copA Gene Research Articles

Microbial fuel cell-assisted composting yields higher performance on metals passivation, antibiotics degradation, and resistance genes removal

Little scientific evidence on metal passivation, antibiotic degradation and resistance genes removal, is available under autogenetic electrochemical reactions during composting process. This study established microbial fuel cell (MFC)-assisted composting procedure to ascertain the removal performance and detoxification mechanisms involving metals, antibiotics and their resistance genes. Compared to control treatment, the bioavailability of zinc (Zn) and copper (Cu) in MFC-assisted treatment decreased by 7.8% and 26.9%, while the content of tetracycline (TCL) and oxytetracycline (OCL) reduced by 100% and 89%, respectively. Organics mineralization and humification were responsible for 80% and 70% of the variations in metal passivation and antibiotic degradation during composting process. A decrease of 54% was found for tetW gene, while copA gene increased by 42% in MFC-assisted composting treatment. These findings highlight the detoxification mechanisms underlying metal passivation and antibiotic degradation during composting process, and potentially offer valuable insights for environmental source protection and agricultural sustainable development.

A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application

BackgroundStructural variants (SVs) such as deletions, duplications, and insertions are known to contribute to phenotypic variation but remain challenging to identify and genotype. A more complete, accessible, and assessable collection of SVs will assist efforts to study SV function in cattle and to incorporate SV genotyping into animal evaluation.ResultsIn this work we produced a large and deeply characterized collection of SVs in Holstein cattle using two popular SV callers (Manta and Smoove) and publicly available Illumina whole-genome sequence (WGS) read sets from 310 samples (290 male, 20 female, mean 20X coverage). Manta and Smoove identified 31 K and 68 K SVs, respectively. In total the SVs cover 5% (Manta) and 6% (Smoove) of the reference genome, in contrast to the 1% impacted by SNPs and indels. SV genotypes from each caller were confirmed to accurately recapitulate animal relationships estimated using WGS SNP genotypes from the same dataset, with Manta genotypes outperforming Smoove, and deletions outperforming duplications. To support efforts to link the SVs to phenotypic variation, overlapping and tag SNPs were identified for each SV, using genotype sets extracted from the WGS results corresponding to two bovine SNP chips (BovineSNP50 and BovineHD). 9% (Manta) and 11% (Smoove) of the SVs were found to have overlapping BovineHD panel SNPs, while 21% (Manta) and 9% (Smoove) have BovineHD panel tag SNPs. A custom interactive database (https://svdb-dc.pslab.ca) containing the identified sequence variants with extensive annotations, gene feature information, and BAM file content for all SVs was created to enable the evaluation and prioritization of SVs for further study. Illustrative examples involving the genes POPDC3, ORM1, G2E3, FANCI, TFB1M, FOXC2, N4BP2, GSTA3, and COPA show how this resource can be used to find well-supported genic SVs, determine SV breakpoints, design genotyping approaches, and identify processed pseudogenes masquerading as deletions.ConclusionsThe resources developed through this study can be used to explore sequence variation in Holstein cattle and to develop strategies for studying SVs of interest. The lack of overlapping and tag SNPs from commonly used SNP chips for most of the SVs suggests that other genotyping approaches will be needed (for example direct genotyping) to understand their potential contributions to phenotype. The included SV genotype assessments point to challenges in characterizing SVs, especially duplications, using short-read data and support ongoing efforts to better characterize cattle genomes through long-read sequencing. Lastly, the identification of previously known functional SVs and additional CDS-overlapping SVs supports the phenotypic relevance of this dataset.

Establishment of a human induced pluripotent stem cell line (NIHTVBi031-A) derived from a COPA syndrome patient with a heterozygous p.Ala239Pro mutation

We have successfully generated human induced pluripotent stem cells (hiPSC) from peripheral blood mononuclear cells (PBMCs) of a patient with COPA Syndrome. The patient, a 6 year old Caucasian male, has a spontaneous de novo missense mutation that replaced alanine with proline in the COPA gene. This paper confirms the differentiation potential of the hiPSC line, the presence of the p.Ala239Pro mutation, and the expression of typical pluripotency markers within the hiPSC line. The hiPSC line is ready for use as a cellular model of COPA Syndrome.

