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Chalka A, Dallman TJ, Vohra P, Stevens MP, Gally DL. The advantage of intergenic regions as genomic features for machine-learning-based host attribution of Salmonella Typhimurium from the USA. Microb Genom 2023; 9:001116. [PMID: 37843883 PMCID: PMC10634445 DOI: 10.1099/mgen.0.001116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023] Open
Abstract
Salmonella enterica is a taxonomically diverse pathogen with over 2600 serovars associated with a wide variety of animal hosts including humans, other mammals, birds and reptiles. Some serovars are host-specific or host-restricted and cause disease in distinct host species, while others, such as serovar S. Typhimurium (STm), are generalists and have the potential to colonize a wide variety of species. However, even within generalist serovars such as STm it is becoming clear that pathovariants exist that differ in tropism and virulence. Identifying the genetic factors underlying host specificity is complex, but the availability of thousands of genome sequences and advances in machine learning have made it possible to build specific host prediction models to aid outbreak control and predict the human pathogenic potential of isolates from animals and other reservoirs. We have advanced this area by building host-association prediction models trained on a wide range of genomic features and compared them with predictions based on nearest-neighbour phylogeny. SNPs, protein variants (PVs), antimicrobial resistance (AMR) profiles and intergenic regions (IGRs) were extracted from 3883 high-quality STm assemblies collected from humans, swine, bovine and poultry in the USA, and used to construct Random Forest (RF) machine learning models. An additional 244 recent STm assemblies from farm animals were used as a test set for further validation. The models based on PVs and IGRs had the best performance in terms of predicting the host of origin of isolates and outperformed nearest-neighbour phylogenetic host prediction as well as models based on SNPs or AMR data. However, the models did not yield reliable predictions when tested with isolates that were phylogenetically distinct from the training set. The IGR and PV models were often able to differentiate human isolates in clusters where the majority of isolates were from a single animal source. Notably, IGRs were the feature with the best performance across multiple models which may be due to IGRs acting as both a representation of their flanking genes, equivalent to PVs, while also capturing genomic regulatory variation, such as altered promoter regions. The IGR and PV models predict that ~45 % of the human infections with STm in the USA originate from bovine, ~40 % from poultry and ~14.5 % from swine, although sequences of isolates from other sources were not used for training. In summary, the research demonstrates a significant gain in accuracy for models with IGRs and PVs as features compared to SNP-based and core genome phylogeny predictions when applied within the existing population structure. This article contains data hosted by Microreact.
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Affiliation(s)
- Antonia Chalka
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
| | - Tim J. Dallman
- Institute for Risk Assessment Sciences (IRAS), University of Utrecht, Heidelberglaan, Utrecht, Netherlands
| | - Prerna Vohra
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
| | - Mark P. Stevens
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
| | - David L. Gally
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
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Melis R, Di Crescenzo S, Cariani A, Ferrari A, Crobe V, Bellodi A, Mulas A, Carugati L, Coluccia E, Follesa MC, Cannas R. I Like This New Me: Unravelling Population Structure of Mediterranean Electric Rays and Taxonomic Uncertainties within Torpediniformes. Animals (Basel) 2023; 13:2899. [PMID: 37760300 PMCID: PMC10525375 DOI: 10.3390/ani13182899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The present study focused on the three species of electric rays known to occur in the Mediterranean Sea: Torpedo torpedo, Torpedo marmorata and Tetronarce nobiliana. Correct identification of specimens is needed to properly assess the impact of fisheries on populations and species. Unfortunately, torpedoes share high morphological similarities, boosting episodes of field misidentification. In this context, genetic data was used (1) to identify specimens caught during fishing operations, (2) to measure the diversity among and within these species, and (3) to shed light on the possible occurrence of additional hidden species in the investigated area. New and already published sequences of COI and NADH2 mitochondrial genes were analyzed, both at a small scale along the Sardinian coasts (Western Mediterranean) and at a large scale in the whole Mediterranean Sea. High levels of genetic diversity were found in Sardinian populations, being significantly different from other areas of the Eastern Mediterranean Sea due to the biotic and abiotic factors here discussed. Sardinian torpedoes can hence be indicated as priority populations/areas to be protected within the Mediterranean Sea. Moreover, sequence data confirmed that only the three species occur in the investigated area. The application of several 'species-delimitation' methods found evidence of cryptic species in the three species outside the Mediterranean Sea, as well as in other genera/families, suggesting the urgent need for future studies and a comprehensive revision of the order Torpediniformes for its effective conservation.
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Affiliation(s)
- Riccardo Melis
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Simone Di Crescenzo
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy; (A.C.); (A.F.); (V.C.)
| | - Alice Ferrari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy; (A.C.); (A.F.); (V.C.)
| | - Valentina Crobe
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy; (A.C.); (A.F.); (V.C.)
| | - Andrea Bellodi
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Antonello Mulas
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Laura Carugati
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Elisabetta Coluccia
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Maria Cristina Follesa
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Rita Cannas
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
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Jacobson DK, Low R, Plucinski MM, Barratt JLN. An improved framework for detecting discrete epidemiologically meaningful partitions in hierarchically clustered genetic data. BIOINFORMATICS ADVANCES 2023; 3:vbad118. [PMID: 37744999 PMCID: PMC10517639 DOI: 10.1093/bioadv/vbad118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/26/2023]
Abstract
Motivation Hierarchical clustering of microbial genotypes has the limitation that hierarchical clusters are nested, where smaller groups of related isolates exist within larger groups that get progressively larger as relationships become increasingly distant. In an epidemiologic context, investigators must dissect hierarchical trees into discrete groupings that are epidemiologically meaningful. We recently described a statistical framework (Method A) for dissecting hierarchical trees that attempts to minimize investigator bias. Here, we apply a modified version of that framework (Method B) to a hierarchical tree constructed from 2111 genotypes of the foodborne parasite Cyclospora, including 639 genotypes linked to epidemiologically defined outbreaks. To evaluate Method B's performance, we examined the concordance between these epidemiologically defined groupings and the genetic partitions identified. We also used the same epidemiologic clusters to evaluate the performance of Method A, plus two tree-dissection methods (cutreeHybrid and cutreeDynamic) available within the Dynamic Tree Cut R package, in addition to the TreeCluster method and PARNAS. Results Compared to the other methods, Method B, TreeCluster, and PARNAS were the most accurate (99.4%) in identifying genetic groups that reflected the epidemiologic groupings, noting that TreeCluster and PARNAS performed identically on our dataset. CutreeHybrid identified groups reflecting patterns in the wider Cyclospora population structure but lacked finer, strain-level discrimination (Simpson's D: cutreeHybrid=0.785). CutreeDynamic displayed good strain discrimination (Simpson's D = 0.933), though lacked sensitivity (77%). At two different threshold/radius settings TreeCluster/PARNAS displayed similar utility to Method B. However, Method B computes a tree-dissection threshold automatically, and the threshold/radius settings used when executing TreeCluster/PARNAS here were computed using Method B. Using a TreeCluster threshold of 0.045 as recommended in the TreeCluster documentation, epidemiologic utility dropped markedly below that of Method B. Availability and implementation Relevant code and data are publicly available. Source code (Method B) and instructions for its use are available here: https://github.com/Joel-Barratt/Hierarchical-tree-dissection-framework.
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Affiliation(s)
- David K Jacobson
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
| | - Ross Low
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
- Oak Ridge Institute of Science and Education, Oak Ridge, TN, 37830, United States
| | - Mateusz M Plucinski
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
| | - Joel L N Barratt
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
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Chen K, Xie M, Dong N, Chan EWC, Zhang R, Chen S. Deciphering mechanisms of bla NDM gene transmission between human and animals: a genomics study of bacterial isolates from various sources in China, 2015 to 2017. Euro Surveill 2023; 28:2200925. [PMID: 37707983 PMCID: PMC10687984 DOI: 10.2807/1560-7917.es.2023.28.37.2200925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/15/2023] [Indexed: 09/16/2023] Open
Abstract
BackgroundIn China, the bla NDM gene has been recovered from human bacterial isolates since 2011. After 2014, detections of this gene in animal and food bacterial isolates have increasingly been reported.AimWe aimed to understand how bla NDM-bearing bacteria could spread between humans, animals, and animal-derived food.MethodsA total of 288 non-duplicate Escherichia coli strains, including 130 bla NDM-carrying and 158 bla NDM-negative strains were collected from clinical (humans), food-producing animals (pigs) and food (retail pork) sources between 2015 and 2017. The strains were whole genome sequenced. Core-genome-multilocus-sequence-typing was conducted. To investigate if sequence types (STs) found in human, animal or food samples could have a prior origin in a clinical, animal or food-borne animal reservoir, discriminant analysis of principal components (DAPC) was used. Plasmids bearing bla NDM were characterised.ResultsThe 130 bla NDM-carrying E. coli strains comprised a total of 60 STs, with ST167 (10/51), ST77 (6/33) and ST48 (6/46) being most prevalent in clinical, animal and food sources, respectively. Some ST10 and ST167 strains were respectively found among all three sources sampled, suggesting they might enable transfer of bla NDM between sources. DAPC analysis indicated possible transmissions of ST167 from humans to animals and ST10 from animals to human. In 114 of 130 bla NDM-carrying isolates, bla NDM was located on an IncX3 plasmid.ConclusionThis study in a Chinese context suggests that cross-species transmission of certain STs of E. coli harbouring bla NDM on mobile elements, may facilitate the spread of carbapenem-resistant Enterobacteriaceae. Stringent monitoring of bla NDM-bearing E. coli in ecosystems is important.
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Affiliation(s)
- Kaichao Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China
- These authors contributed equally to this work
| | - Miaomiao Xie
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China
- These authors contributed equally to this work
| | - Ning Dong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China
| | - Edward Wai Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, China
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China
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Graña-Miraglia L, Morales-Lizcano N, Wang PW, Hwang DM, Yau YCW, Waters VJ, Guttman DS. Predictive modeling of antibiotic eradication therapy success for new-onset Pseudomonas aeruginosa pulmonary infections in children with cystic fibrosis. PLoS Comput Biol 2023; 19:e1011424. [PMID: 37672526 PMCID: PMC10506723 DOI: 10.1371/journal.pcbi.1011424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 09/18/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023] Open
Abstract
Chronic Pseudomonas aeruginosa (Pa) lung infections are the leading cause of mortality among cystic fibrosis (CF) patients; therefore, the eradication of new-onset Pa lung infections is an important therapeutic goal that can have long-term health benefits. The use of early antibiotic eradication therapy (AET) has been shown to clear the majority of new-onset Pa infections, and it is hoped that identifying the underlying basis for AET failure will further improve treatment outcomes. Here we generated machine learning models to predict AET outcomes based on pathogen genomic data. We used a nested cross validation design, population structure control, and recursive feature selection to improve model performance and showed that incorporating population structure control was crucial for improving model interpretation and generalizability. Our best model, controlling for population structure and using only 30 recursively selected features, had an area under the curve of 0.87 for a holdout test dataset. The top-ranked features were generally associated with motility, adhesion, and biofilm formation.
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Affiliation(s)
- Lucía Graña-Miraglia
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nadia Morales-Lizcano
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Pauline W. Wang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - David M. Hwang
- Department of Laboratory Medicine and Pathobiology, Toronto, Ontario, Canada
- Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Yvonne C. W. Yau
- Department of Laboratory Medicine and Pathobiology, Toronto, Ontario, Canada
- Department of Paediatric Laboratory Medicine, Division of Microbiology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Valerie J. Waters
- Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, Toronto, Ontario, Canada
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
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Zhang Z, Wang J, Wang H, Zhang L, Shang W, Li Z, Song L, Li T, Cheng M, Zhang C, Zhao Q, Shen S, Cui M. Molecular Surveillance of MRSA in Raw Milk Provides Insight into MRSA Cross Species Evolution. Microbiol Spectr 2023; 11:e0031123. [PMID: 37260406 PMCID: PMC10433870 DOI: 10.1128/spectrum.00311-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) in foods has been associated with severe infections in humans and animals worldwide. In the present study, the molecular characteristics of livestock-associated MRSA (LA-MRSA) and human-associated MRSA (hMRSA) isolates obtained in China, as well as MRSA isolates obtained from raw milk in 2018, were investigated. In total, 343 (20.38%; 343/1,683) S. aureus isolates were obtained from 1,683 raw milk samples from 100 dairy farms in 11 provinces across China. Among these, 49 (2.91%; 49/1,683) were mecA-positive MRSA. All LA-MRSA isolates were resistant to penicillin and highly resistant to erythromycin, sulfisoxazole, and clindamycin. Bioinformatic analysis the 49 genomes of LA-MRSA and 71 previously published hMRSA genomes isolated from Chinese individuals in 2018 indicated that blaZ, erm, ant(6)-Ia, aph(3')-III, tet(K), cat, and aph(2″)-Ia were more prevalent in MRSA from raw milk (P < 0.05) compared to hMRSA. Additionally, hMRSA isolates were more significantly associated with ST5 (P < 0.01) compared to LA-MRSA; in contrast, ST338 was more prevalent among LA-MRSA isolates (P < 0.01). Likewise, the SCCmec type II was only detected in hMRSA isolates, whereas SCCmec type V and IV were more prevalent among LA-MRSA (P < 0.01). Furthermore, core-genome phylogenetic analysis showed the endemic characteristics of LA-MRSA in local provinces, as well as the close evolutionary relationships between MRSA from cattle and humans. Finally, homology analysis of mecA and blaZ genetic contexts revealed a high possibility of horizontal transmission of MRSA resistance genes among raw milk-associated and hMRSA strains, which increases the risk for public health. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is considered a public health concern as it is resistant to multiple antibiotics, thus being in zoonotic transmission of antibiotic resistance genes. MRSA causes serious public health issues and leads to hard-to-treat infections in humans and animals; therefore, it was meaningful to determine the prevalence of MRSA in raw milk samples and investigate phenotype and genotype of antimicrobial resistance and molecular characteristics in livestock-associated MRSA (LA-MRSA) and human-associated MRSA (hMRSA) in China, which could provide a theoretical basis for preventing and controlling the spread of MRSA between livestock and humans.
