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Thilakarathna SH, Li V, Chui L. A challenging STEC strain isolation from patients' stools: an O166:H15 STEC strain with the stx2 gene. Microbiol Spectr 2024:e0009824. [PMID: 38814093 DOI: 10.1128/spectrum.00098-24] [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: 01/10/2024] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
Two patients with acute gastroenteritis tested positive for Shiga toxin-producing Escherichia coli (STEC) by polymerase chain reaction (PCR), and both strains carried the Shiga toxin 2 encoding gene. Since routine culture using CHROMagar STEC failed to recover these isolates, immunomagnetic separation (IMS) targeting the top six non-O157:H7 serotypes was used for isolate recovery. After two subsequent IMS runs, the STEC strains were isolated from trypticase soy broth with and without overnight enrichment for runs 1 and 2, respectively. Serotyping based on whole-genome sequencing revealed that both patients carried the strain O166:H15 STEC with the stx2 gene. Hence, the magnetic beads used in IMS appeared to have cross-reactivity with other E. coli serotypes. When the STEC isolates from both stools were cultured on CHROMagar STEC and sheep blood agar (BAP), two distinct colony sizes were apparent after overnight incubation. The small and large colonies were picked and separately cultured on both media, and colony growth was observed for 2 weeks at room temperature after an initial overnight incubation at 37°C. After 1 week, the colonies showed concentric ring structures with a darker center and a lighter surrounding on CHROMagar STEC and a "fried egg"-resembling structure with a raised circular center and a flat surrounding on BAP. Both colony types remained morphologically different on CHROMagar STEC throughout the 15 days. However, on BAP, their appearance was comparable by day 7. IMPORTANCE Shiga toxin-producing E. coli (STEC) infections can lead to severe complications such as bloody diarrhea and hemolytic uremic syndrome (HUS), especially in young children and the elderly. Strains that carry the shiga toxin 2 gene (stx2), such as O157:H7, have been mostly linked with severe disease outcomes. In recent years, outbreaks caused by non-O157:H7 strains have increased. E. coli O166:H15 has been previously reported causing a gastroenteritis outbreak in 1996 as a non-STEC strain, however the O166:H15 serotype we recovered carried the stx2 gene. It was particularly challenging to isolate this strain from stools by culture. Consequently, we tested immunomagnetic separation for the STEC recovery, which was a novel approach on clinical stools. Virulence genes were included for the characterization of these isolates.
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Affiliation(s)
- Surangi H Thilakarathna
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Vincent Li
- Alberta Precision Laboratories - Public Health Laboratory (ProvLab), Edmonton, Canada
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Alberta Precision Laboratories - Public Health Laboratory (ProvLab), Edmonton, Canada
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2
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Shi Z, Lan Y, Wang Y, Yan X, Ma X, Hassan FU, Rushdi HE, Xu Z, Wang W, Deng T. Multi-omics strategy reveals potential role of antimicrobial resistance and virulence factor genes responsible for Simmental diarrheic calves caused by Escherichia coli. mSystems 2024:e0134823. [PMID: 38742910 DOI: 10.1128/msystems.01348-23] [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: 12/12/2023] [Accepted: 04/05/2024] [Indexed: 05/16/2024] Open
Abstract
Escherichia coli (E. coli) is reported to be an important pathogen associated with calf diarrhea. Antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) pose a considerable threat to both animal and human health. However, little is known about the characterization of ARGs and VFGs presented in the gut microbiota of diarrheic calves caused by E. coli. In this study, we used multi-omics strategy to analyze the ARG and VFG profiles of Simmental calves with diarrhea caused by E. coli K99. We found that gut bacterial composition and their microbiome metabolic functions varied greatly in diarrheic calves compared to healthy calves. In total, 175 ARGs were identified, and diarrheal calves showed a significantly higher diversity and abundance of ARGs than healthy calves. Simmental calves with diarrhea showed higher association of VFGs with pili function, curli assembly, and ferrienterobactin transport of E. coli. Co-occurrence patterns based on Pearson correlation analysis revealed that E. coli had a highly significant (P < 0.0001) correlation coefficient (>0.8) with 16 ARGs and 7 VFGs. Metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Phylotype analysis of E. coli genomes showed that the predominant phylogroup B1 in diarrheic Simmental calves was associated with 10 ARGs and 3 VFGs. These findings provide an overview of the diversity and abundance of the gut microbiota in diarrheic calves caused by E. coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the calves affected with diarrhea.IMPORTANCESimmental is a well-recognized beef cattle breed worldwide. They also suffer significant economic losses due to diarrhea. In this study, fecal metagenomic analysis was applied to characterize the antibiotic resistance gene (ARG) and virulence factor gene (VFG) profiles of diarrheic Simmental calves. We identified key ARGs and VFGs correlated with Escherichia coli isolated from Simmental calves. Additionally, metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Our findings provide an insight into the diversity and abundance of the gut microbiota in diarrheic calves caused by Escherichia coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the diarrheal calves from cattle hosts.