Isolation, identification, antibiotic resistance profile and molecular analysis of Ornithobacterium rhinotracheal isolates from turkeys.

Ornithobacterium rhinotracheal (ORT) infects numerous birds, particularly chickens and turkeys. ORT is an emerging bacterial pathogen of global concern in the poultry industry. As ORT is rapidly spreading throughout commercial poultry, it requires intensive studies of its epidemiology, diagnostic procedures, molecular typing, virulence genes and antimicrobial resistance. The present study was conducted in isolation and identification of ORT from slaughtered turkeys. Cleft palate swabs of 200 were collected from slaughtered turkeys and cultured on blood agar. ORT was characterized using biochemical tests and PCR targeting the ORT 16S rRNA gene. Virulence genes of isolates were determined targeting adenylate kinase (adk), copA and virulence-associated protein D (vapD) genes. Additionally, diversity of ORT isolates was performed by enterobacterial repetitive intergenic consensus (ERIC) and RAPD PCR. Disk diffusion was used to determine the antibiotic sensitivity of the isolates. ORT was identified in 23 (11.5%) samples using both the biochemical tests and PCR. The result of detecting virulence genes showed that all the isolates (23: 100%) had the adk gene, whereas two (8.7%) isolates had the copA gene, and seven (30.43%) isolates had the vapD gene. Molecular typing of isolates revealed 21 different patterns by RAPD PCR assay using M13 primer and 20 distinct patterns by ERIC PCR test. Both ERIC and RAPD PCR were distinctive methods for investigating the genetic diversity of ORT isolates. The antibiotic resistance test showed that 18 (78.26%) isolates were resistant to gentamicin, amikacin, cefazolin, streptomycin and penicillin. All isolates (100%) were resistant to cloxacillin and fosfomycin. This study showed the prevalence of ORT in turkey and high resistance of this bacterium to many common veterinary antibiotics. Moreover, both ERIC and RAPD PCR are distinctive methods for investigating the genetic diversity of ORT isolates. These data may help monitor antibiotic resistance and typing of ORT in epidemiological studies and serve as the foundation for designing region-specific vaccines for future use.

Comparison of Copper-Tolerance Genes between Different Groups of Acidovorax citrulli.

Acidovorax citrulli populations exhibit genetic and phenotypic variations, particularly in terms of copper tolerance. Group I strains of A. citrulli generally exhibit higher copper tolerance compared to group II strains. This study aims to identify genes involved in copper tolerance to better understand the differences in copper tolerance between group I and group II strains. Representative strains pslb65 (group I) and pslbtw14 (group II) were selected for comparison. Deletion mutants of putative copper-tolerance genes and their corresponding complementary strains were constructed. The copper tolerance of each strain was evaluated using the minimum inhibitory concentration method. The results showed that the copA, copZ, cueR, and cueO genes played major roles in copper tolerance in A. citrulli, while cusC-like, cusA-like, and cusB-like genes had minor effects. The different expression levels of copper-tolerance-related genes in pslb65 and pslbtw14 under copper stress indicated that they had different mechanisms for coping with copper stress. Overall, this study provides insights into the mechanisms of copper tolerance in A. citrulli and highlights the importance of specific genes in copper tolerance.

Bacteria populating freshly appeared supraglacial lake possess metals and antibiotic-resistant genes

Antibiotic resistance (AR) has been extensively studied in natural habitats and clinical applications. AR is mainly reported with the use and misuse of antibiotics; however, little is known about its presence in antibiotic-free remote supraglacial lake environments. This study evaluated bacterial strains isolated from supraglacial lake debris and meltwater in Dook Pal Glacier, northern Pakistan, for antibiotic-resistant genes (ARGs) and metal-tolerant genes (MTGs) using conventional PCR. Several distinct ARGs were reported in the bacterial strains isolated from lake debris (92.5%) and meltwater (100%). In lake debris, 57.5% of isolates harbored the blaTEM gene, whereas 58.3% of isolates in meltwater possessed blaTEM and qnrA each. Among the ARGs, qnrA was dominant in debris isolates (19%), whereas in meltwater isolates, qnrA (15.2%) and blaTEM (15.2%) were dominant. ARGs were widely distributed among the bacterial isolates and different bacteria shared similar types of ARGs. Relatively greater number of ARGs were reported in Gram-negative bacterial strains. In addition, 92.5% of bacterial isolates from lake debris and 83.3% of isolates from meltwater harbored MTGs. Gene copA was dominant in meltwater isolates (50%), whereas czcA was greater in debris bacterial isolates (45%). Among the MTGs, czcA (18.75%) was dominant in debris strains, whereas copA (26.0%) was greater in meltwater isolates. This presents the co-occurrence and co-selection of MTGs and ARGs in a freshly appeared supraglacial lake. The same ARGs and MTGs were present in different bacteria, exhibiting horizontal gene transfer (HGT). Both positive and negative correlations were determined between ARGs and MTGs. The research provides insights into the existence of MTGs and ARGs in bacterial strains isolated from remote supraglacial lake environments, signifying the need for a more detailed study of bacteria harboring ARGs and MTGs in supraglacial lakes.

