic, and phylogenomic analyses, these nine strains represent two novel species within the genus Campylobacter, for which the names Campylobacter felis sp. nov. (Type strain XJK22-1T = GDMCC 1.3684T = JCM 35847T) and Campylobacter ovis sp. nov. (Type strain SYS25-1T = GDMCC 1.3685T) are proposed.

A novel adaptive cubic quasi-Newton optimizer for deep learning based medical image analysis tasks, validated on detection of COVID-19 and segmentation for COVID-19 lung infection, liver tumor, and optic disc/cup.

BACKGROUND: Most of existing deep learning research in medical image analysis is focused on networks with stronger performance. These networks have achieved success, while their architectures are complex and even contain massive parameters ranging from thousands to millions in numbers. The nature of high dimension and nonconvex makes it easy to train a suboptimal model through the popular stochastic first-order optimizers, which only use gradient information. PURPOSE: Our purpose is to design an adaptive cubic quasi-Newton optimizer, which could help to escape from suboptimal solution and improve the performance of deep neural networks on four medical image analysis tasks including: detection of COVID-19, COVID-19 lung infection segmentation, liver tumor segmentation, optic disc/cup segmentation. METHODS: In this work, we introduce a novel adaptive cubic quasi-Newton optimizer with high-order moment (termed ACQN-H) for medical image analysis. The optimizer dynamically captures the curvature of the loss function by diagonally approximated Hessian and the norm of difference between previous two estimates, which helps to escape from saddle points more efficiently. In addition, to reduce the variance introduced by the stochastic nature of the problem, ACQN-H hires high-order moment through exponential moving average on iteratively calculated approximated Hessian matrix. Extensive experiments are performed to access the performance of ACQN-H. These include detection of COVID-19 using COVID-Net on dataset COVID-chestxray, which contains 16 565 training samples and 1841 test samples; COVID-19 lung infection segmentation using Inf-Net on COVID-CT, which contains 45, 5, and 5 computer tomography (CT) images for training, validation, and testing, respectively; liver tumor segmentation using ResUNet on LiTS2017, which consists of 50 622 abdominal scan images for training and 26 608 images for testing; optic disc/cup segmentation using MRNet on RIGA, which has 655 color fundus images for training and 95 for testing. The results are compared with commonly used stochastic first-order optimizers such as Adam, SGD, and AdaBound, and recently proposed stochastic quasi-Newton optimizer Apollo. In task detection of COVID-19, we use classification accuracy as the evaluation metric. For the other three medical image segmentation tasks, seven commonly used evaluation metrics are utilized, that is, Dice, structure measure, enhanced-alignment measure (EM), mean absolute error (MAE), intersection over union (IoU), true positive rate (TPR), and true negative rate. RESULTS: Experiments on four tasks show that ACQN-H achieves improvements over other stochastic optimizers: (1) comparing with AdaBound, ACQN-H achieves 0.49%, 0.11%, and 0.70% higher accuracy on the COVID-chestxray dataset using network COVID-Net with VGG16, ResNet50 and DenseNet121 as backbones, respectively; (2) ACQN-H has the best scores in terms of evaluation metrics Dice, TPR, EM, and MAE on COVID-CT dataset using network Inf-Net. Particularly, ACQN-H achieves 1.0% better Dice as compared to Apollo; (3) ACQN-H achieves the best results on LiTS2017 dataset using network ResUNet, and outperforms Adam in terms of Dice by 2.3%; (4) ACQN-H improves the performance of network MRNet on RIGA dataset, and achieves 0.5% and 1.0% better scores on cup segmentation for Dice and IoU, respectively, compared with SGD. We also present fivefold validation results of four tasks. It can be found that the results on detection of COVID-19, liver tumor segmentation and optic disc/cup segmentation can achieve high performance with low variance. For COVID-19 lung infection segmentation, the variance on test set is much larger than on validation set, which may due to small size of dataset. CONCLUSIONS: The proposed optimizer ACQN-H has been validated on four medical image analysis tasks including: detection of COVID-19 using COVID-Net on COVID-chestxray, COVID-19 lung infection segmentation using Inf-Net on COVID-CT, liver tumor segmentation using ResUNet on LiTS2017, optic disc/cup segmentation using MRNet on RIGA. Experiments show that ACQN-H can achieve some performance improvement. Moreover, the work is expected to boost the performance of existing deep learning networks in medical image analysis.