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Affiliation(s)
- Zhenbiao Zhang
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, People’s Republic of China
| | - Jianzhong Wang
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, People’s Republic of China
| | - Hejia Wang
- China Institute of Veterinary Drug Control, Beijing, People’s Republic of China
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, People’s Republic of China
| | - Liu Zhang
- College of Agricultural Standardization, Shanxi Agricultural University, Jinzhong, Shanxi, People’s Republic of China
| | - Wei Shang
- No.988 Hospital of Joint Logistic Support Force, Zhengzhou, Henan, People’s Republic of China
| | - Zekun Li
- China Institute of Veterinary Drug Control, Beijing, People’s Republic of China
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, People’s Republic of China
| | - Li Song
- China Institute of Veterinary Drug Control, Beijing, People’s Republic of China
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, People’s Republic of China
| | - Ting Li
- China Institute of Veterinary Drug Control, Beijing, People’s Republic of China
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, People’s Republic of China
| | - Min Cheng
- China Institute of Veterinary Drug Control, Beijing, People’s Republic of China
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, People’s Republic of China
| | - Chunping Zhang
- China Institute of Veterinary Drug Control, Beijing, People’s Republic of China
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, People’s Republic of China
| | - Qi Zhao
- China Institute of Veterinary Drug Control, Beijing, People’s Republic of China
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, People’s Republic of China
| | - Shan Shen
- Shandong Provincial Hospital (Group) Ludong Hospital, Yantai, Shandong, People’s Republic of China
| | - Mingquan Cui
- China Institute of Veterinary Drug Control, Beijing, People’s Republic of China
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, People’s Republic of China
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Ma C, Li M, Peng H, Lan M, Tao L, Li C, Wu C, Bai H, Zhong Y, Zhong S, Qin R, Li F, Li J, He J. Mesomycoplasma ovipneumoniae from goats with respiratory infection: pathogenic characteristics, population structure, and genomic features. BMC Microbiol 2023; 23:220. [PMID: 37580659 PMCID: PMC10424369 DOI: 10.1186/s12866-023-02964-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Mycoplasma ovipneumoniae is a critical pathogen that causes respiratory diseases that threaten Caprini health and cause economic damage. A genome-wide study of M. ovipneumoniae will help understand the pathogenic characteristics of this microorganism. RESULTS Toxicological pathology and whole-genome sequencing of nine M. ovipneumoniae strains isolated from goats were performed using an epidemiological survey. These strains exhibited anterior ventral lung consolidation, typical of bronchopneumonia in goats. Average nucleotide identity and phylogenetic analysis based on whole-genome sequences showed that all M. ovipneumoniae strains clustered into two clades, largely in accordance with their geographical origins. The pan-genome of the 23 M. ovipneumoniae strains contained 5,596 genes, including 385 core, 210 soft core, and 5,001 accessory genes. Among these genes, two protein-coding genes were annotated as cilium adhesion and eight as paralog surface adhesins when annotated to VFDB, and no antibiotic resistance-related genes were predicted. Additionally, 23 strains carried glucosidase-related genes (ycjT and group_1595) and glucosidase-related genes (atpD_2), indicating that M. ovipneumoniae possesses a wide range of glycoside hydrolase activities. CONCLUSIONS The population structure and genomic features identified in this study will facilitate further investigations into the pathogenesis of M. ovipneumoniae and lay the foundation for the development of preventive and therapeutic methods.
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Affiliation(s)
- Chunxia Ma
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530001, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Nanning, 530001, Guangxi, China
| | - Ming Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, Nanning, 530021, Guangxi, China
| | - Hao Peng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530001, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Nanning, 530001, Guangxi, China
| | - Meiyi Lan
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530001, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Nanning, 530001, Guangxi, China
| | - Li Tao
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530001, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Nanning, 530001, Guangxi, China
| | - Changting Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530001, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Nanning, 530001, Guangxi, China
| | - Cuilan Wu
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530001, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Nanning, 530001, Guangxi, China
| | - Huili Bai
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530001, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Nanning, 530001, Guangxi, China
| | - Yawen Zhong
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Shuhong Zhong
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530001, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Nanning, 530001, Guangxi, China
| | - Ruofu Qin
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530001, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Nanning, 530001, Guangxi, China
| | - Fengsheng Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530001, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Nanning, 530001, Guangxi, China
| | - Jun Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, 530001, Guangxi, China.
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Nanning, 530001, Guangxi, China.
| | - Jiakang He
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China.
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Barandongo ZR, Dolfi AC, Bruce SA, Rysava K, Huang YH, Joel H, Hassim A, Kamath PL, van Heerden H, Turner WC. The persistence of time: the lifespan of Bacillus anthracis spores in environmental reservoirs. Res Microbiol 2023; 174:104029. [PMID: 36720294 DOI: 10.1016/j.resmic.2023.104029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/30/2023]
Abstract
Anthrax is a lethal bacterial zoonosis primarily affecting herbivorous wildlife and livestock. Upon host death Bacillus anthracis vegetative cells form spores capable of surviving for years in soil. Anthrax transmission requires host exposure to large spore doses. Thus, conditions that facilitate higher spore concentrations or promote spore survival will increase the probability that a pathogen reservoir infects future hosts. We investigated abiotic and pathogen genomic variation in relation to spore concentrations in surface soils (0-1 cm depth) at 40 plains zebra (Equus quagga) anthrax carcass sites in Namibia. Specifically, how initial spore concentrations and spore survival were affected by seasonality associated with the timing of host mortality, local soil characteristics, and pathogen genomic variation. Zebras dying of anthrax in wet seasons-the peak season for anthrax in Etosha National Park-had soil spore concentrations 1.36 orders of magnitude higher than those that died in dry seasons. No other variables considered affected spore concentrations, and spore survival rates did not differ among sites. Surface soils at these pathogen reservoirs remained culture positive for a range of 3.8-10.4 years after host death. Future research could evaluate if seasonal patterns in spore concentrations are driven by differences in sporulation success or levels of terminal bacteremia.
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Affiliation(s)
- Zoë R Barandongo
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Amélie C Dolfi
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Spencer A Bruce
- Department of Biological Sciences, State University of New York, Albany, NY 12222, USA.
| | - Kristyna Rysava
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Yen-Hua Huang
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Hendrina Joel
- Department of Environmental Science, Faculty of Science, University of Namibia, Private Bag 13301, Windhoek, Namibia.
| | - Ayesha Hassim
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa.
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, ME, USA.
| | - Henriette van Heerden
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa.
| | - Wendy C Turner
- U.S. Geological Survey, Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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59
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Bonnin N, Piel AK, Brown RP, Li Y, Connell JA, Avitto AN, Boubli JP, Chitayat A, Giles J, Gundlapally MS, Lipende I, Lonsdorf EV, Mjungu D, Mwacha D, Pintea L, Pusey AE, Raphael J, Wich SA, Wilson ML, Wroblewski EE, Hahn BH, Stewart FA. Barriers to chimpanzee gene flow at the south-east edge of their distribution. Mol Ecol 2023; 32:3842-3858. [PMID: 37277946 PMCID: PMC10421595 DOI: 10.1111/mec.16986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023]
Abstract
Populations on the edge of a species' distribution may represent an important source of adaptive diversity, yet these populations tend to be more fragmented and are more likely to be geographically isolated. Lack of genetic exchanges between such populations, due to barriers to animal movement, can not only compromise adaptive potential but also lead to the fixation of deleterious alleles. The south-eastern edge of chimpanzee distribution is particularly fragmented, and conflicting hypotheses have been proposed about population connectivity and viability. To address this uncertainty, we generated both mitochondrial and MiSeq-based microsatellite genotypes for 290 individuals ranging across western Tanzania. While shared mitochondrial haplotypes confirmed historical gene flow, our microsatellite analyses revealed two distinct clusters, suggesting two populations currently isolated from one another. However, we found evidence of high levels of gene flow maintained within each of these clusters, one of which covers an 18,000 km2 ecosystem. Landscape genetic analyses confirmed the presence of barriers to gene flow with rivers and bare habitats highly restricting chimpanzee movement. Our study demonstrates how advances in sequencing technologies, combined with the development of landscape genetics approaches, can resolve ambiguities in the genetic history of critical populations and better inform conservation efforts of endangered species.
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Affiliation(s)
- Noémie Bonnin
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
| | - Alex K. Piel
- Department of Anthropology, University College London, London, UK
| | - Richard P. Brown
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
| | - Yingying Li
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jesse A. Connell
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alexa N. Avitto
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jean P. Boubli
- School of Science, Engineering & Environment, University of Salford, Salford, UK
| | - Adrienne Chitayat
- Institute of Biodiversity and Ecological Dynamics, University of Amsterdam, The Netherlands
| | - Jasmin Giles
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Madhurima S. Gundlapally
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Iddi Lipende
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Elizabeth V. Lonsdorf
- Department of Psychology, Franklin and Marshall College, Lancaster, PA 17604, USA
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Deus Mjungu
- Gombe Stream Research Centre, The Jane Goodall Institute–Tanzania, P.O. Box 1182, Kigoma, Tanzania
| | - Dismas Mwacha
- Gombe Stream Research Centre, The Jane Goodall Institute–Tanzania, P.O. Box 1182, Kigoma, Tanzania
| | - Lilian Pintea
- Conservation Science Department, the Jane Goodall Institute, Washington, DC, 20036, USA
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | | | - Serge A. Wich
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
- Institute of Biodiversity and Ecological Dynamics, University of Amsterdam, The Netherlands
| | - Michael L. Wilson
- Department of Anthropology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
- Institute on the Environment, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Fiona A. Stewart
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
- Department of Anthropology, University College London, London, UK
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60
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Kasimov V, White RT, Foxwell J, Jenkins C, Gedye K, Pannekoek Y, Jelocnik M. Whole-genome sequencing of Chlamydia psittaci from Australasian avian hosts: A genomics approach to a pathogen that still ruffles feathers. Microb Genom 2023; 9:mgen001072. [PMID: 37486739 PMCID: PMC10438822 DOI: 10.1099/mgen.0.001072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/26/2023] [Indexed: 07/25/2023] Open
Abstract
Chlamydia psittaci is a globally distributed veterinary pathogen with zoonotic potential. Although C. psittaci infections have been reported in various hosts, isolation and culture of Chlamydia is challenging, hampering efforts to produce contemporary global C. psittaci genomes. This is particularly evident in the lack of avian C. psittaci genomes from Australia and New Zealand. In this study, we used culture-independent probe-based whole-genome sequencing to expand the global C. psittaci genome catalogue. Here, we provide new C. psittaci genomes from two pigeons, six psittacines, and novel hosts such as the Australian bustard (Ardeotis australis) and sooty shearwater (Ardenna grisea) from Australia and New Zealand. We also evaluated C. psittaci genetic diversity using multilocus sequence typing (MLST) and major outer membrane protein (ompA) genotyping on additional C. psittaci-positive samples from various captive avian hosts and field isolates from Australasia. We showed that the first C. psittaci genomes sequenced from New Zealand parrots and pigeons belong to the clonal sequence type (ST)24 and diverse 'pigeon-type' ST27 clade, respectively. Australian parrot-derived strains also clustered in the ST24 group, whereas the novel ST332 strain from the Australian bustard clustered in a genetically diverse clade of strains from a fulmar, parrot, and livestock. MLST and ompA genotyping revealed ST24/ompA genotype A in wild and captive parrots and a sooty shearwater, whilst 'pigeon-types' (ST27/35 and ompA genotypes B/E) were found in pigeons and other atypical hosts, such as captive parrots, a little blue penguin/Kororā (Eudyptula minor) and a zebra finch (Taeniopygia guttata castanotis) from Australia and New Zealand. This study provides new insights into the global phylogenomic diversity of C. psittaci and further demonstrates the multi-host generalist capacity of this pathogen.
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Affiliation(s)
- Vasilli Kasimov
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia
| | - Rhys T. White
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, Brisbane, Queensland 4072, Australia
- The University of Queensland, Australian Centre for Ecogenomics, Brisbane, Queensland 4072, Australia
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Jonathan Foxwell
- Animal Health Laboratory, Ministry for Primary Industries, 66 Ward Street, Upper Hutt 5018, New Zealand
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia
| | - Kristene Gedye
- Massey University, School of Veterinary Science, Palmerston North 4442, New Zealand
| | - Yvonne Pannekoek
- University of Amsterdam, Amsterdam UMC, Department of Medical Microbiology and Infection Prevention, Amsterdam 1105, Netherlands
| | - Martina Jelocnik
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia
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61
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Moradigaravand D, Li L, Dechesne A, Nesme J, de la Cruz R, Ahmad H, Banzhaf M, Sørensen SJ, Smets BF, Kreft JU. Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning. Bioinformatics 2023; 39:btad400. [PMID: 37348862 PMCID: PMC10318386 DOI: 10.1093/bioinformatics/btad400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 06/24/2023] Open
Abstract
MOTIVATION Wastewater treatment plants (WWTPs) harbor a dense and diverse microbial community. They constantly receive antimicrobial residues and resistant strains, and therefore provide conditions for horizontal gene transfer (HGT) of antimicrobial resistance (AMR) determinants. This facilitates the transmission of clinically important genes between, e.g. enteric and environmental bacteria, and vice versa. Despite the clinical importance, tools for predicting HGT remain underdeveloped. RESULTS In this study, we examined to which extent water cycle microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e. the ability of cells to receive a plasmid through conjugation, based on data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, representing the range of hosts a plasmid is able to transfer to, for three broad host-range resistance IncP plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.49 for pB10 [95% confidence interval (CI): 0.44-0.55], 0.43 for pKJK5 (0.95% CI: 0.41-0.49), and 0.53 for RP4 (0.95% CI: 0.48-0.57) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite the broad host-range nature of these plasmids. Our results provide a framework that contributes to the assessment of the risk of AMR pollution in wastewater systems. AVAILABILITY AND IMPLEMENTATION The predictive tool is available as an application at https://github.com/DaneshMoradigaravand/PlasmidPerm.
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Affiliation(s)
- Danesh Moradigaravand
- Laboratory of Infectious Disease Epidemiology, KAUST Smart-Health Initiative and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Liguan Li
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
- Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Joseph Nesme
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Roberto de la Cruz
- Center for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Huda Ahmad
- Laboratory of Infectious Disease Epidemiology, KAUST Smart-Health Initiative and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Center for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Manuel Banzhaf
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Jan-Ulrich Kreft
- Center for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
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62
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Ferrari A, Crobe V, Cannas R, Leslie RW, Serena F, Stagioni M, Costa FO, Golani D, Hemida F, Zaera-Perez D, Sion L, Carbonara P, Fiorentino F, Tinti F, Cariani A. To Be, or Not to Be: That Is the Hamletic Question of Cryptic Evolution in the Eastern Atlantic and Mediterranean Raja miraletus Species Complex. Animals (Basel) 2023; 13:2139. [PMID: 37443937 DOI: 10.3390/ani13132139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/25/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Despite a high species diversity, skates (Rajiformes) exhibit remarkably conservative morphology and ecology. Limited trait variations occur within and between species, and cryptic species have been reported among sister and non-sister taxa, suggesting that species complexes may be subject to stabilising selection. Three sibling species are currently recognised in the Raja miraletus complex: (i) R. miraletus occurring along the Portuguese and Mediterranean coasts, (ii) R. parva in the Central-Eastern Atlantic off West Africa and (iii) R. ocellifera in the Western Indian Ocean off South Africa. In the present study, the genetic variation at mitochondrial and nuclear markers was estimated in the species complex by analysing 323 individuals sampled across most of its geographical distribution area to test the hypothesis that restricted gene flow and genetic divergence within species reflect known climate and bio-oceanographic discontinuities. Our results support previous morphological studies and confirm the known taxonomic boundaries of the three recognised species. In addition, we identified multiple weakly differentiated clades in the Northeastern Atlantic Ocean and Mediterranean, at least two additional cryptic taxa off Senegal and Angola, a pronounced differentiation of ancient South African clades. The hidden genetic structure presented here may represent a valuable support to species' conservation action plans.