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Affiliation(s)
- Zhihai Shi
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yali Lan
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yazhou Wang
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiangzhou Yan
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaoya Ma
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Hossam E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Zhaoxue Xu
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Wenjia Wang
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
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Li Y, Zhang Y, Sun X, Wu Y, Yan Z, Ju X, Huang Y, Zhou H, Wang Z, Wang S, Zhang R, Li R. National genomic epidemiology investigation revealed the spread of carbapenem-resistant Escherichia coli in healthy populations and the impact on public health. Genome Med 2024; 16:57. [PMID: 38627827 PMCID: PMC11020349 DOI: 10.1186/s13073-024-01310-x] [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: 10/13/2023] [Accepted: 03/04/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Carbapenem-resistant Escherichia coli (CREC) has been considered as WHO priority pathogens, causing a great public health concern globally. While CREC from patients has been thoroughly investigated, the prevalence and underlying risks of CREC in healthy populations have been overlooked. Systematic research on the prevalence of CREC in healthy individuals was conducted here. We aimed to characterize CREC collected from healthy populations in China between 2020 and 2022 and to compare the genomes of CREC isolates isolated from healthy individuals and clinical patients. METHODS We present a nationwide investigation of CREC isolates among healthy populations in China, employing robust molecular and genomic analyses. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatics were utilized to analyze a cohort of CREC isolates (n = 113) obtained from fecal samples of 5 064 healthy individuals. Representative plasmids were extracted for third-generation nanopore sequencing. We previously collected 113 non-duplicate CREC isolates (59 in 2018, 54 in 2020) collected from ICU patients in 15 provinces and municipalities in China, and these clinical isolates were used to compare with the isolates in this study. Furthermore, we employ comparative genomics approaches to elucidate molecular variations and potential correlations between clinical and non-clinical CREC isolates. RESULTS A total of 147 CREC isolates were identified from 5 064 samples collected across 11 provinces in China. These isolates were classified into 64 known sequence types (STs), but no dominant STs were observed. In total, seven carbapenemase genes were detected with blaNDM-5 (n = 116) being the most prevalent one. Genetic environments and plasmid backbones of blaNDM were conserved in CREC isolated from healthy individuals. Furthermore, we compared clinical and healthy human-originated CRECs, revealing noteworthy distinctions in 23 resistance genes, including blaNDM-1, blaNDM-5, and blaKPC (χ2 test, p < 0.05). Clinical isolates contained more virulence factors associated with iron uptake, adhesion, and invasion than those obtained from healthy individuals. Notably, CREC isolates generally found healthy people are detected in hospitalized patients. CONCLUSIONS Our findings underscore the significance of healthy populations-derived CRECs as a crucial reservoir of antibiotic resistance genes (ARGs). This highlights the need for ongoing monitoring of CREC isolates in healthy populations to accurately assess the potential risks posed by clinical CREC isolates.
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Affiliation(s)
- Yan Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, P. R. China
| | - Yanyan Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Xinran Sun
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, P. R. China
| | - Yuchen Wu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Zelin Yan
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Xiaoyang Ju
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Yonglu Huang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Hongwei Zhou
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, P. R. China
- Jiangsu Key Lab of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Shaolin Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, Zhejiang, P. R. China.