A Large Acute Gastroenteritis Outbreak Associated with Both Campylobacter coli and Human Sapovirus - Beijing Municipality, China, 2021.

What is already known about this topic?: Campylobacter is a significant foodborne pathogen that leads to global outbreaks of acute gastroenteritis (AGE) usually affecting less than 30 individuals. Human sapovirus (HuSaV) is an enteric virus responsible for sporadic cases and outbreaks of AGE worldwide. In a study conducted in Beijing, HuSaV detection ranked second after norovirus. What is added by this report?: We present a discussion of the first large-scale outbreak of AGE caused by both Campylobacter coli (C. coli) and HuSaV. The outbreak involved a total of 996 patients and exhibited two distinct peaks over a period of 17 days. Through case-control studies, we identified exposure to raw water from a secondary water supply system as a significant risk factor. Among 83 patients, 49 samples tested positive for C. coli, 39 samples tested positive for HuSaV, and 27 samples tested positive for both pathogens using real-time polymerase chain reaction detection. Furthermore, whole-genome sequencing of 17 C. coli isolates obtained from 17 patients revealed that all isolates belonged to a highly clonal strain of C. coli. What are the implications for public health practice?: Outbreaks of AGE resulting from multiple pathogen infections warrant increased attention. This report emphasizes the significance of ensuring the safety of drinking water, particularly in secondary supply systems.

Genetic characteristics, antimicrobial resistance, and prevalence of Arcobacter spp. isolated from various sources in Shenzhen, China.

Arcobacter spp. is a globally emerging zoonotic and foodborne pathogen. However, little is known about its prevalence and antimicrobial resistance in China. To investigate the prevalence of Arcobacter spp. isolated from various sources, 396 samples were collected from human feces, chicken cecum, and food specimens including chicken meat, beef, pork, lettuce, and seafood. Arcobacter spp. was isolated by the membrane filtration method. For 92 strains, the agar dilution method and next-generation sequencing were used to investigate their antimicrobial resistance and to obtain whole genome data, respectively. The virulence factor database (VFDB) was queried to identify virulence genes. ResFinder and the Comprehensive Antibiotic Resistance Database (CARD) were used to predict resistance genes. A phylogenetic tree was constructed using the maximum likelihood (ML) method with core single-nucleotide polymorphisms (SNPs). We found that 27.5% of the samples (n = 109) were positive for Arcobacter spp., comprising Arcobacter butzleri (53.0%), Arcobacter cryaerophilus (39.6%), and Arcobacter skirrowii (7.4%). Chicken meat had the highest prevalence (81.2%), followed by seafood (51.9%), pork (43.3%), beef (36.7%), lettuce (35.5%), chicken cecum (8%), and human fecal samples (0%, 0/159). Antimicrobial susceptibility tests revealed that 51 A. butzleri and 40 A. cryaerophilus strains were resistant to streptomycin (98.1, 70%), clindamycin (94.1, 90%), tetracycline (64.7, 52.5%), azithromycin (43.1%, 15%), nalidixic acid (33.4, 35%), and ciprofloxacin (31.3, 35%) but were susceptible to erythromycin, gentamicin, chloramphenicol, telithromycin, and clindamycin (≤10%). A. skirrowii was sensitive to all experimental antibiotics. The virulence factors tlyA, mviN, cj1349, ciaB, and pldA were carried by all Arcobacter spp. strains at 100%, and the following percentages were cadF (95.7%), iroE (23.9%), hecB (2.2%), hecA, and irgA (1.1%). Only one A. butzleri strain (F061-2G) carried a macrolide resistance gene (ereA). One A. butzleri and one A. cryaerophilus harbored resistance island gene clusters, which were isolated from pork and chicken. Phylogenetic tree analysis revealed that A. butzleri, A. cryaerophilus, and A. skirrowii were separated from each other. To our knowledge, this is the first report of the isolation of Arcobacter spp. from vegetables and seafood in China. The resistance island gene cluster found in pork and chicken meat and the presence of virulence factors could be a potential risk to human health.