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Affiliation(s)
- Alice Ferrari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Valentina Crobe
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Rita Cannas
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy
| | - Rob W Leslie
- Branch Fisheries Management, Department Agriculture, Forestry and Fisheries, Cape Town 8018, South Africa
| | - Fabrizio Serena
- Institute for Biological Resources and Marine Biotechnology, National Research Council, 91026 Trapani, Italy
| | - Marco Stagioni
- Laboratory of Marine Biology and Fisheries, Department Biological, Geological and Environmental Sciences, University of Bologna, 61032 Fano, Italy
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Daniel Golani
- Department of Evolution, Systematics and Ecology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Farid Hemida
- Ecole Nationale Supérieure des Sciences de la Mer et de l'Aménagement du Littoral, Campus Universitaire de Dely Ibrahim, Algiers 16320, Algeria
| | | | - Letizia Sion
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy
| | | | - Fabio Fiorentino
- Institute for Biological Resources and Marine Biotechnology, National Research Council, 91026 Trapani, Italy
- Stazione Zoologica Anton Dohrn, 90149 Palermo, Italy
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
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63
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Turbek SP, Funk WC, Ruegg KC. Where to draw the line? Expanding the delineation of conservation units to highly mobile taxa. J Hered 2023; 114:300-311. [PMID: 36815497 DOI: 10.1093/jhered/esad011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
Conservation units (CUs) are an essential tool for maximizing evolutionary potential and prioritizing areas across a species' range for protection when implementing conservation and management measures. However, current workflows for identifying CUs on the basis of neutral and adaptive genomic variation largely ignore information contained in patterns of isolation by distance (IBD), frequently the primary signal of population structure in highly mobile taxa, such as birds, bats, and marine organisms with pelagic larval stages. While individuals located on either end of a species' distribution may exhibit clear genetic, phenotypic, and ecological differences, IBD produces subtle changes in allele frequencies across space, making it difficult to draw clear boundaries for conservation purposes in the absence of discrete population structure. Here, we highlight potential pitfalls that arise when applying common methods for delineating CUs to continuously distributed organisms and review existing methods for detecting subtle breakpoints in patterns of IBD that can indicate barriers to gene flow in highly mobile taxa. In addition, we propose a new framework for identifying CUs in all organisms, including those characterized by continuous genomic differentiation, and suggest several possible ways to harness the information contained in patterns of IBD to guide conservation and management decisions.
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Affiliation(s)
- Sheela P Turbek
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Fort Collins, CO, United States
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64
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Atencio GWG, Zanini R, Deprá M, Romanowski HP. Preliminary population studies of the grassland swallowtail butterfly Euryades corethrus (Lepidoptera, Papilionidae). AN ACAD BRAS CIENC 2023; 95:e20210503. [PMID: 37341269 DOI: 10.1590/0001-3765202320210503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/10/2021] [Indexed: 06/22/2023] Open
Abstract
Euryades corethrus is a Troidini butterfly (Papilionidae, Papilioninae), endemic to grasslands in southern Brazil, Uruguay, Argentina and Paraguay. Formerly abundant, nowadays it is in the Red list of endangered species for those areas. During its larval stage, it feeds on Aristolochia spp, commonly found in southern grasslands. These native grassland areas are diminishing, being converted to crops and pastures, causing habitat loss for Aristolochia and E. corethrus. This study aimed to assess the genetic diversity, population structure and demographic history of E. corethrus. We sampled eight populations from Rio Grande do Sul, Brazil and based on Cytochrome Oxidase subunit I (COI) molecular marker, our results suggest a low genetic variability between populations, presence of gene flow and, consequently, lack of population structure. A single maternally inherited-genetic marker is insufficient for population-level decisions, but barcoding is a useful tool during early stages of population investigation, bringing out genomic diversity patterns within the target species. Those populations likely faced a bottleneck followed by a rapid expansion during the last glaciation and subsequent stabilization in effective population size. Habitat loss is a threat, which might cause isolation, loss of genetic variability and, ultimately, extinction of E. corethrus if no habitat conservation policy is adopted.
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Affiliation(s)
- Guilherme Wagner G Atencio
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Zoologia, Laboratório de Ecologia de Insetos, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43435, Sala 218, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade de Lisboa, Faculdade de Ciências, Centro de Ecologia, Evolução e Alterações Ambientais, Edifício C2, 5.º piso, Sala 2.5.46, Código Postal 1749-016, Campo Grande, Lisboa, Portugal
| | - Rebeca Zanini
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Drosophila, Av. Bento Gonçalves, 9500, Prédio 43323, Sala 210, Agronomia, 90650-001 Porto Alegre, RS, Brazil
- Universidade Nova de Lisboa, Faculdade de Ciências Médicas, Laboratório de Biomedicina Integrativa, Rua do Instituto Bacteriológico 5, Código Postal 1169-056, Lisboa, Portugal
| | - Maríndia Deprá
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Drosophila, Av. Bento Gonçalves, 9500, Prédio 43323, Sala 210, Agronomia, 90650-001 Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Prédio 43312 M, Caixa Postal 15053, Agronomia, 90650-001 Porto Alegre, RS, Brazil
| | - Helena P Romanowski
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Zoologia, Laboratório de Ecologia de Insetos, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43435, Sala 218, Agronomia, 91501-970 Porto Alegre, RS, Brazil
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65
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Mashe T, Thilliez G, Chaibva BV, Leekitcharoenphon P, Bawn M, Nyanzunda M, Robertson V, Tarupiwa A, Al-Khanaq H, Baker D, Gosa M, Kock MM, Midzi S, Witson ML, Jorge M, Jensen JD, Aarestrup FM, Weill FX, Hendriksen RS, Ehlers MM, Kingsley RA. Highly drug resistant clone of Salmonella Kentucky ST198 in clinical infections and poultry in Zimbabwe. NPJ ANTIMICROBIALS AND RESISTANCE 2023; 1:6. [PMID: 39843602 PMCID: PMC11721084 DOI: 10.1038/s44259-023-00003-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/27/2023] [Indexed: 01/24/2025]
Abstract
A highly multidrug-resistant strain of Salmonella enterica serotype Kentucky (S. Kentucky) of sequence type (ST)198 emerged in North Africa and has since spread widely. To investigate the genetic diversity and phylogenetic relationship of S. Kentucky in Zimbabwe and identify potential sources of infection, the whole-genome sequence of 37 S. Kentucky strains isolated from human clinical infections and from poultry farms between 2017 and 2020 was determined. Of 37 S. Kentucky isolates, 36 were ST198 and one was ST152. All ST198 isolates had between six and fifteen antimicrobial resistance (AMR) genes, and 92% carried at least ten AMRs. All ST198 isolates harbored the Salmonella genomic island K-Israel variant (SGI1-KIV) integrated into the chromosome with aac(3)-ld, aac(6)-laa, aadA7, blaTEM-1, sul1, and tetA genes, with occasional sporadic loss of one or more genes noted from five isolates. All ST198 isolates also had mutations in the quinolone resistance-determining region of the gyrA and parC genes. The blaCTX-M-14.1 and fosA3 genes were present in 92% of the ST198 isolates, conferring resistance to extended-spectrum cephalosporins and fosfomycin, respectively, were present on an IncHI2 plasmid with the aadA2b, aadA1, aph(3')-Ib, aph(6')-Id, cmlA1 and sul3 AMR genes. S. Kentucky ST198 isolates from Zimbabwe formed a closely related phylogenetic clade that emerged from a previously reported global epidemic population. The close genetic relationship and population structure of the human clinical and poultry isolates of ST198 in Zimbabwe are consistent with poultry being an important source of highly resistant strains of S. Kentucky in Zimbabwe.
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Affiliation(s)
- Tapfumanei Mashe
- University of Pretoria, Pretoria, South Africa.
- National Microbiology Reference Laboratory, Harare, Zimbabwe.
- World Health Organization, Harare, Zimbabwe.
| | | | | | | | - Matt Bawn
- Quadram Institute Bioscience, Norwich, UK
- Earlham Insitute, Norwich, UK
- University of Leeds, Leeds, UK
| | | | | | - Andrew Tarupiwa
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | | | - Dave Baker
- Quadram Institute Bioscience, Norwich, UK
| | | | - Marleen M Kock
- University of Pretoria, Pretoria, South Africa
- National Health Laboratory Service, Pretoria, South Africa
| | | | | | | | | | | | | | | | - Marthie M Ehlers
- University of Pretoria, Pretoria, South Africa
- National Health Laboratory Service, Pretoria, South Africa
| | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich, UK.
- University of East Anglia, Norwich, UK.
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66
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Hu Y, Wang S, Zhang Y, Wu Y, Liu C, Ju X, Zhou H, Cai C, Zhang R. A comparative study of intestinal Pseudomonas aeruginosa in healthy individuals and ICU inpatients. ONE HEALTH ADVANCES 2023; 1:13. [PMID: 37521531 PMCID: PMC10227385 DOI: 10.1186/s44280-023-00014-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 08/01/2023]
Abstract
The human intestinal tract is considered the most important reservoir of the opportunistic pathogens, including Pseudomonas aeruginosa, which is often overlooked but critical due to its antimicrobial resistance and virulence. Public health interventions to control this pathogen require a comprehensive understanding of its epidemiology and genomics. In the current study, we identified P. aeruginosa strains from 2,605 fecal samples collected between 2021 to 2022. Among these samples, 574 were from ICU inpatients in Zhejiang province, while 2,031 were obtained from healthy individuals residing in ten different provinces in China. The prevalence of P. aeruginosa intestinal carriage was found to be higher in ICU inpatients (10.28%, 95% CI: 7.79%-12.76%) than that in healthy individuals (3.99%, 81/2,031, 95% CI: 3.14%-4.84%). Similarly, the prevalence of carbapenem-resistant P. aeruginosa (CRPA) was higher in ICU inpatients (32.2%) compared to healthy individuals (7.41%). The population structure analysis of our isolates revealed a predominantly non-clonal distribution, with 41 distinct sequence types identified among 59 P. aeruginosa isolates from ICU inpatients and 38 different STs among 81 P. aeruginosa isolates from healthy individuals. These findings suggest that the individual acquisition of P. aeruginosa is more frequent than patient-to-patient transmission, as evidenced by the polyclonal population structure. Antimicrobial susceptibility testing and genome analysis indicated that P. aeruginosa strains from ICU inpatients exhibited significantly higher resistance rates to most antimicrobials and harbored a greater number of acquired resistance genes compared to strains from healthy individuals. Notably, in ICU inpatients, we identified three isolates of ST463, all of which shared the conserved Tn3-TnpR-ISKpn8-blaKPC-ISKpn6 genetic context. Additionally, five isolates carrying the qacE gene were also identified, these findings suggest that small-scale transmission events may still occur within the ICU setting, posing significant challenges for clinical management. With regard to virulence factors, we observed similar profiles between the two groups, except for phzA2, phzB2, and pilA, which were statistically higher in isolates from healthy individuals. This may be because the accumulating resistance mutations in ICU-derived P. aeruginosa are linked to a decrease in virulence.
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Affiliation(s)
- Yanyan Hu
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009 China
| | - Siheng Wang
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009 China
| | - Yanyan Zhang
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009 China
| | - Yuchen Wu
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009 China
| | - Congcong Liu
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009 China
| | - Xiaoyang Ju
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009 China
| | - Hongwei Zhou
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009 China
| | - Chang Cai
- Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology, Zhejiang Agricultural and Forestry University, Hangzhou, China
| | - Rong Zhang
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009 China
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Song Z, Zheng J, Zhao Y, Yin J, Zheng D, Hu H, Liu H, Sun M, Ruan L, Liu F. Population genomics and pathotypic evaluation of the bacterial leaf blight pathogen of rice reveals rapid evolutionary dynamics of a plant pathogen. Front Cell Infect Microbiol 2023; 13:1183416. [PMID: 37305415 PMCID: PMC10250591 DOI: 10.3389/fcimb.2023.1183416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/05/2023] [Indexed: 06/13/2023] Open
Abstract
The Xanthomonas oryzae pv. oryzae (Xoo) is a bacterial pathogen causing bacterial blight disease in rice, resulting in significant yield reductions of up to 50% in rice production. Despite its serious threat to food production globally, knowledge of its population structure and virulence evolution is relatively limited. In this study, we employed whole-genome sequencing to explore the diversity and evolution of Xoo in the main rice-growing areas of China over the past 30 years. Using phylogenomic analysis, we revealed six lineages. CX-1 and CX-2 primarily contained Xoo isolates from South China, while CX-3 represented Xoo isolates from North China. Xoo isolates belonging to CX-5 and CX-6 were the most prevalent across all studied areas, persisting as dominant lineages for several decades. Recent sporadic disease outbreaks were primarily caused by Xoo isolates derived from the two major lineages, CX-5 and CX-6, although Xoo isolates from other lineages also contributed to these outbreaks. The lineage and sub-lineage distributions of Xoo isolates were strongly correlated with their geographical origin, which was found to be mainly determined by the planting of the two major rice subspecies, indica and japonica. Moreover, large-scale virulence testing was conducted to evaluate the diversity of pathogenicity for Xoo. We found rapid virulence evolution against rice, and its determinant factors included the genetic background of Xoo, rice resistance genes, and planting environment of rice. This study provides an excellent model for understanding the evolution and dynamics of plant pathogens in the context of their interactions with their hosts, which are shaped by a combination of geographical conditions and farming practices. The findings of this study may have important implications for the development of effective strategies for disease management and crop protection in rice production systems.
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Affiliation(s)
- Zhiwei Song
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Yancun Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jiakang Yin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Dehong Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Huifeng Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Hongxia Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Jiang T, Li G, Huang L, Ding D, Ruan Z, Yan J. Genomic and Phylogenetic Analysis of a Multidrug-Resistant blaNDM-carrying Klebsiella michiganensis in China. Infect Drug Resist 2023; 16:3109-3116. [PMID: 37228660 PMCID: PMC10202706 DOI: 10.2147/idr.s409544] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023] Open
Abstract
Objective Klebsiella michiganensis is an emerging hospital-acquired bacterial pathogen. However, there is a dearth of knowledge on the antimicrobial resistance and transmission of K. michiganensis. Here, we characterized the microbiological and genomic features of a carbapenem-resistant K. michiganensis strain harboring the blaNDM-1 gene in China. Methods K. michiganensis strain 2563 was recovered from the sputum sample of a hospitalized patient with pulmonary infection. Whole-genome sequencing of K. michiganensis strain 2563 was conducted using both the short-read Illumina and long-read MinION platforms to thoroughly characterize the genetic context of blaNDM-carrying plasmid in K. michiganensis 2563. Furthermore, BacWGSTdb server was utilized to perform in silico multilocus sequence typing (MLST), identify antimicrobial resistance genes, and conduct genomic epidemiological analyses of the closely related isolates deposited in the public database. Results K. michiganensis 2563 was resistant to piperacillin, aztreonam, meropenem, imipenem, amoxicillin-clavulanic acid, ampicillin, cefotaxime, cefazolin, ampicillin/sulbactam, cefepime, piperacillin-tazobactam, and ceftazidime. It belonged to sequence type (ST) 43, and the blaNDM-1 gene was found to be located on the plasmid p2563_NDM (54,035 bp). This plasmid showed remarkable similarity to other blaNDM-1-encoding plasmids found in various Enterobacterium species in the public database. The occurrence of global ST43 K. michiganensis was primarily sporadic, and the closest relative of K. michiganensis 2563 was another ST43 isolate 12,084 recovered from China in 2013, which differed by 171 SNPs. Conclusion Our study reports the genome characteristics of a carbapenem-resistant K. michiganensis strain carrying the blaNDM-1 gene in China, highlighting the need for ongoing surveillance of this pathogen in clinical settings.