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, P. R. China.
- Jiangsu Key Lab of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, P. R. China.
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China.
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Grinevich D, Harden L, Thakur S, Callahan B. Serovar-level identification of bacterial foodborne pathogens from full-length 16S rRNA gene sequencing. mSystems 2024; 9:e0075723. [PMID: 38319092 PMCID: PMC10949465 DOI: 10.1128/msystems.00757-23] [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: 07/31/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024] Open
Abstract
The resolution of variation within species is critical for interpreting and acting on many microbial measurements. In the key foodborne pathogens Salmonella and Escherichia coli, the primary subspecies classification scheme used is serotyping: differentiating variants within these species by surface antigen profiles. Serotype prediction from whole-genome sequencing (WGS) of isolates is now seen as comparable or preferable to traditional laboratory methods where WGS is available. However, laboratory and WGS methods depend on an isolation step that is time-consuming and incompletely represents the sample when multiple strains are present. Community sequencing approaches that skip the isolation step are, therefore, of interest for pathogen surveillance. Here, we evaluated the viability of amplicon sequencing of the full-length 16S rRNA gene for serotyping Salmonella enterica and E. coli. We developed a novel algorithm for serotype prediction, implemented as an R package (Seroplacer), which takes as input full-length 16S rRNA gene sequences and outputs serovar predictions after phylogenetic placement into a reference phylogeny. We achieved over 89% accuracy in predicting Salmonella serotypes on in silico test data and identified key pathogenic serovars of Salmonella and E. coli in isolate and environmental test samples. Although serotype prediction from 16S rRNA gene sequences is not as accurate as serotype prediction from WGS of isolates, the potential to identify dangerous serovars directly from amplicon sequencing of environmental samples is intriguing for pathogen surveillance. The capabilities developed here are also broadly relevant to other applications where intraspecies variation and direct sequencing from environmental samples could be valuable.IMPORTANCEIn order to prevent and stop outbreaks of foodborne pathogens, it is important that we can detect when pathogenic bacteria are present in a food or food-associated site and identify connections between specific pathogenic bacteria present in different samples. In this work, we develop a new computational technology that allows the important foodborne pathogens Escherichia coli and Salmonella enterica to be serotyped (a subspecies level classification) from sequencing of a single-marker gene, and the 16S rRNA gene often used to surveil bacterial communities. Our results suggest current limitations to serotyping from 16S rRNA gene sequencing alone but set the stage for further progress that we consider likely given the rapid advance in the long-read sequencing technologies and genomic databases our work leverages. If this research direction succeeds, it could enable better detection of foodborne pathogens before they reach the public and speed the resolution of foodborne pathogen outbreaks.
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Affiliation(s)
- Dmitry Grinevich
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Lyndy Harden
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Benjamin Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
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Moinet M, Rogers L, Biggs P, Marshall J, Muirhead R, Devane M, Stott R, Cookson A. High-resolution genomic analysis to investigate the impact of the invasive brushtail possum (Trichosurus vulpecula) and other wildlife on microbial water quality assessments. PLoS One 2024; 19:e0295529. [PMID: 38236841 PMCID: PMC10796070 DOI: 10.1371/journal.pone.0295529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/21/2023] [Indexed: 01/22/2024] Open
Abstract