Prevalence of the copA Gene in Escherichia coli Isolated from Common Carp in Sulaymaniyah Province

Prevalence of the copA Gene in Escherichia coli Isolated from Common Carp in Sulaymaniyah Province

The Prevalence of some Heavy Metal Resistance Genes in Pseudomonas aeruginosa Isolated from Hospital Environments

Metal resistance genes were phenotyped in a group of 31 Pseudomonas aeruginosa strains gathered from medical facilities, such as clinical and environmental samples. The strains were evaluated for resistance based on their origin and the likelihood of exposure to heavy metals and chemicals. To determine the presence of metal resistance-encoding genes, PCR was conducted using specific primers for copA, copB, czcA, and merA. Positive amplification signals were obtained for copA, copB, and czcA genes in all 5 (100.0%) strains gathered from clinical samples, while the merA gene was detected in only 40% of strains found in clinical specimens. Metal resistance genes were found in all 7 (100.00%) environmental sample isolates for czcA and in 6 (85.7%) for copA and copB. Unfortunately, none of the environmental isolate amplified with merA. The current isolates containing resistance-encoding genes suggest a possible correlation to gaining resistance traits from external determinants.

Study of Copper Resistant Pseudomonas Strains Isolated from Soil in Sarcheshmeh Copper Mine, in Iran and Investigation of the Mechanisms Involved in Copper Resistance

Heavy metal contaminated sites are the potential source of metal resistance microorganisms. The major focus of this study is to isolate and identify copper ions resistant Pseudomonas from the soil samples collected from mining and refining sites of Sarcheshmeh copper mine in the Kerman Province of Iran and investigate on possible mechanisms for copper resistance. Isolates were selected based on high level of copper ions resistance. The screened isolate was identified as Pseudomonas putida Cu-2 by morphological, biochemical and 16S rDNA gene sequencing analysis. A high degree of copper ions resistance associated with multiple antibiotic resistances was also detected in the screened isolate. The growth pattern of screened isolate with all the studied Cu concentrations was similar to that of control (without Cu ions) indicating that Cu ions would not affect the growth of isolated strain. A decrease in the amount of exopolysaccharides (EPS) was detected after Cu ions – P. Putida Cu-2 culture supernatant interaction. The Fourier transform infrared spectroscopy (FT-IR) peaks for the EPS extracted from the bacterial culture supernatant and the interacted Cu ions were nearly similar. The EPS covering of the Cu ions was established by FT-IR. The study of bacterial EPS covered Cu ions with E. coli PTCC 1338 and S. aureus PTCC 1113 exhibited less toxicity compared to uncoated Cu ions. The presence of copA gene that encodes for the multi-copper oxidase was investigated in the selected strain. The present study suggests that the capping of Cu ions by bacterially produced EPS and the presence of copA gene serve as the probable mechanisms of copper resistance.

Evaluating clinical factors for improved utilization of targeted gene panel testing for inborn errors of immunity in a U.S. tertiary care pediatric hospital