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Affiliation(s)
- Tian Jiang
- Department of Clinical Laboratory, The Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, People’s Republic of China
| | - Guoli Li
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Linyao Huang
- Department of Clinical Laboratory, The Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, People’s Republic of China
| | - Ding Ding
- Department of Clinical Laboratory, The Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, People’s Republic of China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Jianxin Yan
- Department of Clinical Laboratory, The Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, People’s Republic of China
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Li Y, Chen J, Wang S, Jiang K, Zhou J, Zhu R, Gao C, Bu W, Xue H. Out of East Asia: Early Warning of the Possible Invasion of the Important Bean Pest Stalk-Eyed Seed Bug Chauliops fallax (Heteroptera: Malcidae: Chauliopinae). INSECTS 2023; 14:insects14050433. [PMID: 37233061 DOI: 10.3390/insects14050433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/27/2023]
Abstract
The short stay at the beginning of the invasion process is a critical time for invasive species identification and preventing invasive species from developing a wider distribution and significant economic impact. The stalk-eyed seed bug Chauliops fallax is an important agricultural pest of soybean and was first reported to occur outside East Asia. Here, we reported the native evolutionary history, recent invasion history, and potential invasion threats of C. fallax for the first time based on population genetic methods and ecological niche modelling. The results showed that four native East Asian genetic groups (EA, WE, TL, and XZ) were well supported, showing an east-west differentiation pattern consistent with the geographical characteristics of three-step landforms in China. Two main haplotypes existed: Hap1 might have experienced a rapid northwards expansion process after the LGM period, and Hap5 reflected local adaptation to the environment in southeastern China. The Kashmir sample was found to come from the recent invasion of populations in the coastal areas of southern China. Ecological niche modelling results suggested that North America has a high risk of invasion, which might pose a serious threat to local soybean production. In addition, with future global warming, the suitable habitat in Asia will move towards the higher latitude region and gradually deviate from the soybean planting area, which indicates the threat of C. fallax to soybean production in Asia will decrease in the future. The results could provide new insights into the monitoring and management of this agricultural pest in the early invasion stage.
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Affiliation(s)
- Yanfei Li
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Juhong Chen
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shujing Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Kun Jiang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiayue Zhou
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Runqi Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Cuiqing Gao
- Co-Innovation Center for the Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
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Liu KD, Jin WJ, Li RB, Zhang RM, Sun J, Liu YH, Wang MG, Liao XP. Prevalence and molecular characteristics of mcr-1-positive Escherichia coli isolated from duck farms and the surrounding environments in coastal China. Microbiol Res 2023; 270:127348. [PMID: 36867961 DOI: 10.1016/j.micres.2023.127348] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/30/2023] [Accepted: 02/26/2023] [Indexed: 03/04/2023]
Abstract
The emergence of colistin-resistance is considered a threat to public health and colistin-resistant bacteria have recently been reported in animal, environmental and human sources. Whereas, the epidemic and dissemination of colistin-resistant bacteria in duck farms have not been surveyed, especially the surrounding environmental contamination from duck farms. We investigated the prevalence and molecular characteristics of mcr-1-positive E. coli from duck farms in coastal China. 360 mcr-1-positive E. coli isolates were collected from 1112 samples from duck farms and surrounding environments. The prevalence of mcr-1-positive E. coli in Guangdong province was higher than other two provinces we examined. PFGE analysis indicated clonal spread of mcr-1-positive E. coli between duck farms and surrounding environments, including water and soil. MLST analysis demonstrated that ST10 was more common than ST1011, ST117, and ST48. Phylogenomic analysis also suggested mcr-1-positive E. coli collected from distinct cities were assigned to the same lineage and mcr-1 was primarily located on IncI2 and IncHI2 plasmids. Genomic environment analysis showed mobile gene elements ISApl1 most likely plays a key role in the horizontal transmission of mcr-1. WGS further revealed that mcr-1 was found associated with 27 different ARGs. Our findings emphasize the urgent need for effective colistin resistance surveillance in humans, animals and the environment.
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Affiliation(s)
- Kai-Di Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
| | - Wen-Jie Jin
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
| | - Run-Bo Li
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
| | - Rong-Min Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, PR China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, PR China
| | - Min-Ge Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China.
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, PR China.
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Tiwari SK, van der Putten BCL, Fuchs TM, Vinh TN, Bootsma M, Oldenkamp R, La Ragione R, Matamoros S, Hoa NT, Berens C, Leng J, Álvarez J, Ferrandis-Vila M, Ritchie JM, Fruth A, Schwarz S, Domínguez L, Ugarte-Ruiz M, Bethe A, Huber C, Johanns V, Stamm I, Wieler LH, Ewers C, Fivian-Hughes A, Schmidt H, Menge C, Semmler T, Schultsz C. Genome-wide association reveals host-specific genomic traits in Escherichia coli. BMC Biol 2023; 21:76. [PMID: 37038177 PMCID: PMC10088187 DOI: 10.1186/s12915-023-01562-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/10/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Escherichia coli is an opportunistic pathogen which colonizes various host species. However, to what extent genetic lineages of E. coli are adapted or restricted to specific hosts and the genomic determinants of such adaptation or restriction is poorly understood. RESULTS We randomly sampled E. coli isolates from four countries (Germany, UK, Spain, and Vietnam), obtained from five host species (human, pig, cattle, chicken, and wild boar) over 16 years, from both healthy and diseased hosts, to construct a collection of 1198 whole-genome sequenced E. coli isolates. We identified associations between specific E. coli lineages and the host from which they were isolated. A genome-wide association study (GWAS) identified several E. coli genes that were associated with human, cattle, or chicken hosts, whereas no genes associated with the pig host could be found. In silico characterization of nine contiguous genes (collectively designated as nan-9) associated with the human host indicated that these genes are involved in the metabolism of sialic acids (Sia). In contrast, the previously described sialic acid regulon known as sialoregulon (i.e. nanRATEK-yhcH, nanXY, and nanCMS) was not associated with any host species. In vitro growth experiments with a Δnan-9 E. coli mutant strain, using the sialic acids 5-N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc) as sole carbon source, showed impaired growth behaviour compared to the wild-type. CONCLUSIONS This study provides an extensive analysis of genetic determinants which may contribute to host specificity in E. coli. Our findings should inform risk analysis and epidemiological monitoring of (antimicrobial resistant) E. coli.
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Affiliation(s)
- Sumeet K Tiwari
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Program, Norwich Research Park, Norwich, UK
| | - Boas C L van der Putten
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Thilo M Fuchs
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Trung N Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Faculty of Veterinary Medicine, College of Agriculture, Can Tho University, Can Tho, Vietnam
| | | | - Rik Oldenkamp
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Life and Environment, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Roberto La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Sebastien Matamoros
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ngo T Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Tropical medicine and global health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Microbiology- Parasitology Unit, Biomedical Research Center and Microbiology Department, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Christian Berens
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Joy Leng
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Julio Álvarez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | | | - Jenny M Ritchie
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Angelika Fruth
- Robert Koch Institute, Enteropathogenic Bacteria and Legionella, Wernigerode, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Lucas Domínguez
- Tropical medicine and global health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Microbiology- Parasitology Unit, Biomedical Research Center and Microbiology Department, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Astrid Bethe
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Charlotte Huber
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Vanessa Johanns
- Robert Koch Institute, Advanced Light and Electron Microscopy, Berlin, Germany
| | - Ivonne Stamm
- Vet Med Labor GmbH, Division of IDEXX Laboratories, Kornwestheim, Germany
| | | | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Giessen, Germany
| | - Amanda Fivian-Hughes
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Herbert Schmidt
- Institute of Food Science and Biotechnology, Department of Food Microbiology and Hygiene, University of Hohenheim, Stuttgart, Germany
| | - Christian Menge
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Torsten Semmler
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany.
| | - Constance Schultsz
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.
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Mason LCE, Greig DR, Cowley LA, Partridge SR, Martinez E, Blackwell GA, Chong CE, De Silva PM, Bengtsson RJ, Draper JL, Ginn AN, Sandaradura I, Sim EM, Iredell JR, Sintchenko V, Ingle DJ, Howden BP, Lefèvre S, Njampeko E, Weill FX, Ceyssens PJ, Jenkins C, Baker KS. The evolution and international spread of extensively drug resistant Shigella sonnei. Nat Commun 2023; 14:1983. [PMID: 37031199 PMCID: PMC10082799 DOI: 10.1038/s41467-023-37672-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/24/2023] [Indexed: 04/10/2023] Open
Abstract
Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with men (MSM). Multidrug resistance in S. sonnei is common including against World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently, an MSM-associated outbreak of extended-spectrum β-lactamase producing, extensively drug resistant S. sonnei was reported in the United Kingdom. Here, we aimed to identify the genetic basis, evolutionary history, and international dissemination of the outbreak strain. Our genomic epidemiological analyses of 3,304 isolates from the United Kingdom, Australia, Belgium, France, and the United States of America revealed an internationally connected outbreak with a most recent common ancestor in 2018 carrying a low-fitness cost resistance plasmid, previously observed in travel associated sublineages of S. flexneri. Our results highlight the persistent threat of horizontally transmitted antimicrobial resistance and the value of continuing to work towards early and open international sharing of genomic surveillance data.
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Affiliation(s)
- Lewis C E Mason
- NIHR HPRU in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - David R Greig
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, UK
| | | | - Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Elena Martinez
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Grace A Blackwell
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Charlotte E Chong
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - P Malaka De Silva
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Rebecca J Bengtsson
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Jenny L Draper
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Andrew N Ginn
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
- Douglass Hanly Moir Pathology, Macquarie Park, NSW, Australia
| | - Indy Sandaradura
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Eby M Sim
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Microbiology Research, Westmead Hospital, Westmead, NSW, Australia
| | - Danielle J Ingle
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sophie Lefèvre
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Elisabeth Njampeko
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | | | - Claire Jenkins
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, UK
| | - Kate S Baker
- NIHR HPRU in Gastrointestinal Infections at University of Liverpool, Liverpool, UK.
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK.
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73
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Sun XY, Yuan JJ, Dong ZE. Small population of the largest water strider after the late Pleistocene and the implications for its conservation. Gene 2023; 859:147219. [PMID: 36702394 DOI: 10.1016/j.gene.2023.147219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023]
Abstract
Climate oscillation and its synergistic impacts on habitat fragmentation have been identified as threatening the survival of some extant species. However, the mechanisms by which semi-aquatic insects impacted by such events remain poorly understood. Herein, we studied the largest water strider in the world, Gigantometra gigas, to explore the effect of these two factors on its evolutionary history. The sequences of mitogenomic and nrDNA cluster were utilized to reconstruct phylogenetic relationship among G. gigas populations and its demographic history. Mitochondrial genes were separately reconstructed topologies of that populations and detected remarkable differences. We found that G. gigas populations conform to the isolation-by-distance model, and decline occurred at about 120 ka, which was probably influenced by the climate change during the late Pleistocene and eventually maintained a small effective population size (Ne) around 85,717. The populations in Guangdong Province of China are worthy of note in that they exhibit low genetic diversity, a small Ne around 18,899 individuals, and occupy an area with little suitable future habitat for G. gigas. This work recommends that conservation efforts are implemented to ensure the long-term survival of small G. gigas populations, and notes that further evaluation of their extinction risk under the impacts of human activities is required.
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Affiliation(s)
- Xiao-Ya Sun
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China.
| | - Juan-Juan Yuan
- College of Life Sciences, Zaozhuang University, Shandong 277160, China
| | - Zhuo-Er Dong
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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74
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Du Z, Zhao Q, Wang X, Sota T, Tian L, Song F, Cai W, Zhao P, Li H. Climatic oscillation promoted diversification of spinous assassin bugs during Pleistocene glaciation. Evol Appl 2023; 16:880-894. [PMID: 37124089 PMCID: PMC10130555 DOI: 10.1111/eva.13543] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/28/2023] Open
Abstract
Insect speciation is among the most fascinating topics in evolutionary biology; however, its underlying mechanisms remain unclear. Allopatric speciation represents one of the major types of speciation and is believed to have frequently occurred during glaciation periods, when climatic oscillation may have caused suitable habitats to be fragmented repeatedly, creating geographical isolation among populations. However, supporting evidence for allopatric speciation of insects in East Asia during the Pleistocene glaciation remains lacking. We aim to investigate the effect of climatic oscillation during the Pleistocene glaciation on the diversification pattern and evolutionary history of hemipteran insects and to test the hypothesis of Pleistocene species stability using spinous assassin bugs Sclomina (Hemiptera: Reduviidae), a small genus widely distributed in southern China but was later found to have cryptic species diversity. Here, using the whole mitochondrial genome (mitogenome) and nuclear ribosomal RNA genes, we investigated both interspecific and intraspecific diversification patterns of spinous assassin bugs. Approximate Bayesian computation, ecological niche modeling, and demographic history analyses were also applied to understand the diversification process and driven factors. Our data suggest that the five species of Sclomina are highly diverged, despite three of them currently being cryptic. Speciation occurred during the Pleistocene when suitable distribution areas were possibly fragmented. Six phylogeographic groups in the type species S. erinacea were identified, among which two groups underwent expansion during the early Last Glacial Period and after Last Glacier Maximum. Our analyses suggest that this genus may have experienced climate-driven habitat fragmentation and postglacial expansion in the Pleistocene, promoting allopatric speciation and intraspecific diversification. Our results reveal underestimated species diversity in a small insect group and illustrate a remarkable example of allopatric speciation of insects in East Asia promoted by Pleistocene climatic oscillations. These findings provide important insights into the speciation processes and aid the conservation of insect species diversity.
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Affiliation(s)
- Zhenyong Du
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
| | - Qian Zhao
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
| | - Xuan Wang
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
| | - Teiji Sota
- Department of Zoology, Graduate School of ScienceKyoto University, SakyoKyotoJapan
| | - Li Tian
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
| | - Fan Song
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
| | - Wanzhi Cai
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
| | - Ping Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf (Ministry of Education) and Guangxi Key Laboratory of Earth Surface Processes and Intelligent SimulationNanning Normal UniversityNanningChina
| | - Hu Li
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
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75
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Liu X, He J, Du Z, Zhang R, Cai W, Li H. Weak genetic structure of flower thrips Frankliniella intonsa in China revealed by mitochondrial genomes. Int J Biol Macromol 2023; 231:123301. [PMID: 36657550 DOI: 10.1016/j.ijbiomac.2023.123301] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/01/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023]
Abstract
Human activities facilitate long-distance dispersal of insects beyond their native range. In particular, the transportation of live plants offers diffusion opportunities for some insects with weak flight abilities. The increase in urban afforestation also help insect reside in urban habitats. The flower thrips, Frankliniella intonsa, is a widespread pest that causes serious damage to many economically important plants. Human activities are likely to facilitate the dispersal of this pest, however, the population genetic structure of this pest remains unclear. Herein, high-throughput sequencing was used to obtain 149 whole mitochondrial genomes of flower thrips from 28 geographic populations in China. Population genetic analyses, phylogenetic reconstruction, and inference of demographic history were then performed. A weak genetic structure was found among all populations across large geographic distance in China, in which five mitochondrial haplotype lineages were resolved. One of the lineages was identified to be shared among most samples collected from central city areas, which may be derived from the surrounding areas. Demographic history analyses suggested a recent population expansion of F. intonsa. Overall, the present population genetic structure of flower thrips in China may be promoted by human-mediated urban afforestation across the country.