Escherichia coli are routine indicators of fecal contamination in water quality assessments. Contrary to livestock and human activities, brushtail possums (Trichosurus vulpecula), common invasive marsupials in Aotearoa/New Zealand, have not been thoroughly studied as a source of fecal contamination in freshwater. To investigate their potential role, Escherichia spp. isolates (n = 420) were recovered from possum gut contents and feces and were compared to those from water, soil, sediment, and periphyton samples, and from birds and other introduced mammals collected within the Mākirikiri Reserve, Dannevirke. Isolates were characterized using E. coli-specific real-time PCR targeting the uidA gene, Sanger sequencing of a partial gnd PCR product to generate a gnd sequence type (gST), and for 101 isolates, whole genome sequencing. Escherichia populations from 106 animal and environmental sample enrichments were analyzed using gnd metabarcoding. The alpha diversity of Escherichia gSTs was significantly lower in possums and animals compared with aquatic environmental samples, and some gSTs were shared between sample types, e.g., gST535 (in 85% of samples) and gST258 (71%). Forty percent of isolates gnd-typed and 75% of reads obtained by metabarcoding had gSTs shared between possums, other animals, and the environment. Core-genome single nucleotide polymorphism (SNP) analysis showed limited variation between several animal and environmental isolates (<10 SNPs). Our data show at an unprecedented scale that Escherichia clones are shared between possums, other wildlife, water, and the wider environment. These findings support the potential role of possums as contributors to fecal contamination in Aotearoa/New Zealand freshwater. Our study deepens the current knowledge of Escherichia populations in under-sampled wildlife. It presents a successful application of high-resolution genomic methods for fecal source tracking, thereby broadening the analytical toolbox available to water quality managers. Phylogenetic analysis of isolates and profiling of Escherichia populations provided useful information on the source(s) of fecal contamination and suggest that comprehensive invasive species management strategies may assist in restoring not only ecosystem health but also water health where microbial water quality is compromised.
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Affiliation(s)
- Marie Moinet
- Hopkirk Research Institute, AgResearch, Palmerston North, New Zealand
| | - Lynn Rogers
- Hopkirk Research Institute, AgResearch, Palmerston North, New Zealand
| | - Patrick Biggs
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Jonathan Marshall
- School of Mathematical and Computational Sciences, Massey University, Palmerston North, New Zealand
| | | | - Megan Devane
- Institute of Environmental Science and Research Ltd. (ESR), Christchurch, New Zealand
| | - Rebecca Stott
- National Institute of Water and Atmospheric Research (NIWA), Hamilton, New Zealand
| | - Adrian Cookson
- Hopkirk Research Institute, AgResearch, Palmerston North, New Zealand
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
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Sudhakari PA, Ramisetty BCM. Resistome Diversity in Escherichia coli Isolates of Global Wastewaters. Microb Drug Resist 2024; 30:37-49. [PMID: 38150178 DOI: 10.1089/mdr.2022.0296] [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] [Indexed: 12/28/2023] Open
Abstract
Antimicrobial resistance (AMR) is a global health threat requiring urgent attention and effective strategies for containment. AMR is fueled by wastewater mismanagement and global mobility, disseminating multidrug-resistant (MDR) strains worldwide. While global estimates of AMR burden have been informative, community-level understanding has received little attention despite reports of high AMR prevalence in healthy communities. We assessed the "invasion" of antibiotic resistance genes (ARGs) into the normal human flora by characterizing AMR Escherichia coli in local wastewaters contributed by a healthy youth population. This study estimated 26% (out of 300 isolates) resistant and 59% plasmid-bearing E. coli in local wastewater. Of the 78 AMR isolates, the frequency of mono-resistance was higher against tetracycline (32%), followed by kanamycin (17%) and chloramphenicol (9%). Five isolates were potentially MDR. We further sequenced four MDRs and four sensitive strains to comprehend the genome and resistome diversity in comparison to the global wastewater E. coli (genomes from the PATRIC database). The whole-genome analysis revealed extensive genome similarity among global isolates, suggesting global dissemination and colonization of E. coli. Global wastewater resistome majorly comprised ARGs against aminoglycosides (26%), beta-lactam (17%), sulfonamide (11%), and trimethoprim (8%). Resistance to colistin, a last-resort antibiotic, was prevalent in MDRs of European and South Asian isolates. A systems approach is required to address the AMR crisis on a global scale, reduce antibiotic usage, and increase the efficiency of wastewater management and disinfection.