Species classification and novel plasmid identifications in Arcobacter cryaerophilus and Arcobacter cryaerophilus-like organisms.

The Arcobacter is a globally emerging foodborne and zoonotic pathogen that can cause diarrhea in humans. It is relatively homogenous and clearly distinguishes the group from other Epsilonproteobacteria. Arcobacter cryaerophilus (A. cryaerophilus) is a heterogeneous species and little is known about its genomic characterization in China. This study aims to determine the genetic and plasmid features of A. cryaerophilus based on whole-genome sequence (WGS). Average Nucleotide Identity (ANI) and in silico DNA-DNA hybridization (isDDH) were used for the species classification for 90 initially identified A. cryaerophilus strains. One complete genome and 42 draft genomes were obtained by whole genome sequencing. The genomic characteristics were determined using various bioinformatics software. The genomes of the strains examined were estimated to vary from 1.81 to 2.28 Mb in length, with a G + C content of around 27%. ANI and isDDH results indicated that 90 initially identified A. cryaerophilus strains should be reclassified into four new species (ANI > 96% or isDDH > 70%). Two clades (four subclades) were identified among 90 genomes with the phylogenetic analysis. The phylogenetic tree indicated these 90 genomes exhibited a high intra-species genomic diversity. No clustering was assorted with the host or geographic location among these genomes. Aminoglycoside resistance genes, such as aph(2'')-Ih, AAC(6')-Ie-APH(2'')-Ia, aac(6')-IIa, ant(6), and streptothricin resistance gene SAT-4 were detected in the chromosomes from a third of the Chinese strains. Virulence-related genes were identified in all the sequenced strains. A novel large multiple drug-resistant plasmid (named pCNAC48 with 161,992 bp in length) was identified in strain ICDCAC48. Two antibiotic-resistance islands were found in the plasmid with lengths of 7,950 and 25,137 bp and G + C content of 38.23 and 32.39%, respectively. The drug resistance genes and some transposable elements were cross-distributed among the islands in the plasmid. Antimicrobial susceptibility tests indicated these resistance genes in the plasmid were functional. Plasmid conjugation and curing experiments proved pCNAC48 was stable in strain ICDCAC48. It was the first identified multiple drug resistance plasmid in A. cryaerophilus-like.

Estrogen Suppresses Cytokines Release in cc4821 Neisseria meningitidis Infection via TLR4 and ERß-p38-MAPK Pathway.

Estrogen has long been known to possess immune-modulatory effects in diseases, and multiple pathological conditions show great sex disparities. However, the impact of estrogen in Neisseria meningitidis infection has not been determined. The present study aimed to investigate the role of estrogen in N. meningitidis infection and the molecular mechanism. We selected 35 N. meningitidis isolates representing different clonal complexes (cc), serogroups, and isolation sources to infect the HBMEC cell line. Results showed that the expression of estrogen receptor (ER) ß in N. meningitidis-infected cells was downregulated compared with that in normal cells. The expression of ERß induced by invasive isolates was lower than that in carriers. Serogroup C isolates induced the lowest expression of ERß compared with serogroup A and B isolates. We used four cc4821 N. meningitidis isolates to infect two kinds of host cells (human brain microvascular endothelial cells and meningeal epithelial cells). The results showed that 17 ß-estradiol (E2) could inhibit the release of inflammatory factors interleukin (IL)-6, IL-8, and tumor necrosis factor-α after N. meningitidis infection via TLR4. E2 could inhibit the activation of the p38-MAPK signal pathway induced by N. meningitidis infection through binding to ERß, and significantly inhibit the release of inflammatory factors in N. meningitidis-infected host cells. This study demonstrated that estrogen plays a protective role in N. meningitidis infection. ERß is potentially associated with the release of inflammatory cytokines in N. meningitidis infection, which sheds light on a possible therapeutic strategy for the treatment of invasive diseases caused by N. meningitidis.