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Affiliation(s)
- Xinzhi Liu
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Jia He
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, China; Ningxia Key Lab of Plant Disease and Pest Control, Yinchuan 750002, China
| | - Zhenyong Du
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Rong Zhang
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, China; Ningxia Key Lab of Plant Disease and Pest Control, Yinchuan 750002, China
| | - Wanzhi Cai
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Hu Li
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572025, China.
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76
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Li F, Li X, Cheng CC, Bujdoš D, Tollenaar S, Simpson DJ, Tasseva G, Perez-Muñoz ME, Frese S, Gänzle MG, Walter J, Zheng J. A phylogenomic analysis of Limosilactobacillus reuteri reveals ancient and stable evolutionary relationships with rodents and birds and zoonotic transmission to humans. BMC Biol 2023; 21:53. [PMID: 36907868 PMCID: PMC10010030 DOI: 10.1186/s12915-023-01541-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 02/09/2023] [Indexed: 03/14/2023] Open
Abstract
BACKGROUND Gut microbes play crucial roles in the development and health of their animal hosts. However, the evolutionary relationships of gut microbes with vertebrate hosts, and the consequences that arise for the ecology and lifestyle of the microbes are still insufficiently understood. Specifically, the mechanisms by which strain-level diversity evolved, the degree by which lineages remain stably associated with hosts, and how their evolutionary history influences their ecological performance remain a critical gap in our understanding of vertebrate-microbe symbiosis. RESULTS This study presents the characterization of an extended collection of strains of Limosilactobacillus reuteri and closely related species from a wide variety of hosts by phylogenomic and comparative genomic analyses combined with colonization experiments in mice to gain insight into the long-term evolutionary relationship of a bacterial symbiont with vertebrates. The phylogenetic analysis of L. reuteri revealed early-branching lineages that primarily consist of isolates from rodents (four lineages) and birds (one lineage), while lineages dominated by strains from herbivores, humans, pigs, and primates arose more recently and were less host specific. Strains from rodent lineages, despite their phylogenetic divergence, showed tight clustering in gene-content-based analyses. These L. reuteri strains but not those ones from non-rodent lineages efficiently colonize the forestomach epithelium of germ-free mice. The findings support a long-term evolutionary relationships of L. reuteri lineages with rodents and a stable host switch to birds. Associations of L. reuteri with other host species are likely more dynamic and transient. Interestingly, human isolates of L. reuteri cluster phylogenetically closely with strains from domesticated animals, such as chickens and herbivores, suggesting zoonotic transmissions. CONCLUSIONS Overall, this study demonstrates that the evolutionary relationship of a vertebrate gut symbiont can be stable in particular hosts over time scales that allow major adaptations and specialization, but also emphasizes the diversity of symbiont lifestyles even within a single bacterial species. For L. reuteri, symbiont lifestyles ranged from autochthonous, likely based on vertical transmission and stably aligned to rodents and birds over evolutionary time, to allochthonous possibly reliant on zoonotic transmission in humans. Such information contributes to our ability to use these microbes in microbial-based therapeutics.
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Affiliation(s)
- Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Xudong Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Christopher C Cheng
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Dalimil Bujdoš
- School of Microbiology, and Department of Medicine, APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Stephanie Tollenaar
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - David J Simpson
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Guergana Tasseva
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Maria Elisa Perez-Muñoz
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Steven Frese
- Department of Nutrition, University of Nevada, Reno, NV, 89557, USA
| | - Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada. .,Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E1, Canada. .,School of Microbiology, and Department of Medicine, APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China.
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Cabrera A, Pita S, González T, Viera A, Verger L, Piegas S, Willat G, Fresia P, Basmadjián Y. Genetic variability highlights the invasion route of the Lutzomyia longipalpis complex, the main vector of Visceral Leishmaniasis in Uruguay. Zoonoses Public Health 2023. [PMID: 36898974 DOI: 10.1111/zph.13036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 03/12/2023]
Abstract
In the Americas, the sandfly Lutzomyia longipalpis is the main vector of the parasitic protozoa Leishmania infantum, the etiological agent of visceral leishmaniasis (VL). The Lu. longipalpis species complex is currently discontinuously distributed across the Neotropical region, from Mexico to the north of Argentina and Uruguay. During its continental spreading, it must have adapted to several biomes and temperature amplitudes, when founder events should have contributed to the high genetic divergence and geographical structure currently observed, reinforcing the speciation process. The first report of Lu. longipalpis in Uruguay was in 2010, calling the attention of Public Health authorities. Five years later, the parasite Le. infantum was recorded and in 2015 the first case of VL in canids was reported. Hitherto seven human cases by VL have been reported in Uruguay. Here, we publish the first DNA sequences from the mitochondrial genes ND4 and CYTB of Lu. longipalpis collected in Uruguay, and we used these molecular markers to investigate their genetic variability and population structure. We described four new ND4 haplotypes in a total of 98 (4/98) and one CYTB in a total of 77 (1/77). As expected, we were able to establish that the Lu. longipalpis collected in two localities (i.e. Salto and Bella Unión) from the north of Uruguay are closely related to the populations from neighbouring countries. We also propose that the possible route for the vector arrival to the region may have been through vegetation and forest corridors of the Uruguay River system, as well as it may have benefited from landscape modifications generated by commercial forestation. The ecological-scale processes shaping Lu. longipalpis populations, the identification of genetically homogeneous groups and the gene flow among them must be carefully investigated by using highly sensible molecular markers (i.e. genome wide SNPs) since it will help to the understanding of VL transmission and contribute to the planification of public policies on its control.
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Affiliation(s)
- Andrés Cabrera
- Departamento de Parasitología y Micología, Instituto de Higiene, Facultad de Medicina, UdelaR, Montevideo, Uruguay.,Laboratorio de Interacciones Hospedero-Patógeno, Institut Pasteur Montevideo, Montevideo, Uruguay.,Unidad de Microbiología, Departamento de Patobiología, Facultad de Veterinaria, UdelaR, Montevideo, Uruguay
| | - Sebastián Pita
- Laboratorio de Interacciones Hospedero-Patógeno, Institut Pasteur Montevideo, Montevideo, Uruguay.,Sección Genética Evolutiva, Facultad de Ciencias, UdelaR, Montevideo, Uruguay
| | - Telma González
- Departamento de Parasitología y Micología, Instituto de Higiene, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Ana Viera
- Departamento de Parasitología y Micología, Instituto de Higiene, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Lorenzo Verger
- Ministerio de Salud Pública, Uruguay, Montevideo, Uruguay
| | - Sofia Piegas
- Ministerio de Salud Pública, Uruguay, Montevideo, Uruguay
| | | | - Pablo Fresia
- Unidad Mixta Pasteur+INIA (UMPI), Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Yester Basmadjián
- Departamento de Parasitología y Micología, Instituto de Higiene, Facultad de Medicina, UdelaR, Montevideo, Uruguay
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78
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Wu Y, Dong N, Cai C, Zeng Y, Lu J, Liu C, Wang H, Zhang Y, Huang L, Zhai W, Shao D, Li R, Liu D, Chen S, Zhang R. Aeromonas spp. from hospital sewage act as a reservoir of genes resistant to last-line antibiotics. Drug Resist Updat 2023; 67:100925. [PMID: 36696835 DOI: 10.1016/j.drup.2023.100925] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 12/13/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
BACKGROUND Aeromonas species are opportunistic pathogens distributed widely in the ecosystem. They are known to be capable of acquiring antibiotic resistance genes, including those encoding proteins against last-line antibiotics, such as the tmexCD-toprJ, mcr and carbapenemase genes. We investigated the genomic and phenotypic characteristics of tmexCD-toprJ-positive Aeromonas strains collected from human, animals, and water samples, particularly those from hospital wastewater in China. METHODS Samples were collected from living animals, meat, water and human. Aeromonas strains in these samples were isolated in selective media. Antimicrobial resistance profiles of all Aeromonas strains were tested by the broth microdilution method. The presence of tmexCD-toprJ was verified by polymerase chain reaction (PCR). All tmexCD-toprJ-positive (n = 36) and selected tmexCD-toprJ-negative (n = 18) Aeromonas strains were subjected to whole genome sequencing. Carriage of antimicrobial resistance genes, the genetic environment of tmexCD-toprJ and genetic diversity of tmexCD-toprJ-positive Aeromonas strains were determined by bioinformatics analysis. Phylogenetic tree of the Aeromonas strains was built by using the Harvest Suite. FINDINGS Among the 636 Aeromonas strains isolated from different sources, 36 were positive for tmexCD-toprJ, with the highest prevalence of tmexCD-toprJ being found in fishes (8.8%, 95 CI% 3.6-17.2%), followed by hospital wastewater (6.5%, 95 CI% 4.3-9.3%), river water (2.0%, 0.1-10.9) and duck (1.2%, 95 CI% 3.6-17.2%). All tmexCD-toprJ-positive Aeromonas strains carried multiple antimicrobial resistance genes and exhibited resistance to different classes of antibiotics. Co-existence of tmexCD-toprJ, mcr and blaKPC-2 were identified in 21 strains. The tmexCD-toprJ-positive Aeromonas strains were genetically diverse and found to belong to four different species that could be clustered into three major lineages. The tmexCD-toprJ gene clusters were predominantly located in the chromosome (35/36) of Aeromonas spp., with only one strain carrying the plasmid-borne tmexCD-toprJ cluster. The tmexCD-toprJ genes were associated with seven different types of genetic environments, each of which carried distinct types of mobile elements that may be responsible for mediating transmission of this gene cluster.
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Affiliation(s)
- Yuchen Wu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Ning Dong
- Department of Medical Microbiology, School of Biology and Basic Medical Science, Medical College of Soochow University, Suzhou, China; Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Soochow University, Suzhou, China
| | - Chang Cai
- China Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology, Zhejiang Agricultural and Forestry University, Hangzhou, China
| | - Yu Zeng
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen, China
| | - Jiayue Lu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Congcong Liu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Hanyu Wang
- New Jersey Institute of Technology, NJ, United States
| | - Yanyan Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Ling Huang
- Department of Clinical Laboratory, The Women's and Children's Hospital of Linping District, Hangzhou, China
| | - Weishuai Zhai
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Dongyan Shao
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Jiangsu, China
| | - Dejun Liu
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China.
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.
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Vega M, Quintero‐Corrales C, Mastretta‐Yanes A, Casas A, López‐Hilario V, Wegier A. Multiple domestication events explain the origin of Gossypium hirsutum landraces in Mexico. Ecol Evol 2023; 13:e9838. [PMID: 36911302 PMCID: PMC9994486 DOI: 10.1002/ece3.9838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 03/14/2023] Open
Abstract
Several Mesoamerican crops constitute wild-to-domesticated complexes generated by multiple initial domestication events, and continuous gene flow among crop populations and between these populations and their wild relatives. It has been suggested that the domestication of cotton (Gossypium hirsutum) started in the northwest of the Yucatán Peninsula, from where it spread to other regions inside and outside of Mexico. We tested this hypothesis by assembling chloroplast genomes of 23 wild, landraces, and breeding lines (transgene-introgressed and conventional). The phylogenetic analysis showed that the evolutionary history of cotton in Mexico involves multiple events of introgression and genetic divergence. From this, we conclude that Mexican landraces arose from multiple wild populations. Our results also revealed that their structural and functional chloroplast organizations had been preserved. However, genetic diversity decreases as a consequence of domestication, mainly in transgene-introgressed (TI) individuals (π = 0.00020, 0.00001, 0.00016, 0, and 0, of wild, TI-wild, landraces, TI-landraces, and breeding lines, respectively). We identified homologous regions that differentiate wild from domesticated plants and indicate a relationship among the samples. A decrease in genetic diversity associated with transgene introgression in cotton was identified for the first time, and our outcomes are therefore relevant to both biosecurity and agrobiodiversity conservation.
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Affiliation(s)
- Melania Vega
- Genética de la Conservación, Jardín BotánicoInstituto de Biología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Christian Quintero‐Corrales
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
- Departamento de BotánicaInstituto de Biología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Alicia Mastretta‐Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO)Ciudad de MéxicoMexico
- Consejo Nacional de Ciencia y Tecnología (CONACYT) Programa de Investigadores e Investigadoras por MéxicoCiudad de MéxicoMexico
| | - Alejandro Casas
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de MéxicoMoreliaMexico
| | | | - Ana Wegier
- Genética de la Conservación, Jardín BotánicoInstituto de Biología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
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Carriage and Transmission of mcr-1 in Salmonella Typhimurium and Its Monophasic 1,4,[5],12:i:- Variants from Diarrheal Outpatients: a 10-Year Genomic Epidemiology in Guangdong, Southern China. Microbiol Spectr 2023; 11:e0311922. [PMID: 36629419 PMCID: PMC9927551 DOI: 10.1128/spectrum.03119-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The banning of colistin as a feed additive for food-producing animals in mainland China in 2017 caused the decline in the prevalence of Escherichia coli-mobilized colistin resistance (mcr-1) in China. Salmonella Typhimurium and its monophasic 1,4,[5],12:i:- variants are also the main species associated with the spread of mcr-1; however, the evidence of the prevalence and transmission of mcr-1 among Salmonella is lacking. Herein, the 5,354 Salmonella isolates recovered from fecal samples of diarrheal patients in Guangdong, Southern China, from 2009 to 2019 were screened for colistin resistance and mcr-1, and mcr-1-positive isolates were characterized based on whole-genome sequencing (WGS) data. Relatively high prevalence rates of colistin resistance and mcr-1 (4.05%/4.50%) were identified, and more importantly, the prevalence trends of colistin-resistant and mcr-1-positive Salmonella isolates had a similar dynamic profile, i.e., both were first detected in 2012 and rapidly increased during 2013 to 2016, followed by a sharp decrease since 2017. WGS and phylogenetic analysis indicate that, whether before or after the ban, the persistence and cross-hospital transmission of mcr-1 are primarily determined by IncHI2 plasmids with similar backbones and sequence type 34 (ST34) Salmonella in specific clades that are associated with a high prevalence of IncHI2 plasmids and clinically important antimicrobial resistance genes, including blaCTX-M-14-fosA3-oqxAB-floR genotypes. Our work reveals the difference in the prevalence rate of mcr-1 in clinical Salmonella before and after the Chinese colistin ban, whereas mcr-1 transmission was closely linked to multidrug-resistant IncHI2 plasmid and ST34 Salmonella across diverse hospitals over 10 years. Continued surveillance is required to explore the factors related to a sharp decrease in mcr-1 after the recent ban and determine whether the ban has affected the carriage of mcr-1 in Salmonella circulating in the health care system. IMPORTANCE Colistin is one of the last-line antibiotics for the clinical treatment of Enterobacteriaceae. However, the emergence of the mobilized colistin resistance (mcr-1) gene has spread throughout the entire human health system and largely threatens the usage of colistin in the clinical setting. In this study, we investigated the existence of mcr-1 in clinical Salmonella from a 10-year continuous surveillance and genomic study. Overall, the colistin resistance rate and mcr-1 carriage of Salmonella in tertiary hospitals in Guangdong (2009 to 2019) were relatively high and, importantly, rapidly increased from 2013 to 2016 and significantly decreased after the Chinese colistin withdrawal. However, before or after the ban, the MDR IncHI2 plasmid with a similar backbone and ST34 Salmonella were the main vectors involved in the spread of mcr-1. Interestingly, these Chinese mcr-1-carrying Salmonella obtain phylogenetically and phylogeographically distinct patterns compared with those from other continents and are frequently associated with clinically important ARGs including the extended-spectrum β-lactamases. Our data confirmed that the national stewardship intervention seems to be successful in blocking antibiotic resistance determinants and that continued surveillance of colistin resistance in clinical settings, farm animals, and related products is necessary.