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Affiliation(s)
- Pavithra Anantharaman Sudhakari
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Bhaskar Chandra Mohan Ramisetty
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
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Aswal M, Singhal N, Kumar M. Genomic analysis of phylogroup D Escherichia coli strains using novel de-novo reference-based guided assembly. Sci Data 2023; 10:573. [PMID: 37658065 PMCID: PMC10474267 DOI: 10.1038/s41597-023-02444-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 08/04/2023] [Indexed: 09/03/2023] Open
Abstract
Escherichia coli are highly diverse bacteria with different pathogenic types, serotypes and phylogenetic types/phylotypes. In recent years, infections with E. coli have increased worldwide and so has the emergence of antibiotic resistant strains. In the present study we have assembled, annotated and analysed genome sequences of three strains of the phylogroup D of E. coli. These strains were isolated from the river Yamuna, a prominent anthropogenic urban river of northern India. These strains showed varied antibiotic susceptibilities, one was susceptible to all the antibiotics tested except ampicillin while of the other two, one was multi-β-lactam resistant and the other was multi-drug resistant (resistant to multiple β-lactams, fluoroquinolones and kanamycin). The short-sequence reads were assembled into contigs using the de-novo approach and further, scaffolding of contigs was performed by using the best reference genome for a particular isolate which resulted in a significant increase in the N50 value of each assembly. The bioinformatics assembly approach used in this study could be easily applied to study other bacterial genomes.
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Affiliation(s)
- Manisha Aswal
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Neelja Singhal
- Department of Biophysics, University of Delhi South Campus, New Delhi, India.
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India.
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Boutzoukas AE, Komarow L, Chen L, Hanson B, Kanj SS, Liu Z, Salcedo Mendoza S, Ordoñez K, Wang M, Paterson DL, Evans S, Ge L, Giri A, Hill C, Baum K, Bonomo RA, Kreiswirth B, Patel R, Arias CA, Chambers HF, Fowler VG, van Duin D. International Epidemiology of Carbapenemase-Producing Escherichia coli. Clin Infect Dis 2023; 77:499-509. [PMID: 37154071 PMCID: PMC10444003 DOI: 10.1093/cid/ciad288] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Carbapenemase-producing (CP) Escherichia coli (CP-Ec) are a global public health threat. We aimed to describe the clinical and molecular epidemiology and outcomes of patients from several countries with CP-Ec isolates obtained from a prospective cohort. METHODS Patients with CP-Ec were enrolled from 26 hospitals in 6 countries. Clinical data were collected, and isolates underwent whole-genome sequencing. Clinical and molecular features and outcomes associated with isolates with or without metallo-β-lactamases (MBLs) were compared. The primary outcome was desirability of outcome ranking (DOOR) at 30 days after the index culture. RESULTS Of the 114 CP-Ec isolates in Consortium on resistance against carbapenems in Klebsiella and other Enterobacterales-2 (CRACKLE-2), 49 harbored an MBL, most commonly blaNDM-5 (38/49, 78%). Strong regional variations were noted with MBL-Ec predominantly found among patients in China (23/49). Clinically, MBL-Ec were more often from urine sources (49% vs 29%), less often met criteria for infection (39% vs 58%, P = .04), and had lower acuity of illness when compared with non-MBL-Ec. Among patients with infection, the probability of a better DOOR outcome for a randomly selected patient with MBL-Ec as compared with non-MBL-Ec was 62% (95% CI: 48.2-74.3%). Among infected patients, non-MBL-Ec had increased 30-day (26% vs 0%; P = .02) and 90-day (39% vs 0%; P = .001) mortality compared with MBL-Ec. CONCLUSIONS Emergence of CP-Ec was observed with important geographic variations. Bacterial characteristics, clinical presentations, and outcomes differed between MBL-Ec and non-MBL-Ec. Mortality was higher among non-MBL isolates, which were more frequently isolated from blood, but these findings may be confounded by regional variations.