Two-Stage CNN Model for Joint Demosaicing and Denoising of Burst Bayer Images.

In the classical image processing pipeline, demosaicing and denoising are separated steps that may interfere with each other. Joint demosaicing and denoising utilizes the shared image prior information to guide the image recovery process. It is expected to have better performance by the joint optimization of the two problems. Besides, learning recovered images from burst (continuous exposure images) can further improve image details. This article proposes a two-stage convolutional neural network model for joint demosaicing and denoising of burst Bayer images. The proposed CNN model consists of a single-frame joint demosaicing and denoising module, a multiframe denoising module, and an optional noise estimation module. It requires a two-stage training scheme to ensure that the model converges to a good solution. Experiments on multiframe Bayer images with simulated Gaussian noise show that the proposed method has obvious performance advantages and speed advantages compared with similar approaches. Experiments on actual multiframe Bayer images verify the denoising effect and detail retention ability of the proposed method.

AdaCN: An Adaptive Cubic Newton Method for Nonconvex Stochastic Optimization.

In this work, we introduce AdaCN, a novel adaptive cubic Newton method for nonconvex stochastic optimization. AdaCN dynamically captures the curvature of the loss landscape by diagonally approximated Hessian plus the norm of difference between previous two estimates. It only requires at most first order gradients and updates with linear complexity for both time and memory. In order to reduce the variance introduced by the stochastic nature of the problem, AdaCN hires the first and second moment to implement and exponential moving average on iteratively updated stochastic gradients and approximated stochastic Hessians, respectively. We validate AdaCN in extensive experiments, showing that it outperforms other stochastic first order methods (including SGD, Adam, and AdaBound) and stochastic quasi-Newton method (i.e., Apollo), in terms of both convergence speed and generalization performance.

Geographic distribution of the cagA, vacA, iceA, oipA and dupA genes of Helicobacter pylori strains isolated in China.

BACKGROUND: There are geographic variations in the genotypes of Helicobacter pylori (H. pylori) cagA, vacA, iceA, oipA and dupA. The aim of the study was to investigate the distribution of these genotypes among H. pylori strains from five regions of China and their association with clinical outcomes. MATERIALS AND METHODS: Gastric biopsy specimens were obtained from 348 patients with different gastrointestinal diseases in the five regions of China. The regional distribution was 89 patients from Shandong, 91 from Guangxi, 57 from Hunan, 58 from Qinghai and 53 from Heilongjiang. The presence of cagA, vacA, iceA, oipA and dupA genotypes was determined by polymerase chain reaction (PCR) from H. pylori DNA. RESULTS: A total of 269 H. pylori isolates were obtained, of which 74 isolates were from Shandong, 78 from Guangxi, 46 from Hunan, 33 from Qinghai and 38 from Heilongjiang. The cagA-positive status was predominant in the five regions. The predominant vacA genotypes were s1c (73.4%), m2 (70.6%) and i1 (92.9%). In strains from Shandong, s1a and m1 were dominant. By contrast, s1c was dominant in Guangxi and i1 was dominant in Hunan and Heilongjiang. The prevalence of m2 subtype in Qinghai (78.8%) was significantly higher than that in other regions (P < 0.05). The predominant iceA genotype was iceA1 and the frequency of iceA1 was significantly more prevalent in Hunan than in other regions (P < 0.05). The oipA status "on" gene was more frequent in Shandong (91.9%) and Guangxi (91%) than in Heilongjiang (71.7%) (P < 0.05). Conversely, the dupA-positive status was less than half in Shandong (31.1%) and Guangxi (15.4%), whereas it was 73.9% in Hunan and 81.8% in Qinghai (P < 0.001). There were no significant associations between the cagA, vacA, iceA, oipA genotypes and clinical outcomes. The dupA-positive strains were more common in peptic ulcer disease (PUD) patients than in non-ulcer dyspepsia (NUD) patients in Shandong and Guangxi (P < 0.05), but the association was not observed in other geographic regions. CONCLUSIONS: There was significant geographic diversity of H. pylori genotypes in different regions of China and the presence of dupA gene can be considered as a marker for the development of gastroduodenal diseases. However, the cagA, iceA, vacA and oipA genes cannot be regarded for prediction of the clinical presentation of H. pylori infection in China.