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Novel Multilocus Sequence Typing and Global Sequence Clustering Schemes for Characterizing the Population Diversity of Streptococcus mitis. J Clin Microbiol 2023; 61:e0080222. [PMID: 36515506 PMCID: PMC9879099 DOI: 10.1128/jcm.00802-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Streptococcus mitis is a common oral commensal and an opportunistic pathogen that causes bacteremia and infective endocarditis; however, the species has received little attention compared to other pathogenic streptococcal species. Effective and easy-to-use molecular typing tools are essential for understanding bacterial population diversity and biology, but schemes specific for S. mitis are not currently available. We therefore developed a multilocus sequence typing (MLST) scheme and defined sequence clusters or lineages of S. mitis using a comprehensive global data set of 322 genomes (148 publicly available and 174 newly sequenced). We used internal 450-bp sequence fragments of seven housekeeping genes (accA, gki, hom, oppC, patB, rlmN, and tsf) to define the MLST scheme and derived the global S. mitis sequence clusters using the PopPUNK clustering algorithm. We identified an initial set of 259 sequence types (STs) and 258 global sequence clusters. The schemes showed high concordance (100%), capturing extensive S. mitis diversity with strains assigned to multiple unique STs and global sequence clusters. The tools also identified extensive within- and between-host S. mitis genetic diversity among isolates sampled from a cohort of healthy individuals, together with potential transmission events, supported by both phylogeny and pairwise single nucleotide polymorphism (SNP) distances. Our novel molecular typing and strain clustering schemes for S. mitis allow for the integration of new strain data, are electronically portable at the PubMLST database (https://pubmlst.org/smitis), and offer a standardized approach to understanding the population structure of S. mitis. These robust tools will enable new insights into the epidemiology of S. mitis colonization, disease and transmission.
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Gostev VV, Sulian O, Pavlova P, Nesterova E, Kalinogorskaya O, Chulkova P, Trofimova N, Ageevets V, Ageevets I, Sidorenko SV. Genomic characterization of oxacillin-susceptible mecA-positive Staphylococcus aureus ST59. CLINICAL MICROBIOLOGY AND ANTIMICROBIAL CHEMOTHERAPY 2023; 25:116-122. [DOI: 10.36488/cmac.2023.2.116-122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
Abstract
Objective.
To characterize the genomes of oxacillin-susceptible mecA-positive Staphylococcus aureus ST59 isolated in St. Petersburg.
Materials and Methods.
Nine oxacillin-susceptible mecA-positive of S. aureus isolates (OS-MRSA) of ST59 were included in the study. The isolates were obtained from children who showed no clinical signs of staphylococcal infections during nasal screening of S. aureus in St. Petersburg in 2018–2019. One isolate was obtained from an adult patient with skin and soft tissue infection (SSTI). The susceptibility to antibiotics and whole genome sequencing were performed. The analysis included 242 genomes of S. aureus ST59 from open access databases.
Results.
By employing the broth serial dilution and VITEK, the isolates’ phenotypic susceptibility to oxacillin was determined. The cefoxitin inhibition zones ranged from 17 to 22 mm. All isolates showed a penicillinclavulanate MIC ≤ 0.5 µg/mL. Isolates obtained from carriers belonged to the ST59-t1950-SCCmec Vb (seb+) genotype whereas the isolate obtained from SSTI belonged to the ST59-t437-SCCmec Vb (seb/ lukF/lukS+) genotype. Nucleotide position -33 (C/T) of mecA promoter and mutations in PBP2a (S225R + E246G) were present in all isolates. Based on phylogenetic analysis and Bayesian clustering the ST59 genomes were divided into four clusters and all Russian genomes belonged to the East Asian ST59 sublineage. The PVL toxin was present in the genomes of the first cluster of the East Asian ST59 sublineage. Pairwise comparisons of nucleotide substitutions among the genomes of Russian isolates showed a high similarity: median 13, interquartile range 8–18. All ST59 clusters were characterized by the presence of enterotoxin B, as well as mutations in PBP2a (S225R and E246G) and the promoter regions of the mecA gene (-7 G/A or -33 C/T). The genomes of the Russian isolates differed from the globally spread ST59 by specific mutations at the following loci (relative to the reference genome of S. aureus M013TW): lactose catabolism regulator RS03495 (N168D), ribosomal protein L28 (V47A), putative glyoxalase RS07825 (V42A), and the hypothetical protein RS13235 (K32E).
Conclusions.
Russian MRSA-ST59 isolates belong to the East Asian sublineage and are characterized by the presence of the enterotoxin B gene. Oxacillin susceptibility and borderline resistance to cefoxitin are specific characteristics of MRSA-ST59. OS-MRSA phenotypes have a risk of improper sensitivity testing leading to ineffective antibiotic treatment. Detection of mecA gene is the most accurate method for differentiating between MSSA and MRSA.
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Affiliation(s)
- Vladimir V. Gostev
- Children Scientific Clinical Center of Infectious Disease; North-Western State Medical University named after I.I. Mechnikov (Saint-Petersburg, Russia)
| | - O.S. Sulian
- Children Scientific Clinical Center of Infectious Diseases (Saint-Petersburg, Russia)
| | - P.A. Pavlova
- Children Scientific Clinical Center of Infectious Diseases; Saint-Petersburg State University (Saint-Petersburg, Russia)
| | - E.V. Nesterova
- City Skin and Venereal Diseases Dispensary (Saint-Petersburg, Russia)
| | - O.S. Kalinogorskaya
- Children Scientific Clinical Center of Infectious Diseases (Saint-Petersburg, Russia)
| | - P.S. Chulkova
- Children Scientific Clinical Center of Infectious Diseases (Saint-Petersburg, Russia)
| | - N.N. Trofimova
- City Skin and Venereal Diseases Dispensary (Saint-Petersburg, Russia)
| | - V.A. Ageevets
- Children Scientific Clinical Center of Infectious Diseases (Saint-Petersburg, Russia)
| | - I.V. Ageevets
- Children Scientific Clinical Center of Infectious Diseases (Saint-Petersburg, Russia)
| | - Sergey V. Sidorenko
- Children Scientific Clinical Center of Infectious Disease; North-Western State Medical University named after I.I. Mechnikov (Saint-Petersburg, Russia)
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Wang S, Li Y, Zhou J, Jiang K, Chen J, Ye Z, Xue H, Bu W. The anthropogenic effect of land use on population genetics of Malcus inconspicuus. Evol Appl 2023; 16:98-110. [PMID: 36699121 PMCID: PMC9850013 DOI: 10.1111/eva.13512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022] Open
Abstract
Since the beginning of the Holocene era, human activities have seriously impacted animal habitats and vegetative environments. Species that are dependent on natural habitats or with narrow niches might be more severely affected by habitat changes. Malcus inconspicuus is distributed in subtropical China and highly dependent on the mountain environment. Our study investigated the role of the mountainous landscape in the historical evolution of M. inconspicuus and the impact of Holocene human activities on it. A phylogeographical approach was implemented with integrative datasets including double-digest restriction site-associated DNA (ddRAD), mitochondrial data, and distribution data. Three obvious clades and an east-west phylogeographical pattern were found in subtropical China. Mountainous landscape has "multifaceted" effects on the evolutionary history of M. inconspicuus, it has contributed to population differentiation, provided glacial refuges, and provided population expansion corridors during the postglacial period. The effective population size (Ne) of M. inconspicuus showed a sharp decline during the Holocene era, which revealed a significantly negative correlation with the development of cropland in a hilly area at the same time and space. It supported that the species which are highly dependent on natural habitats might undergo greater impact when the habitat was damaged by agricultural activities and we should pay more attention to them, especially in the land development of their distribution areas.
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Affiliation(s)
- Shujing Wang
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Yanfei Li
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Jiayue Zhou
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Kun Jiang
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Juhong Chen
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Zhen Ye
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Huaijun Xue
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Wenjun Bu
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
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Santos PD, Günther A, Keller M, Homeier-Bachmann T, Groschup MH, Beer M, Höper D, Ziegler U. An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany. Virus Evol 2023; 9:vead013. [PMID: 37197362 PMCID: PMC10184446 DOI: 10.1093/ve/vead013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/13/2023] [Accepted: 03/16/2023] [Indexed: 05/19/2023] Open
Abstract
West Nile virus (WNV) is the most widespread arthropod-borne (arbo) virus and the primary cause of arboviral encephalitis globally. Members of WNV species genetically diverged and are classified into different hierarchical groups below species rank. However, the demarcation criteria for allocating WNV sequences into these groups remain individual and inconsistent, and the use of names for different levels of the hierarchical levels is unstructured. In order to have an objective and comprehensible grouping of WNV sequences, we developed an advanced grouping workflow using the 'affinity propagation clustering' algorithm and newly included the 'agglomerative hierarchical clustering' algorithm for the allocation of WNV sequences into different groups below species rank. In addition, we propose to use a fixed set of terms for the hierarchical naming of WNV below species level and a clear decimal numbering system to label the determined groups. For validation, we applied the refined workflow to WNV sequences that have been previously grouped into various lineages, clades, and clusters in other studies. Although our workflow regrouped some WNV sequences, overall, it generally corresponds with previous groupings. We employed our novel approach to the sequences from the WNV circulation in Germany 2020, primarily from WNV-infected birds and horses. Besides two newly defined minor (sub)clusters comprising only three sequences each, Subcluster 2.5.3.4.3c was the predominant WNV sequence group detected in Germany from 2018 to 2020. This predominant subcluster was also associated with at least five human WNV infections in 2019-20. In summary, our analyses imply that the genetic diversity of the WNV population in Germany is shaped by enzootic maintenance of the dominant WNV subcluster accompanied by sporadic incursions of other rare clusters and subclusters. Moreover, we show that our refined approach for sequence grouping yields meaningful results. Although we primarily aimed at a more detailed WNV classification, the presented workflow can also be applied to the objective genotyping of other virus species.
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Affiliation(s)
| | | | - Markus Keller
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, 17493, Greifswald-Insel Riems, Germany
| | | | - Martin H Groschup
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, 17493, Greifswald-Insel Riems, Germany
- German Centre for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, 17493, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, 17493, Greifswald-Insel Riems, Germany
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85
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Liao M, Wu J, Li Y, Lu X, Tan H, Chen S, Huang W, Lian X, Sun J, Liao X, Liu Y, Feng S, Zhang R. Prevalence and Persistence of Ceftiofur-Resistant Escherichia coli in A Chicken Layer Breeding Program. Animals (Basel) 2022; 13:ani13010090. [PMID: 36611699 PMCID: PMC9817529 DOI: 10.3390/ani13010090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
We determined the longitudinal persistence of ceftiofur-resistant Escherichia coli from a chicken breeding farm in China. A total of 150 samples were collected from 5 breeding periods in a flock of layer hens, and the prevalence of ceftiofur-resistant E. coli fluctuated across the 5 chicken breeding stages: eggs, 3.33%; growing period, 100%; early laying period, 36.7%; peak laying period, 66.7% and late laying period, 80%. The most prevalent ceftiofur resistance genes were blaCTX-M-55, blaCMY and blaNDM, and ST101 was the most prevalent and persistent sequence type across the breeding periods. Our results indicated that this breeder flock was heavily contaminated by ST101 ceftiofur-resistant E. coli and that its presence should be intensively monitored on chicken farms.
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Affiliation(s)
- Meina Liao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Jiaen Wu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Yafei Li
- Institute of Quality Standard and Monitoring Technology for Agro-Products, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiaoqing Lu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Huizhen Tan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Shanshan Chen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Wenqing Huang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Xinlei Lian
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Jian Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoping Liao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Yahong Liu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Saixiang Feng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (S.F.); (R.Z.)
| | - Rongmin Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (S.F.); (R.Z.)
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86
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Zhang Y, Li W, Tian X, Sun R, Zhou S, Jia L, Sun J, Liao XP, Liu YH, Yu Y. Phenotypic and Genotypic Characterization of Carbapenem-Resistant Enterobacteriaceae Recovered from a Single Hospital in China, 2013 to 2017. Infect Drug Resist 2022; 15:7679-7690. [PMID: 36582450 PMCID: PMC9793792 DOI: 10.2147/idr.s393155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/09/2022] [Indexed: 12/25/2022] Open
Abstract
Objective Carbapenem-resistant Enterobacteriaceae (CRE) have become an increasingly common cause of healthcare-related infections and present a serious challenge to clinical treatment. This study examined the phenotypic, genotypic characterization, clinical, and microbiological data of CRE in the Huizhou Municipal Central Hospital. Methods We conducted a phenotypic susceptibility evaluation and whole genome sequence analysis for 52 CRE strains isolated from 37 patients and 2 medical device-related samples during 2013-2017 to characterize risk factors, antimicrobial resistance profiles, dominant clones and hospital transmission. Results Long-term hospitalization, treatment time with antibiotics and use of invasive devices were linked to the risk of CRE infection. The carbapenem resistance genes (CRGs) we found included blaNDM (82.7%), blaIMP (19.2%) and blaKPC (3.8%), Escherichia coli (44.2%) and Klebsiella pneumoniae (44.2%) were the dominant species we identified, and the type of CRG carried by isolates was highly correlated with species. The coexistence of CRGs with a variety of other antibiotic resistance genes leads to an increased prevalence of high resistance levels for CRE to β-lactams and other antibiotic classes such as aminoglycosides and fluoroquinolones. These isolates were sensitive only to colistin and tigecycline. In addition to this, we observed significantly genomic diversity of CRE isolates in this hospital. Importantly, we found that long-term transmission of multiple CRE clones had occurred at this hospital between various wards. Conclusion Evaluating and improving the current infection control strategies may be necessary, and reducing nosocomial transmission remains the primary control element for CRE infections in China.