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Affiliation(s)
- Angelique E Boutzoukas
- Division of Infectious Diseases, Duke University, Durham, North Carolina, USA
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - Lauren Komarow
- The Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Blake Hanson
- Center for Infectious Diseases and Microbial Genomics, UTHealth, McGovern School of Medicine at Houston, Houston, Texas, USA
| | - Souha S Kanj
- Division of Infectious Diseases, and Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
| | - Zhengyin Liu
- Infectious Disease Section, Department of Internal Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Soraya Salcedo Mendoza
- Servicio de Infectología, Organizacion Clinica General del Norte, Barranquilla, Colombia
| | - Karen Ordoñez
- Department of Infectious Diseases, E.S.E. Hospital Universitario, San Jorge de Pereira, Pereira, Colombia
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - David L Paterson
- ADVANCE-ID, Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Scott Evans
- The Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Lizhao Ge
- The Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Abhigya Giri
- The Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Carol Hill
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - Keri Baum
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- VA–Case Center for Antibiotic Resistance and Epidemiology (Case-VA CARES), Cleveland, Ohio, USA
| | - Barry Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, and Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Cesar A Arias
- Division of Infectious Diseases and Center for Infectious Diseases, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Henry F Chambers
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Vance G Fowler
- Division of Infectious Diseases, Duke University, Durham, North Carolina, USA
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
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Cave R, Ter-Stepanyan MM, Mkrtchyan HV. Short- and Long-Read Sequencing Reveals the Presence and Evolution of an IncF Plasmid Harboring blaCTX-M-15 and blaCTX-M-27 Genes in Escherichia coli ST131. Microbiol Spectr 2023; 11:e0035623. [PMID: 37466446 PMCID: PMC10433869 DOI: 10.1128/spectrum.00356-23] [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: 01/23/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
Escherichia coli sequence type 131 (ST131) has contributed to the spread of extended-spectrum beta-lactamase (ESBL) and has emerged as the dominant cause of hospital- and community-acquired urinary tract infections. Here, we report for the first time an in-depth analysis of whole-genome sequencing (WGS) of 4 ESBL-producing E. coli ST131 isolates recovered from patients in two hospitals in Armenia using Illumina short-read sequencing for accurate base calling to determine their genotype and to infer their phylogeny and using Oxford Nanopore Technologies long-read sequencing to resolve plasmid and chromosomal genetic elements. Genotypically, the four Armenian isolates were identified as part of the H30Rx/clade C2 (n = 2) and H41/clade A (n = 2) lineages and were phylogenetically closely related to isolates from the European Nucleotide Archive (ENA) database previously recovered from patients in the United States, Australia, and New Zealand. The Armenian isolates recovered in this study had chromosomal integration of the blaCTX-M-15 gene in the H30Rx isolates and a high number of virulence genes found in the H41 isolates associated with the carriage of a rare genomic island (in the context of E. coli ST131) containing the S fimbrial, salmochelin siderophore, and microcin H47 virulence genes. Furthermore, our data show the evolution of the IncF[2:A2:B20] plasmid harboring both blaCTX-M-15 and blaCTX-M-27 genes, derived from the recombination of genes from an IncF[F2:A-:B-] blaCTX-M-15-associated plasmid into the IncF[F1:A2:B20] blaCTX-M-27-associated plasmid backbone seen in two genetically closely related H41 Armenian isolates. IMPORTANCE Combining short and long reads from whole-genome sequencing analysis provided a genetic context for uncommon genes of clinical importance to better understand transmission and evolutionary features of ESBL-producing uropathogenic E. coli (UPEC) ST131 isolates recovered in Armenia. Using hybrid genome assembly in countries lacking genomic surveillance studies can inform us about new lineages not seen in other countries with genes encoding high virulence and antibiotic resistance harbored on mobile genetic elements.