RationaleThere has been an increased use of targeted gene panels to evaluate inborn errors of immunity (IEI) due to increased availability and reduced costs. Refinements to clinical indications for targeted gene panels may improve yields for the test. MethodA retrospective chart review on 140 patients aged ≤18 years old with suspected IEI who had clinical targeted gene panel testing (Invitae®) for primary immune deficiency at a tertiary pediatric hospital in the U.S. Relevant clinical information and basic immunology labs, consisting of complete blood count, immunoglobulins, vaccine titers, immune competence, and other relevant lab tests, were evaluated. Additional patients with targeted gene panels sent over the course of 5 years are being reviewed to confirm these initial findings. ResultOf 140 patients (median age 3.9 years [IQR 1.6–9.5], 62% male, 85% Caucasian suspected of IEI and had the targeted gene panel sent, 9% had positive findings that led to a change in diagnosis and/or treatment plan. The most common indications for IEI workups in our cohort were infections (37%), organ-specific inflammation (30%), and periodic fevers (17%), Table 1. Of 52 patients with infections, 3 had pathogenic, or likely pathogenic variants in TNFRSF13B, CD40LG, and XLA genes. All patients with infections and normal clinical-based immunology testing had negative gene panels. Only one patient with organ-specific inflammation had a variant in STAT3 explaining her clinical features. Of 10 patients presenting with systemic autoimmune disease or polyautoimmunity, 5 had positive findings (STAT5B, TNFAIP3, NLRP12, COPA, and NLRC4 genes). Two of 24 patients with periodic fevers had variants in TNFAIP3 and MEFV, one had elevated inflammatory markers and one had positive family history. Of 9 patients who had WES after negative genetic panel, one patient had positive finding that explains his syndromic manifestations (PTEN).Table 1Primary Indication of sending targeted IEI panel and resultsPrimary Indications of sending targeted IEI gene panel N = 140)Number of patients with positive genetic testing that led to changes in diagnosis and/or treatment plans (n(%))Affected genes (each with n = 1)Infections (n = 52, 37%)3(6%)TNFRSF13B CD40LG XLAOrgan-specific inflammation (n = 42, 30%)1(2%)STAT3 LOF• Skin lesion (14)• Inflammatory bowel disease (9)• Cytopenias including ITP, Evan'ssyndrome and HLH (7)• Lymphadenopathy (3)• Others: enteropathy (3), pericarditis(2), arthritis (1), autoimmune hepatitis(1), endocrinologic disease (1), SNHL(1)Periodic fevers (n = 24,17%)2(8%)TNFAIP3 MEFVAbnormal newborn screening or1(9%)ATMabnormal immunology labs (n = 11, 8%)• Abnormal SCID screen (4)• Abnormal immunology labs (7)Systemic autoimmune disease or5 (50%)STAT5Bpolyautoimmunity (n = 10, 7%)TNFAIP3• Systemic autoimmune disease (4)NLRP12• Polyautoimmunity (6)COPANLRC4Family history (n = 1,1%)1 (100%)ATM• Pathogenic variant in ATMgene in identical twinIEI, inborn error of immunity; ITP, immune thrombocytopenia; HLH, hemophagocytic lymphohistiocytosis; SNHL, sensorineural hearing loss; SCID, severe combined immunodeficiency. ConclusionTargeted gene panel testing has the highest yield in patients with polyautoimmunity. Low yields of targeted gene panel were found in organ-specific inflammation, infections with normal clinical testing, and periodic fevers with normal inflammatory markers and a negative family history of IEI. Limitations included potentially missed cases from chart review.

ArfGAP3 regulates vesicle transport and glucose uptake in myoblasts

Skeletal muscle injuries are common, and damaged myofibers are repaired through proliferation and differentiation of muscle satellite cells. GLUT4 is enriched in GLUT4 storage vesicles (GSVs) and plays a crucial role in the maintenance of muscle function. ArfGAP3 regulates the vesicle transport especially for COPI coat assembly, but its effects on GSVs and the repair process after skeletal muscle injury remains unclear. In this study, datasets related to skeletal muscle injury and myoblast differentiation GSE469, GSE5413, GSE45577 and GSE108040 were retrieved through the GEO database and the expression of heptameric coat protein complex I (COPI) and Golgi vesicle transport-related genes in various datasets, as well as the expression correlation between ArfGAP2, ArfGAP3 and COPI-related genes COPA, COPB1, COPB2, COPE, COPZ1, COPZ2 were analyzed. The results suggested that ArfGAP3 was expressed in the process of repair after skeletal muscle injury and myoblast differentiation and that ArfGAP3 was positively correlated with COPI-related genes. In vitro experimental results showed that ArfGAP3 was colocalized with COPA, COPB, COPG protein, and GLUT4 in C2C12 myoblasts. After the downregulation of ArfGAP3 expression, intracellular vesicle transport, and glucose uptake were blocked, the proliferation of myoblasts under low glucose culture conditions was impaired, the proportion of apoptosis increased, and myotube differentiation was impaired. In summary, ArfGAP3 regulates COPI-associated vesicle and GSVs transport and affects the proliferation and differentiation ability of myoblasts by influencing glucose uptake, thereby modulating the repair process after skeletal muscle injury.