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Affiliation(s)
- Yan Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Wenjie Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Xiaomin Tian
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Ruanyang Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Shidan Zhou
- Intensive Care Unit, Huizhou Municipal Central Hospital, Huizhou, People’s Republic of China
| | - Ling Jia
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Jian Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, People’s Republic of China,Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Science, Guangzhou, People’s Republic of China,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, People’s Republic of China
| | - Xiao-Ping Liao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, People’s Republic of China,Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Science, Guangzhou, People’s Republic of China,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, People’s Republic of China
| | - Ya-Hong Liu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, People’s Republic of China,Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Science, Guangzhou, People’s Republic of China,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, People’s Republic of China
| | - Yang Yu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, People’s Republic of China,Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Science, Guangzhou, People’s Republic of China,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, People’s Republic of China,Correspondence: Yang Yu, Email
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87
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Impact of international travel and diarrhea on gut microbiome and resistome dynamics. Nat Commun 2022; 13:7485. [PMID: 36470885 PMCID: PMC9722912 DOI: 10.1038/s41467-022-34862-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/08/2022] [Indexed: 12/11/2022] Open
Abstract
International travel contributes to the global spread of antimicrobial resistance. Travelers' diarrhea exacerbates the risk of acquiring multidrug-resistant organisms and can lead to persistent gastrointestinal disturbance post-travel. However, little is known about the impact of diarrhea on travelers' gut microbiomes, and the dynamics of these changes throughout travel. Here, we assembled a cohort of 159 international students visiting the Andean city of Cusco, Peru and applied next-generation sequencing techniques to 718 longitudinally-collected stool samples. We find that gut microbiome composition changed significantly throughout travel, but taxonomic diversity remained stable. However, diarrhea disrupted this stability and resulted in an increased abundance of antimicrobial resistance genes that can remain high for weeks. We also identified taxa differentially abundant between diarrheal and non-diarrheal samples, which were used to develop a classification model that distinguishes between these disease states. Additionally, we sequenced the genomes of 212 diarrheagenic Escherichia coli isolates and found those from travelers who experienced diarrhea encoded more antimicrobial resistance genes than those who did not. In this work, we find the gut microbiomes of international travelers' are resilient to dysbiosis; however, they are also susceptible to colonization by multidrug-resistant bacteria, a risk that is more pronounced in travelers with diarrhea.
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Shen Y, Zhang R, Shao D, Yang L, Lu J, Liu C, Wang X, Jiang J, Wang B, Wu C, Parkhill J, Wang Y, Walsh TR, Gao GF, Shen Z. Genomic Shift in Population Dynamics of mcr-1-positive Escherichia coli in Human Carriage. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1168-1179. [PMID: 36481457 DOI: 10.1016/j.gpb.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 11/07/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Emergence of the colistin resistance gene, mcr-1, has attracted worldwide attention. Despite the prevalence of mcr-1-positive Escherichia coli (MCRPEC) strains in human carriage showing a significant decrease between 2016 and 2019, genetic differences in MCRPEC strains remain largely unknown. We therefore conducted a comparative genomic study on MCRPEC strains from fecal samples of healthy human subjects in 2016 and 2019. We identified three major differences in MCRPEC strains between these two time points. First, the insertion sequence ISApl1 was often deleted and the percentage of mcr-1-carrying IncI2 plasmids was increased in MCRPEC strains in 2019. Second, the antibiotic resistance genes (ARGs), aac(3)-IVa and blaCTX-M-1, emerged and coexisted with mcr-1 in 2019. Third, MCRPEC strains in 2019 contained more virulence genes, resulting in an increased proportion of extraintestinal pathogenic E. coli (ExPEC) strains (36.1%) in MCRPEC strains in 2019 compared to that in 2016 (10.5%), which implies that these strains could occupy intestinal ecological niches by competing with other commensal bacteria. Our results suggest that despite the significant reduction in the prevalence of MCRPEC strains in humans, mcr-1 is now associated with more stable genetic structures as well as the widespread IncI2 plasmid exhibits increased coexistence with other clinically important ARGs, and is increasingly associated with ExPEC strains, thus posing a potential public health threat.
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Affiliation(s)
- Yingbo Shen
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510641, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rong Zhang
- The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Dongyan Shao
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Lu Yang
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jiayue Lu
- The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Congcong Liu
- The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Xueyang Wang
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Junyao Jiang
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Boxuan Wang
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Congming Wu
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510641, China
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Yang Wang
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510641, China
| | - Timothy R Walsh
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK.
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Zhangqi Shen
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510641, China.
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89
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Leigh RJ, McKenna C, McWade R, Lynch B, Walsh F. Comparative genomics and pangenomics of vancomycin-resistant and susceptible Enterococcus faecium from Irish hospitals. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction.
Enterococcus faecium
has emerged as an important nosocomial pathogen, which is increasingly difficult to treat due to the genetic acquisition of vancomycin resistance. Ireland has a recalcitrant vancomycin-resistant bloodstream infection rate compared to other developed countries.
Hypothesis/Gap statement. Vancomycin resistance rates persist amongst
E. faecium
isolates from Irish hospitals. The evolutionary genomics governing these trends have not been fully elucidated.
Methodology. A set of 28 vancomycin-resistant isolates was sequenced to construct a dataset alongside 61 other publicly available Irish genomes. This dataset was extensively analysed using in silico methodologies (comparative genomics, pangenomics, phylogenetics, genotypics and comparative functional analyses) to uncover distinct evolutionary, coevolutionary and clinically relevant population trends.
Results. These results suggest that a stable (in terms of genome size, GC% and number of genes), yet genetically diverse population (in terms of gene content) of
E. faecium
persists in Ireland with acquired resistance arising via plasmid acquisition (vanA) or, to a lesser extent, chromosomal recombination (vanB). Population analysis revealed five clusters with one cluster partitioned into four clades which transcend isolation dates. Pangenomic and recombination analyses revealed an open (whole genome and chromosomal specific) pangenome illustrating a rampant evolutionary pattern. Comparative resistomics and virulomics uncovered distinct chromosomal and mobilomal propensity for multidrug resistance, widespread chromosomal point-mutation-mediated resistance and chromosomally harboured arsenals of virulence factors. Interestingly, a potential difference in biofilm formation strategies was highlighted by coevolutionary analysis, suggesting differential biofilm genotypes between vanA and vanB isolates.
Conclusions. These results highlight the evolutionary history of Irish
E. faecium
isolates and may provide insight into underlying infection dynamics in a clinical setting. Due to the apparent ease of vancomycin resistance acquisition over time, susceptible
E. faecium
should be concurrently reduced in Irish hospitals to mitigate potential resistant infections.
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Affiliation(s)
- Robert J. Leigh
- Department of Biology, Maynooth University, Mariavilla, Maynooth, Co. Kildare, Ireland
| | - Chloe McKenna
- Department of Biology, Maynooth University, Mariavilla, Maynooth, Co. Kildare, Ireland
| | - Robert McWade
- Department of Microbiology, Mater Misericordiae University Hospital, Eccles St., Dublin 7, D07 R2WY, Ireland
| | - Breda Lynch
- Department of Microbiology, Mater Misericordiae University Hospital, Eccles St., Dublin 7, D07 R2WY, Ireland
| | - Fiona Walsh
- Department of Biology, Maynooth University, Mariavilla, Maynooth, Co. Kildare, Ireland
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90
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Xu Z, Yuan C. Molecular Epidemiology of Staphylococcus aureus in China Reveals the Key Gene Features Involved in Epidemic Transmission and Adaptive Evolution. Microbiol Spectr 2022; 10:e0156422. [PMID: 36190436 PMCID: PMC9603185 DOI: 10.1128/spectrum.01564-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/12/2022] [Indexed: 12/31/2022] Open
Abstract
Staphylococcus aureus is a Gram-positive pathogen that causes various infections in humans and domestic animals. In China, S. aureus is the most common Gram-positive pathogen that causes clinical infections. However, there are few comprehensive genome-based molecular epidemiology studies to investigate the genotypic background of the major S. aureus clones that are epidemic in China. Here, four S. aureus isolates that were recovered from hospital personnel were sequenced. In combination with whole-genome sequencing (WGS) data of 328 S. aureus strains as references, we performed a comprehensive molecular epidemiology study to reveal the molecular epidemic characterization of S. aureus that is epidemic in China. It was found that 332 S. aureus isolates were phylogenetically categorized into 4 major epidemic groups with different epidemiology phenotypes. Each group has exclusive features in virulence genotypic profiles, antimicrobial resistance genotypic profiles, core and pangenome features representing the differences involved in genetic features, evolutionary processes, and potential future evolutionary directions. Moreover, a comparative core genome analysis of 332 S. aureus isolates indicated several key genes that contributed to differences in molecular epidemic characterization and promoted the adaptive evolutionary process of each group. This study provides a comprehensive understanding of molecular epidemiological characteristics and adaptive evolutionary directions of major S. aureus clones that are epidemic in China. IMPORTANCE Staphylococcus aureus is an important Gram-positive pathogen that is epidemic worldwide and causes various infections in humans and domestic animals. However, there has been relatively little research on comprehensive molecular epidemiology in China. In this research, we reconstructed the phylogenetic relationship based on whole-genome data of strains almost all over China, screened for resistance and virulence genes, and took core and pan genome analysis to perform a comprehensive molecular epidemiology study of S. aureus that is epidemic in China. Our results highlight that there are 4 major epidemic groups with different epidemiology phenotypes after phylogenetic categorization with exclusive genetic features in virulence genotypic profiles, antimicrobial-resistance genotypic profiles, and core and pangenome features, and we found key gene features involved in epidemic transmission and adaptive evolution. Our findings are critical in describing molecular characteristic profiles of S. aureus infection, which could update existing preventive measures and take appropriate strategies.
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Affiliation(s)
- Zhen Xu
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Tianjin Medical University, Tianjin, PR China
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin, PR China
- Center for International Collaborative Research on Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, PR China
| | - Chao Yuan
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Tianjin Medical University, Tianjin, PR China
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin, PR China
- Center for International Collaborative Research on Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Tianjin, PR China
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91
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Molecular Epidemiology of Plasmid-Mediated Types 1 and 3 Fimbriae Associated with Biofilm Formation in Multidrug Resistant Escherichia coli from Diseased Food Animals in Guangdong, China. Microbiol Spectr 2022; 10:e0250321. [PMID: 35969065 PMCID: PMC9603762 DOI: 10.1128/spectrum.02503-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Types 1 and 3 fimbriae in Enterobacteriaceae play versatile roles in bacterial physiology including attachment, invasion, cell motility as well as with biofilm formation and urinary tract infections. Herein, we investigated the prevalence and transmission of plasmid-mediated types 1 and 3 fimbriae from 1753 non-duplicate Enterobacteriaceae from diseased food Animals. We identified 123 (7.01%) strong biofilm producers and all was identified as E. coli. WGS analysis of 43 selected strong biofilm producers revealed that they harbored multiple ARGs, including ESBLs, PMQR and mcr-1. The gene clusters mrkABCDF and fimACDH encoding types 1 and 3 fimbriae, respectively, were identified among 43 (34.96%) and 7 (5.7%) of 123 strong biofilm isolates, respectively. These two operons were able to confer strong biofilm-forming ability to an E. coli weak-biofilm forming laboratory strain. Plasmid analysis revealed that mrk and fim operons were found to co-exist with ARGs and were primarily located on IncX1 and IncFII plasmids with similar backbones, respectively. mrkABCDF operons was present in all of 9457 Klebsiella pneumoniae using archived WGS data, and shared high homology to those on plasmids of 8 replicon types and chromosomes from 6 Enterobacteriaceae species from various origins and countries. In contrast, fimACDH operons was present in most of Enterobacter cloacae (62.15%), and shared high homology to those with only a small group of plasmids and Enterobacteriaceae species. This is the first comprehensive report of the prevalence, transmission and homology of plasmid-encoded type 1 and 3 fimbriae among the Enterobacteriaceae. Our findings indicated that plasmid-encoded mrkABCDF and fimACDH were major contributors to enhanced biofilm formation among E. coli and these two operons, in particular mrk could be as a potential anti-biofilm target. IMPORTANCE Biofilms allow bacteria to tolerate disinfectants and antimicrobials, as well as mammalian host defenses, and are therefore difficult to treat clinically. Most research concerning biofilm-related infections is typically focused on chromosomal biofilm-associated factors, including types 1 and 3 fimbriae of biofilm-forming Enterobacterium. However, the transmission and homology of the mobile types 1 and 3 fimbriae among Enterobacteriaceae is largely unknown. The findings revealed that the plasmid-encoded type 3 fimbriae encoded by mrkABCDF and type 1 fimbriae encoded by fimACDH were major contributors to enhancing biofilm formation among strong biofilm E. coli from diseased food producing animals. Additionally, mrk operon with high homology at an amino acid sequence was present both on plasmids of various replicon types and on chromosomes from diverse Enterobacteriaceae species from numerous origins and countries. These findings provide important information on the transmission of the mobile types 1 and 3 fimbriae among Enterobacteriaceae, indicating a potential antibiofilm target.
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92
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Li L, Guo X, Zhang X, Zhao L, Li L, Wang Y, Xie T, Yin Q, Jing Q, Hu T, Li Z, Wu R, Zhao W, Xin SX, Shi B, Liu J, Xia S, Peng Z, Yang Z, Zhang F, Chen XG, Zhou X. A unified global genotyping framework of dengue virus serotype-1 for a stratified coordinated surveillance strategy of dengue epidemics. Infect Dis Poverty 2022; 11:107. [PMID: 36224651 PMCID: PMC9556283 DOI: 10.1186/s40249-022-01024-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/01/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Dengue is the fastest spreading arboviral disease, posing great challenges on global public health. A reproduceable and comparable global genotyping framework for contextualizing spatiotemporal epidemiological data of dengue virus (DENV) is essential for research studies and collaborative surveillance. METHODS Targeting DENV-1 spreading prominently in recent decades, by reconciling all qualified complete E gene sequences of 5003 DENV-1 strains with epidemiological information from 78 epidemic countries/areas ranging from 1944 to 2018, we established and characterized a unified global high-resolution genotyping framework using phylogenetics, population genetics, phylogeography, and phylodynamics. RESULTS The defined framework was discriminated with three hierarchical layers of genotype, subgenotype and clade with respective mean pairwise distances 2-6%, 0.8-2%, and ≤ 0.8%. The global epidemic patterns of DENV-1 showed strong geographic constraints representing stratified spatial-genetic epidemic pairs of Continent-Genotype, Region-Subgenotype and Nation-Clade, thereby identifying 12 epidemic regions which prospectively facilitates the region-based coordination. The increasing cross-transmission trends were also demonstrated. The traditional endemic countries such as Thailand, Vietnam and Indonesia displayed as persisting dominant source centers, while the emerging epidemic countries such as China, Australia, and the USA, where dengue outbreaks were frequently triggered by importation, showed a growing trend of DENV-1 diffusion. The probably hidden epidemics were found especially in Africa and India. Then, our framework can be utilized in an accurate stratified coordinated surveillance based on the defined viral population compositions. Thereby it is prospectively valuable for further hampering the ongoing transition process of epidemic to endemic, addressing the issue of inadequate monitoring, and warning us to be concerned about the cross-national, cross-regional, and cross-continental diffusions of dengue, which can potentially trigger large epidemics. CONCLUSIONS The framework and its utilization in quantitatively assessing DENV-1 epidemics has laid a foundation and re-unveiled the urgency for establishing a stratified coordinated surveillance platform for blocking global spreading of dengue. This framework is also expected to bridge classical DENV-1 genotyping with genomic epidemiology and risk modeling. We will promote it to the public and update it periodically.