Genetic and Transcriptomic Variations for Amoxicillin Resistance in Helicobacter pylori under Cryopreservation.

Some amoxicillin-resistant strains of H. pylori show a sharp decrease in amoxicillin resistance after freezing. In China, most clinical gastric mucosal specimens are frozen and transported for isolation and drug susceptibility testing for H. pylori, which may lead to an underestimation of the amoxicillin resistance. The objective of this study is to investigated reasons for the decreased amoxicillin resistance after cryopreservation. A high-level amoxicillin-resistant clone (NX24r) was obtained through amoxicillin pressure screening. After cryopreservation at -80 °C for 3 months, the minimum inhibitory concentration (MIC) of NX24r was reduced sharply. Mutations and changes of transcriptome were analyzed after amoxicillin screening and cryopreservation. Mutations in PBP1 (I370T, E428K, T556S) and HefC (M337K, L378F, D976V) were detected in NX24r, which may be the main reason for the induced amoxicillin resistance. No mutations were found in PBP1 or HefC after cryopreservation. However, transcriptome analysis showed that down-regulated genes in the cryopreserved clone were significantly enriched in plasma membrane (GO:0005886), including lepB, secD, gluP, hp0871 and hp1071. These plasma membrane genes are involved in the biosynthesis and transport function of the membrane. The decreased amoxicillin resistance after cryopreservation may be related to the down-regulation of genes involved in membrane structure and transport function.

Diversity of 3' variable region of cagA gene in Helicobacter pylori strains isolated from Chinese population.

BACKGROUND: The cytotoxin-associated gene A (cagA) is one of the most important virulence factors of Helicobacter pylori (H. pylori). There is a highly polymorphic Glu-Pro-Ile-Tyr-Ala (EPIYA) repeat region in the C-terminal of CagA protein. This repeat region is thought to play an important role in the pathogenesis of gastrointestinal diseases. The aim of this study was to investigate the diversity of cagA 3' variable region and the amino acid polymorphisms in the EPIYA segments of the CagA C-terminal region of H. pylori, and their association with gastroduodenal diseases. METHODS: A total of 515 H. pylori strains from patients in 14 different geographical regions of China were collected. The genomic DNA from each strain was extracted and the cagA 3' variable region was amplified by polymerase chain reaction (PCR). The PCR products were sequenced and analyzed using MEGA 7.0 software. RESULTS: A total of 503 (97.7%) H. pylori strains were cagA-positive and 1,587 EPIYA motifs were identified, including 12 types of EPIYA or EPIYA-like sequences. In addition to the four reported major segments, several rare segments (e.g., B', B″ and D') were defined and 20 different sequence types (e.g., ABD, ABC) were found in our study. A total of 481 (95.6%) strains carried the East Asian type CagA, and the ABD subtypes were most prevalent (82.1%). Only 22 strains carried the Western type CagA, which included AC, ABC, ABCC and ABCCCC subtypes. The CagA-ABD subtype had statistical difference in different geographical regions (P = 0.006). There were seven amino acid polymorphisms in the sequences surrounding the EPIYA motifs, among which amino acids 893 and 894 had a statistical difference with gastric cancer (P = 0.004). CONCLUSIONS: In this study, 503 CagA sequences were studied and analyzed in depth. In Chinese population, most H. pylori strains were of the CagA-ABD subtype and its presence was associated with gastroduodenal diseases. Amino acid polymorphisms at residues 893 and 894 flanking the EPIYA motifs had a statistically significant association with gastric cancer.