A toddler with an unusually severe polyarticular arthritis and a lung involvement: a case report

BackgroundCOPA syndrome is a rare hereditary inflammatory disease caused by mutations in the gene encoding the coatomer protein subunit alpha, causing excessive production of type I interferon.This case is a reminder for the general paediatrician, highlighting the relevance of the association between arthritis and lung involvement in toddlers.Case presentationWe report the case of a 2-year-old girl with intermittent limping and joint pain. Her family history was relevant for a Still disease with lung involvement in the mother. Physical examination showed moderate wrist swelling. Laboratory findings on admission showed an increase in inflammatory markers, positive rheumatoid factor, antibodies antinuclear antibody (ANA) and cyclic citrullinated peptide (anti-CCP). Wrists’ ultrasound documented synovial thickening, and chest X-rays showed an unexpected severe interstitial pneumopathy. Genetic testing confirmed the diagnosis of a heterozygous mutation of the COPA gene in c.841C > T (p.R281W). Janus kinase treatment was started (baricitinib, 4 mg daily per os) with a remarkable improvement in limping and joint pain after two weeks.ConclusionsIn cases of recurrent arthritis with family history and multiple involvement organs, a genetic disorder should be suspected and genetic testing should be performed. Furthermore, this case suggests that therapy with jak inhibitors may be effective and safe in interferonopathies.

Lack of evidence for ribosomal frameshifting in ATP7B mRNA decoding

SummaryThe research article describing the discovery of ribosomal frameshifting in the bacterial CopA gene also reported the occurrence of frameshifting in the expression of the human ortholog ATP7B based on assays using dual luciferase reporters. An examination of the publicly available ribosome profiling data and the phylogenetic analysis of the proposed frameshifting site cast doubt on the validity of this claim and prompted us to reexamine the evidence. We observed similar apparent frameshifting efficiencies as the original authors using the same type of vector that synthesizes both luciferases as a single polyprotein. However, we noticed anomalously low absolute luciferase activities from the N-terminal reporter that suggests interference of reporter activity or levels by the ATP7B test cassette. When we tested the same proposed ATP7B frameshifting cassette in a more recently developed reporter system in which the reporters are released without being included in a polyprotein, no frameshifting was detected above background levels.

Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes

Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging. In this study, we developed a sequence-based functional metagenomics procedure for mining the diversity of copper (Cu) resistance gene copA in global microbiomes, by combining the metagenomic assembly technology, local BLAST, evolutionary trace analysis (ETA), chemical synthesis, and conventional functional genomics. In total, 87 metagenomes were collected from a public database and subjected to copA detection, resulting in 93,899 hits. Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates, which were further subjected to ETA. Eventually, 175 novel copA sequences of high quality were discovered. Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins, with 55 sequences from totally unknown species. Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli (ΔcopA). The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake. One recombinant harboring copA-like 15 (copAL15) successfully restored Cu resistance of the host with a substantially enhanced Cu uptake. Two novel copA genes were fused with the gfp gene and expressed in E. coli for microscopic observation. Imaging results showed that they were successfully expressed and their proteins were localized to the membrane. The results here greatly expand the diversity of known CopA proteins, and the sequence-based procedure developed overcomes biases in length, screening methods, and abundance of conventional functional metagenomics.