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Affiliation(s)
- Rory Cave
- School of Biomedical Sciences, University of West London, London, United Kingdom
| | - Mary M. Ter-Stepanyan
- Yerevan State Medical University after M. Heratsi, Faculty of Public Health, Department of Epidemiology, Yerevan, Republic of Armenia
- Research Center of Maternal and Child Health Protection, Yerevan, Armenia
| | - Hermine V. Mkrtchyan
- School of Biomedical Sciences, University of West London, London, United Kingdom
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10
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Safar HA, Alatar F, Nasser K, Al-Ajmi R, Alfouzan W, Mustafa AS. The impact of applying various de novo assembly and correction tools on the identification of genome characterization, drug resistance, and virulence factors of clinical isolates using ONT sequencing. BMC Biotechnol 2023; 23:26. [PMID: 37525145 PMCID: PMC10391896 DOI: 10.1186/s12896-023-00797-3] [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: 02/02/2023] [Accepted: 07/21/2023] [Indexed: 08/02/2023] Open
Abstract
Oxford Nanopore sequencing technology (ONT) is currently widely used due to its affordability, simplicity, and reliability. Despite the advantage ONT has over next-generation sequencing in detecting resistance genes in mobile genetic elements, its relatively high error rate (10-15%) is still a deterrent. Several bioinformatic tools are freely available for raw data processing and obtaining complete and more accurate genome assemblies. In this study, we evaluated the impact of using mix-and-matched read assembly (Flye, Canu, Wtdbg2, and NECAT) and read correction (Medaka, NextPolish, and Racon) tools in generating complete and accurate genome assemblies, and downstream genomic analysis of nine clinical Escherichia coli isolates. Flye and Canu assemblers were the most robust in genome assembly, and Medaka and Racon correction tools significantly improved assembly parameters. Flye functioned well in pan-genome analysis, while Medaka increased the number of core genes detected. Flye, Canu, and NECAT assembler functioned well in detecting antimicrobial resistance genes (AMR), while Wtdbg2 required correction tools for better detection. Flye was the best assembler for detecting and locating both virulence and AMR genes (i.e., chromosomal vs. plasmid). This study provides insight into the performance of several read assembly and read correction tools for analyzing ONT sequencing reads for clinical isolates.
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Affiliation(s)
- Hussain A Safar
- OMICS Research Unit, Health Science Centre, Kuwait University, Hawalli Governorate, Kuwait
| | - Fatemah Alatar
- Serology and Molecular Microbiology Reference Laboratory, Mubarak Al-Kabeer Hospital, Ministry of Health, Hawalli Governorate, Kuwait
| | - Kother Nasser
- Serology and Molecular Microbiology Reference Laboratory, Mubarak Al-Kabeer Hospital, Ministry of Health, Hawalli Governorate, Kuwait
| | - Rehab Al-Ajmi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Hawalli Governorate, Kuwait
| | - Wadha Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Hawalli Governorate, Kuwait
- Microbiology Unit, Farwaniya Hospital, Ministry of Health, Al Farwaniyah Governorate, Kuwait
| | - Abu Salim Mustafa
- Department of Microbiology, Faculty of Medicine, Kuwait University, Hawalli Governorate, Kuwait.
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11
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Libuit KG, Doughty EL, Otieno JR, Ambrosio F, Kapsak CJ, Smith EA, Wright SM, Scribner MR, Petit III RA, Mendes CI, Huergo M, Legacki G, Loreth C, Park DJ, Sevinsky JR. Accelerating bioinformatics implementation in public health. Microb Genom 2023; 9:mgen001051. [PMID: 37428142 PMCID: PMC10438813 DOI: 10.1099/mgen.0.001051] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/24/2023] [Indexed: 07/11/2023] Open
Abstract
We have adopted an open bioinformatics ecosystem to address the challenges of bioinformatics implementation in public health laboratories (PHLs). Bioinformatics implementation for public health requires practitioners to undertake standardized bioinformatic analyses and generate reproducible, validated and auditable results. It is essential that data storage and analysis are scalable, portable and secure, and that implementation of bioinformatics fits within the operational constraints of the laboratory. We address these requirements using Terra, a web-based data analysis platform with a graphical user interface connecting users to bioinformatics analyses without the use of code. We have developed bioinformatics workflows for use with Terra that specifically meet the needs of public health practitioners. These Theiagen workflows perform genome assembly, quality control, and characterization, as well as construction of phylogeny for insights into genomic epidemiology. Additonally, these workflows use open-source containerized software and the WDL workflow language to ensure standardization and interoperability with other bioinformatics solutions, whilst being adaptable by the user. They are all open source and publicly available in Dockstore with the version-controlled code available in public GitHub repositories. They have been written to generate outputs in standardized file formats to allow for further downstream analysis and visualization with separate genomic epidemiology software. Testament to this solution meeting the requirements for bioinformatic implementation in public health, Theiagen workflows have collectively been used for over 5 million sample analyses in the last 2 years by over 90 public health laboratories in at least 40 different countries. Continued adoption of technological innovations and development of further workflows will ensure that this ecosystem continues to benefit PHLs.