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Affiliation(s)
- Liqiang Li
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xiang Guo
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoqing Zhang
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Lingzhai Zhao
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510060, Guangdong, China
| | - Li Li
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Yuji Wang
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Tian Xie
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Qingqing Yin
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Qinlong Jing
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China
| | - Tian Hu
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Ziyao Li
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Rangke Wu
- School of Foreign Studies, Southern Medical University, Guangzhou, 510515, China
| | - Wei Zhao
- BSL-3 Laboratory (Guangdong), School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Sherman Xuegang Xin
- Laboratory of Biophysics, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Benyun Shi
- School of Computer Science and Technology, Nanjing Tech University, Nanjing, 211816, China
| | - Jiming Liu
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China
| | - Shang Xia
- National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, Shanghai, People's Republic of China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhiqiang Peng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China
| | - Zhicong Yang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China
| | - Fuchun Zhang
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510060, Guangdong, China.
| | - Xiao-Guang Chen
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China.
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
| | - Xiaohong Zhou
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China.
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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93
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Lees JA, Tonkin-Hill G, Yang Z, Corander J. Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210237. [PMID: 35989601 PMCID: PMC9393562 DOI: 10.1098/rstb.2021.0237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In less than a decade, population genomics of microbes has progressed from the effort of sequencing dozens of strains to thousands, or even tens of thousands of strains in a single study. There are now hundreds of thousands of genomes available even for a single bacterial species, and the number of genomes is expected to continue to increase at an accelerated pace given the advances in sequencing technology and widespread genomic surveillance initiatives. This explosion of data calls for innovative methods to enable rapid exploration of the structure of a population based on different data modalities, such as multiple sequence alignments, assemblies and estimates of gene content across different genomes. Here, we present Mandrake, an efficient implementation of a dimensional reduction method tailored for the needs of large-scale population genomics. Mandrake is capable of visualizing population structure from millions of whole genomes, and we illustrate its usefulness with several datasets representing major pathogens. Our method is freely available both as an analysis pipeline (https://github.com/johnlees/mandrake) and as a browser-based interactive application (https://gtonkinhill.github.io/mandrake-web/). This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
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Affiliation(s)
- John A Lees
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton CB10 1SD, UK
| | | | - Zhirong Yang
- Department of Computer Science, Norwegian University of Science and Technology, 7491 Trondheim, Norway.,Aalto University, 02150 Espoo, Finland
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, 0317 Oslo, Norway.,Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1SA, UK.,Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, 00100 Helsinki, Finland
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94
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Didelot X, Parkhill J. A scalable analytical approach from bacterial genomes to epidemiology. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210246. [PMID: 35989600 PMCID: PMC9393561 DOI: 10.1098/rstb.2021.0246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/17/2022] [Indexed: 12/21/2022] Open
Abstract
Recent years have seen a remarkable increase in the practicality of sequencing whole genomes from large numbers of bacterial isolates. The availability of this data has huge potential to deliver new insights into the evolution and epidemiology of bacterial pathogens, but the scalability of the analytical methodology has been lagging behind that of the sequencing technology. Here we present a step-by-step approach for such large-scale genomic epidemiology analyses, from bacterial genomes to epidemiological interpretations. A central component of this approach is the dated phylogeny, which is a phylogenetic tree with branch lengths measured in units of time. The construction of dated phylogenies from bacterial genomic data needs to account for the disruptive effect of recombination on phylogenetic relationships, and we describe how this can be achieved. Dated phylogenies can then be used to perform fine-scale or large-scale epidemiological analyses, depending on the proportion of cases for which genomes are available. A key feature of this approach is computational scalability and in particular the ability to process hundreds or thousands of genomes within a matter of hours. This is a clear advantage of the step-by-step approach described here. We discuss other advantages and disadvantages of the approach, as well as potential improvements and avenues for future research. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.
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Affiliation(s)
- Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
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95
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Wright JJ, Bruce SA, Sinopoli DA, Palumbo JR, Stewart DJ. Phylogenomic analysis of the bowfin (Amia calva) reveals unrecognized species diversity in a living fossil lineage. Sci Rep 2022; 12:16514. [PMID: 36192509 PMCID: PMC9529906 DOI: 10.1038/s41598-022-20875-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022] Open
Abstract
The Bowfin (Amia calva), as currently recognized, represents the sole living member of the family Amiidae, which dates back to approximately 150 Ma. Prior to 1896, 13 species of extant Bowfins had been described, but these were all placed into a single species with no rationale or analysis given. This situation has persisted until the present day, with little attention given to re-evaluation of those previously described nominal forms. Here, we present a phylogenomic analysis based on over 21,000 single nucleotide polymorphisms (SNPs) from 94 individuals that unambiguously demonstrates the presence of at least two independent evolutionary lineages within extant Amia populations that merit species-level standing, as well as the possibility of two more. These findings not only expand the recognizable species diversity in an iconic, ancient lineage, but also demonstrate the utility of such methods in addressing previously intractable questions of molecular systematics and phylogeography in slowly evolving groups of ancient fishes.
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Affiliation(s)
- Jeremy J Wright
- Research & Collections, New York State Museum, 3140 Cultural Education Center, Albany, NY, USA.
| | - Spencer A Bruce
- Department of Information Technology Services, University at Albany-State University of New York, Albany, NY, USA
| | - Daniel A Sinopoli
- Department of Biological Sciences, Museum of Natural Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Jay R Palumbo
- Department of Environmental Science & Ecology, State University of New York at Brockport, Brockport, NY, USA
| | - Donald J Stewart
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA.
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96
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White RT, Anstey SI, Kasimov V, Jenkins C, Devlin J, El-Hage C, Pannekoek Y, Legione AR, Jelocnik M. One clone to rule them all: Culture-independent genomics of Chlamydia psittaci from equine and avian hosts in Australia. Microb Genom 2022; 8. [PMID: 36269227 PMCID: PMC9676050 DOI: 10.1099/mgen.0.000888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Chlamydia psittaci is an avian pathogen with zoonotic potential. In Australia, C. psittaci has been well reported as a cause of reproductive loss in mares which subsequently have been the source of infection and illness in some in-contact humans. To date, molecular typing studies describe the predominant and clonal C. psittaci sequence type (ST)24 strains in horse, psittacine, and human infections. We sought to assess the clonality between ST24 strains and the emergence of equine ST24 with a comprehensive genomics approach. We used culture-independent probe-based and metagenomic whole-genome sequencing to investigate 13 C. psittaci genomes from horses, psittacines, and a pigeon from Australia. Published genomes of 36 C. psittaci strains were also used to contextualise our Australian dataset and investigate lineage diversity. We utilised a single-nucleotide polymorphism (SNP) based clustering and multi-locus sequence typing (MLST) approach. C. psittaci has four major phylogenetic groups (PG1-4) based on core-genome SNP-based phylogeny. PG1 contained clonal global and Australian equine, psittacine, and human ST24 genomes, with a median pairwise SNP distance of 68 SNPs. PG2, PG3, and PG4 had greater genomic diversity, including diverse STs collected from birds, livestock, human, and horse hosts from Europe and North America and a racing pigeon from Australia. We show that the clustering of C. psittaci by MLST was congruent with SNP-based phylogeny. The monophyletic ST24 clade has four major sub-lineages. The genomes of 17 Australian human, equine, and psittacine strains collected between 2008 and 2021 formed the predominant ST24 sub-lineage 1 (emerged circa 1979). Despite a temporal distribution of 13 years, the genomes within sub-lineage 1 had a median pairwise SNP distance of 32 SNPs, suggesting a recent population expansion or potential cross-host transmission. However, two C. psittaci genomes collected in 2015 from Victorian parrots clustered into distinct ST24 sub-lineage 4 (emerged circa 1965) with ovine strain C19/98 from Germany. This work describes a comprehensive phylogenomic characterisation of ST24 and identifies a timeline of potential bird-to-equine spillover events.
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Affiliation(s)
- Rhys T White
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia.,The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, Brisbane, Queensland 4072, Australia.,The University of Queensland, Australian Centre for Ecogenomics, Brisbane, Queensland 4072, Australia
| | - Susan I Anstey
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia
| | - Vasilli Kasimov
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia
| | - Joanne Devlin
- The University of Melbourne, Melbourne Veterinary School, Asia Pacific Centre for Animal Health, Parkville, Victoria 3010, Australia
| | - Charles El-Hage
- The University of Melbourne, Melbourne Veterinary School, Asia Pacific Centre for Animal Health, Parkville, Victoria 3010, Australia
| | - Yvonne Pannekoek
- University of Amsterdam, Amsterdam UMC, Department of Medical Microbiology and Infection Prevention, Amsterdam 1105, The Netherlands
| | - Alistair R Legione
- The University of Melbourne, Melbourne Veterinary School, Asia Pacific Centre for Animal Health, Parkville, Victoria 3010, Australia
| | - Martina Jelocnik
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia
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97
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Konowalik K. Phylogeography and colonization pattern of subendemic round-leaved oxeye daisy from the Dinarides to the Carpathians. Sci Rep 2022; 12:16443. [PMID: 36180475 PMCID: PMC9525303 DOI: 10.1038/s41598-022-19619-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
The Carpathians are an important biodiversity hotspot and a link between mountain ranges on the European continent. This study investigated the phylogeography of one the Carpathian subendemics, Leucanthemum rotundifolium, which is distributed throughout the range and in one isolated population outside it. Range-wide sampling was used to examine phylogeographic patterns by sequencing uniparentally inherited chloroplast markers that exemplify seed dispersal. Reconstruct Ancestral State in Phylogenies (RASP) software, Bayesian binary Markov Chain Monte Carlo (BBM) analysis, and ecological niche modeling based on concatenated results of five algorithms were used to infer migration routes and examine links with other species through phylogeny. The round-leaved oxeye daisy is an example of organisms that reached the Carpathians through a southern "Dacian" migration route, most probably through long-distance dispersal. Dating placed the events in the Pleistocene and supported migrations during cooler periods and stasis/isolation followed by separation in the interglacials. Haplotype diversification indicated that after L. rotundifolium reached the area around the Fagaras Mountains, several migration events occurred leading to colonization of the Southern Carpathians followed by migration to the Apuseni Mountains, the Eastern Carpathians, and finally the Western Carpathians. The results are consistent with previous phylogeographic studies in this region and indicate several novel patterns.
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Affiliation(s)
- Kamil Konowalik
- Department of Botany and Plant Ecology, Wrocław University of Environmental and Life Sciences, pl. Grunwaldzki 24a, PL-50-363, Wroclaw, Poland.
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Chong CE, Bengtsson RJ, Horsburgh MJ. Comparative genomics of Staphylococcus capitis reveals species determinants. Front Microbiol 2022; 13:1005949. [PMID: 36246238 PMCID: PMC9563023 DOI: 10.3389/fmicb.2022.1005949] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/05/2022] [Indexed: 11/27/2022] Open
Abstract
Staphylococcus capitis is primarily described as a human skin commensal but is now emergent as an opportunistic pathogen isolated from the bloodstream and prosthetic joint infections, and neonatal intensive care unit (NICU)-associated sepsis. We used comparative genomic analyses of S. capitis to provide new insights into commensal scalp isolates from varying skin states (healthy, dandruff lesional, and non-lesional), and to expand our current knowledge of the species populations (scalp isolates, n = 59; other skin isolates, n = 7; publicly available isolates, n = 120). A highly recombinogenic population structure was revealed, with genomes including the presence of a range of previously described staphylococcal virulence factors, cell wall-associated proteins, and two-component systems. Genomic differences between the two described S. capitis subspecies were explored, which revealed the determinants associated exclusively with each subspecies. The subspecies ureolyticus was distinguished from subspecies capitis based on the differences in antimicrobial resistance genes, β-lactam resistance genes, and β-class phenol soluble modulins and gene clusters linked to biofilm formation and survival on skin. This study will aid further research into the classification of S. capitis and virulence-linked phylogroups to monitor the spread and evolution of S. capitis.
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99
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Bhat SV, Maughan H, Cameron ADS, Yost CK. Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations. Microb Genom 2022; 8:mgen000864. [PMID: 36107145 PMCID: PMC9676026 DOI: 10.1099/mgen.0.000864] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/15/2022] [Indexed: 04/01/2024] Open
Abstract
Delftia is a diverse betaproteobacterial genus with many strains having agricultural and industrial relevance, including plant-growth promotion, bioremediation of hydrocarbon-contaminated soils, and heavy metal immobilization. Delftia spp. are broadly distributed in the environment, and have been isolated from plant hosts as well as healthy and diseased animal hosts, yet the genetic basis of this ecological versatility has not been characterized. Here, we present a phylogenomic comparison of published Delftia genomes and show that the genus is divided into two well-supported clades: one 'Delftia acidovorans' clade with isolates from soils and plant rhizospheres, and a second 'Delftia lacustris and Delftia tsuruhatensis' clade with isolates from humans and sludge. The pan-genome inferred from 61 Delftia genomes contained over 28 000 genes, of which only 884 were found in all genomes. Analysis of industrially relevant functions highlighted the ecological versatility of Delftia and supported their role as generalists.
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Affiliation(s)
- Supriya V. Bhat
- Department of Biology, University of Regina, Regina, SK, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, SK, Canada
| | | | - Andrew D. S. Cameron
- Department of Biology, University of Regina, Regina, SK, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, SK, Canada
| | - Christopher K. Yost
- Department of Biology, University of Regina, Regina, SK, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, SK, Canada
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100
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Mellor KC, Blackwell GA, Cawthraw SA, Mensah NE, Reid SWJ, Thomson NR, Petrovska L, Mather AE. Contrasting long-term dynamics of antimicrobial resistance and virulence plasmids in Salmonella Typhimurium from animals. Microb Genom 2022; 8. [PMID: 35997596 PMCID: PMC9484752 DOI: 10.1099/mgen.0.000826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plasmids are mobile elements that can carry genes encoding traits of clinical concern, including antimicrobial resistance (AMR) and virulence. Population-level studies of Enterobacterales, including Escherichia coli, Shigella and Klebsiella, indicate that plasmids are important drivers of lineage expansions and dissemination of AMR genes. Salmonella Typhimurium is the second most common cause of salmonellosis in humans and livestock in the UK and Europe. The long-term dynamics of plasmids between S. Typhimurium were investigated using isolates collected through national surveillance of animals in England and Wales over a 25-year period. The population structure of S. Typhimurium and its virulence plasmid (where present) were inferred through phylogenetic analyses using whole-genome sequence data for 496 isolates. Antimicrobial resistance genes and plasmid markers were detected in silico. Phenotypic plasmid characterization, using the Kado and Liu method, was used to confirm the number and size of plasmids. The differences in AMR and plasmids between clades were striking, with livestock clades more likely to carry one or more AMR plasmid and be multi-drug-resistant compared to clades associated with wildlife and companion animals. Multiple small non-AMR plasmids were distributed across clades. However, all hybrid AMR–virulence plasmids and most AMR plasmids were highly clade-associated and persisted over decades, with minimal evidence of horizontal transfer between clades. This contrasts with the role of plasmids in the short-term dissemination of AMR between diverse strains in other Enterobacterales in high-antimicrobial-use settings, with implications for predicting plasmid dissemination amongst S. Typhimurium.
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Affiliation(s)
- Kate C Mellor
- Royal Veterinary College, Hatfield, UK.,London School of Hygiene and Tropical Medicine, London, UK
| | - Grace A Blackwell
- European Bioinformatics Institute, Hinxton, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | | | | | | | - Nicholas R Thomson
- London School of Hygiene and Tropical Medicine, London, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Alison E Mather
- Quadram Institute Bioscience, Norwich, UK.,University of East Anglia, Norwich, UK
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