Genomic analysis uncovers laccase-coding genes and biosynthetic gene clusters encoding antimicrobial compounds in laccase-producing Acinetobacter baumannii

Laccases are multicopper oxidase family enzymes that can oxidize various substrates. In this study, we isolated laccase-producing Acinetobacter spp. from the environment, and one isolate of laccase-producing Acinetobacter baumannii, designated NI-65, was identified. The NI-65 strain exhibited constitutive production of extracellular laccase in a crude extract using 2,6-dimethoxyphenol as a substrate when supplemented with 2 mM CuSO4. Whole-genome sequencing of the NI-65 strain revealed a genome size of 3.6 Mb with 3,471 protein-coding sequences. The phylogenetic analysis showed high similarity to the genome of A. baumannii NCIMB8209. Three laccase proteins, PcoA and CopA, that belong to bacterial CopA superfamilies, and LAC-AB, that belongs to the I-bacterial bilirubin oxidase superfamily, were identified. These proteins were encoded by three laccase-coding genes (pcoA, copA, and lac-AB). The lac-AB gene showed a sequence similar to that of polyphenol oxidase (PPO). Gene clusters encoding the catabolized compounds involved in the utilization of plant substances and secondary metabolite biosynthesis gene clusters encoding antimicrobial compounds were identified. This is the first report of whole-genome sequencing of laccase-producing A. baumannii, and the data from this study help to elucidate the genome of A. baumannii to facilitate its application in synthetic biology for enzyme production.

Disinfectant and heavy metal resistance profiles in extended spectrum β-lactamase (ESBL) producing Escherichia coli isolates from chicken meat samples

Biocidal compounds are frequently used as disinfectants in poultry industry and their widespread usage has risen concern due to the co-selection and persistence of antimicrobial resistance among bacteria. In this study, extended spectrum β-lactamase producing (ESBL) Escherichia coli isolates (n = 60) obtained from chicken meat were characterized by Pulsed Field Gel Electrophoresis (PFGE) and further tested for disinfectant and heavy metal resistance phenotypically and genotypically. Plasmid replicon types of these isolates were also determined. ESBL producing E. coli isolates were found to be resistant to ciprofloxacin (48.3 %) and gentamicin (15 %). The majority of these isolates (46.5 %) carried blaCTX-M-55 gene. The isolates showed higher minimal inhibitory concentrations to cetylpyridinium chloride (90 %), cetyltrimethylammonium bromide (50 %), hexadecyltrimethylammonium bromide (46.7 %), triclosan (38.3 %), benzalkonium chloride (28.3 %), chlorhexidine (21.7 %), acriflavine (3.3 %), benzethonium chloride (1.7 %) and N-alkyl dimethyl benzyl ammonium chloride (1.7 %), but 18.3 % of the isolates were resistant to triclosan. Of the quaternary ammonium compounds (QACs) tolerance genes, mdfA, sugE(c), ydgE and ydgF were most present in all isolates, but the qacE, qacG, oqxA and oqxB genes were not detected. Of genes mediating the heavy metal resistance, the zitB gene was detected in all isolates, whereas the copA and cueO genes were detected in 96.67 % and 95 % of isolates, respectively. The IncFIB plasmid was commonly present (93.3 %) in ESBL producing E. coli isolates. Consequently, given the detection of genes mediating disinfectant and heavy metal resistance commonly in ESBL producing E. coli isolates as well as high rate of MICs against disinfectant compounds, the use of QACs for decontamination of the facilities may not be as effective as expected in poultry sector in Turkey.

Identification of mutant gene for Black crystal coat and non-allelic gene interactions in Neogale vison

Sable (Martes zibellina) and American mink (Neogale vison) are valuable species characterized by a variety of coat colour produced on fur farms. Black crystal fur phenotype is Mendelian codominant trait: heterozygous animals (Cr/ +) have white guard hairs scattered predominantly on the spine and the head, while homozygous (Cr/Cr) minks have coats resembling the Himalayan (ch/ch) or white Hedlund (h/h) types. It is one of the most recent of more than 35 currently known phenotypic traits of fur colour in American mink. Black crystal fur phenotype was first described in 1984 in the Russian population of mink, which had undergone selection for domestic defensive response to humans. Here, we performed whole-genome sequencing of American mink with Cr/Cr phenotype. We identified a missense mutation in the gene encoding the α-COP subunit of the COPI complex (COPA). The COPI complex mediates retrograde trafficking from the Golgi system to the endoplasmic reticulum and sorting of transmembrane proteins. We observed an interaction between a newly identified mutation in the COPA gene and a mutation in the microphthalmia-associated transcription factor (MITF), the latter mutation led to the formation of the white Hedlund (h/h) phenotype. Double heterozygotes for these mutations have an entirely white coat and a black-eyed phenotype similar to the phenotype of Cr/Cr or h/h minks. Our data could be useful for tracking economically valuable fur traits in mink breeding programs to contribute to global fur production.