Alterations of Fucosyltransferase Genes and Fucosylated Glycans in Gastric Epithelial Cells Infected with Helicobacter pylori.

Helicobacter pylori (H. pylori) adhesion to human gastric epithelial cells is closely linked with fucosylated glycans. Therefore, investigation of fucosylation in the interaction of gastric epithelial cells with H. pylori is critical. In this study we used lectin microarrays to detect the expression of fucosylated glycans in gastric epithelial cells (GES-1) infected with H. pylori strains isolated from patients with different diseases including chronic gastritis, duodenal ulcers, and gastric cancer (each containing two strains) at 4 h. In addition, we investigated the time-course expression of fucosyltransferase (FUT) 1-6 genes in GES-1 cells stimulated with H. pylori strains at 0.5-8 h. At 4 h post-infection, Lotus, AAA, BC2LCN, PA-IIL, CNL and ACG lectins had increased signals in H. pylori-infected GES-1 cells compared to uninfected cells. Higher expression of FUT1 and FUT2 was detected in all H. pylori-infected GES-1 cells within 2 h, regardless of the H. pylori strain. In particular, the expression of FUT2 was higher in H. pylori-infected GES-1 cells with a higher fold change in levels of BC2LCN lectin specific to α1-2 linked fucose (Fuc) at 4 h. The results suggest that the high levels of α1, 2-linked Fuc synthesized by FUT1/2, might play a role in the preliminary stage of H. pylori infection. This provides us with pivotal information to understand the adhesion of H. pylori to human gastric epithelial cells.

Comparative genomics of Helicobacter pullorum from different countries.

BACKGROUND: Helicobacter pullorum commonly colonized in the gastrointestinal tract of poultry and caused gastroenteritis. This bacterium could be transmitted to humans through contaminated food and caused colitis and hepatitis. Currently, the genetic characteristics of the H. pullorum were not recognized enough. In this study, the genomes of 23 H. pullorum strains from different counties were comparatively analyzed. Among them, H. pullorum 2013BJHL was the first isolated and reported in China. RESULTS: The genomes of the studied strains were estimated to vary from 1.55 to 2.03 Mb, with a GC content of ~ 34%. 4064 pan genes and 1267 core genes were obtained from the core-pan genome analysis using the Roary pipeline. Core genome SNPs (cg-SNPs) were obtained using Snippy4 software. Two groups were identified with the phylogenetic analysis based on the cg-SNPs. Some adhesion-related, immune regulation, motility-related, antiphagocytosis-related, toxin-related and quorum sensing related genes were identified as virulence factors. APH(3')-IIIa, APH(2'')-If, and AAC(6')-Ie-APH(2'')-Ia were identified as antibiotic resistance genes among the H. pullorum genomes. cat, SAT-4 and tetO genes were only identified in 2013BJHL, and tet(C) was identified in MIT98-5489. MIC determination revealed that the 2013BJHL showed acquired resistance to ciprofloxacin, nalidixic acid, tetracycline, gentamicin, streptomycin and erythromycin, only sensitive to ampicillin. The antibiotic resistance genetic determinants on the 2013BJHL genome correlate well with observed antimicrobial susceptibility patterns. Two types of VI secretion system (T6SS) were identified in 52.2% (12/23) the studied strains. CONCLUSION: In this study, we obtained the genetic characteristics of H. pullorum from different sources in the world. The comprehensive genetic characteristics of H. pullorum were first described. H. pullorum showed highly genetic diversity and two sub-types of T6SSs were first identified in H. pullorum. 2013BJHL was found to be multidrug resistant as it was resistant to at least three different antibiotic classes.