Pseudomonas aeruginosa from pet Chinese stripe-necked turtles (Ocadia sinensis) demonstrating antimicrobial and heavy metal resistance

Leading nosocomial pathogen Pseudomonas aeruginosa has increasingly been reported to be an opportunistic pathogen. In this study, a total of twenty P. aeruginosa isolates were isolated from 40 pet Chinese stripe-necked turtles and examined for their antimicrobial and heavy metal resistance properties. All isolates were multidrug resistance by scoring multiple antimicrobial resistance indices ≥0.2. In the disc distribution test, 100% resistance to ampicillin and oxacillin were detected. In addition to that, 14 (70%) isolate demonstrated amoxicillin resistance. Imipenem, fosfomycin, gentamycin, tobramycin and piperacillin resistance were detected in 40%, 15%, 20%, 10% and 5% of the isolates, respectively. The ESBLs gene that predominated in this study was blaSHV (55%), followed by blaTEM (50%), blaCTX (10%) and blaOXA (5%). The most frequent aminoglycoside resistance gene in this study was aac(6´)-Ib (40%). Class1 integron integrase gene intI1 and class 1 integron gene cassette gene aadA1 were detected in 45% and 35% of the isolates, respectively. All P. aeruginosa isolates demonstrated Cu and Cd resistance. CzcA and CopA genes were detected in 65% and 30% of the isolates, respectively. These findings reveal the presence of pet turtle-born P. aeruginosa can be a potential risk to public health and cannot be excluded as a non-nosocomial source of infections.

Talaromyces marneffei infection associated with bronchiolitis obliterans in an HIV-negative child: a case report

BackgroundTalaromyces marneffei is an opportunistic pathogen that infects immunodeficient and immunocompromised patients. We presented a pediatric patient with a diagnosis of T. marneffei infection who was followed up in the Guangzhou Women and Children’s Medical Centre.Case presentationThe child was a 5-year-old girl with persistent cough and gasping over 2 months who was confirmed with T. marneffei infection by bronchoalveolar lavage fluid culture and high-throughput sequencing technology. Human immunodeficiency virus (HIV) was negative according to a serum-specific antibody test. She was treated with amphotericin B and itraconazole as antifungal agents, with good clinical response. At follow-up, high-resolution computed tomography showed a mosaic sign in the whole lung field with a diagnosis of post-infectious bronchiolitis obliterans (PIBO) as the sequela. She has a mutated COPA gene with uncertain pathogenic potential on whole-exome sequencing.ConclusionsClinicians should consider PIBO as a possible sequela in an HIV-negative paediatric patient with T. marneffei infection.

The Influence of Copper Homeostasis Genes copA and copB on Xylella fastidiosa Virulence Is Affected by Sap Copper Concentration.

Xylella fastidiosa is a xylem-limited plant pathogenic bacterium that causes diseases worldwide in crops such as grape, citrus, and olive. Although copper (Cu)-containing compounds are not used for management of X. fastidiosa-caused diseases, they are widely used in X. fastidiosa hosts in vineyards and orchards. The accumulation of Cu in soils and, therefore, plant saps, could be a challenge for X. fastidiosa survival. Here, the molecular basis of Cu homeostasis was studied in relation to virulence. Although homologous Cu-related genes copA (X. fastidiosa loci PD0100) and copB (PD0101) have been characterized in other bacteria, their functions differ among bacterial species. In vitro, both copA and copB mutants were more sensitive to Cu than the wild-type (WT) strain. Interestingly, the copA mutant was more sensitive to Cu shock, while the copB mutant was more sensitive to chronic Cu treatments. In tobacco greenhouse experiments with normal watering, both mutants reduced virulence compared with WT. But when Cu was added as a drench treatment, both copA and copB mutants had increased disease severity approximately 20 and 50% compared with mutants without Cu added, respectively, which were significantly higher than the approximately 5% observed for WT under the same conditions. These results indicate that the pathogen's Cu homeostasis affects virulence and is influenced by Cu concentration in the environment. Understanding Cu homeostasis in X. fastidiosa will help discern the outcome of Cu treatments and the adaptation of this pathogen to the xylem of plants that have been exposed to high Cu concentrations because of agricultural practices.