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Affiliation(s)
- Kevin G. Libuit
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Emma L. Doughty
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - James R. Otieno
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Frank Ambrosio
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Curtis J. Kapsak
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Emily A. Smith
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Sage M. Wright
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Michelle R. Scribner
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Robert A. Petit III
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
- Wyoming Public Health Laboratory, 208 S College Dr, Cheyenne, WY 82007, USA
| | - Catarina Inês Mendes
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Marcela Huergo
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Gregory Legacki
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Christine Loreth
- Broad Institute of Harvard and MIT, 415 Main St, Cambridge, MA 02142, USA
| | - Daniel J. Park
- Broad Institute of Harvard and MIT, 415 Main St, Cambridge, MA 02142, USA
| | - Joel R. Sevinsky
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
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12
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Yang Y, Dufault-Thompson K, Yan W, Cai T, Xie L, Jiang X. Deciphering Phage-Host Specificity Based on the Association of Phage Depolymerases and Bacterial Surface Glycan with Deep Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545366. [PMID: 37503040 PMCID: PMC10370184 DOI: 10.1101/2023.06.16.545366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Phage tailspike proteins are depolymerases that target diverse bacterial surface glycans with high specificity, determining the host-specificity of numerous phages. To address the challenge of identifying tailspike proteins due to their sequence diversity, we developed SpikeHunter, an approach based on the ESM-2 protein language model. Using SpikeHunter, we successfully identified 231,965 tailspike proteins from a dataset comprising 8,434,494 prophages found within 165,365 genomes of five common pathogens. Among these proteins, 143,035 tailspike proteins displayed strong associations with serotypes. Moreover, we observed highly similar tailspike proteins in species that share closely related serotypes. We found extensive domain swapping in all five species, with the C-terminal domain being significantly associated with host serotype highlighting its role in host range determination. Our study presents a comprehensive cross-species analysis of tailspike protein to serotype associations, providing insights applicable to phage therapy and biotechnology.
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Affiliation(s)
- Yiyan Yang
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Wei Yan
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Tian Cai
- Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Lei Xie
- Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, NY 10016, USA
- Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, USA *
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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Okuno M, Arimizu Y, Miyahara S, Wakabayashi Y, Gotoh Y, Yoshino S, Harada T, Seto K, Yamamoto T, Nakamura K, Hayashi T, Ogura Y. Escherichia cryptic clade I is an emerging source of human intestinal pathogens. BMC Biol 2023; 21:81. [PMID: 37055811 PMCID: PMC10100065 DOI: 10.1186/s12915-023-01584-4] [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: 12/12/2022] [Accepted: 03/30/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Within the genus Escherichia, several monophyletic clades other than the traditionally defined species have been identified. Of these, cryptic clade I (C-I) appears to represent a subspecies of E. coli, but due to the difficulty in distinguishing it from E. coli sensu stricto, the population structure and virulence potential of C-I are unclear. RESULTS We defined a set of true C-I strains (n = 465), including a Shiga toxin 2a (Stx2a)-producing isolate from a patient with bloody diarrhoea identified by the retrospective analyses using a C-I-specific detection system. Through genomic analysis of 804 isolates from the cryptic clades, including these C-I strains, we revealed their global population structures and the marked accumulation of virulence genes and antimicrobial resistance genes in C-I. In particular, half of the C-I strains contained hallmark virulence genes of Stx-producing E. coli (STEC) and/or enterotoxigenic E. coli (ETEC). We also found the host-specific distributions of virulence genes, which suggests bovines as the potential source of human infections caused by STEC- and STEC/ETEC hybrid-type C-I strains, as is known in STEC. CONCLUSIONS Our findings demonstrate the emergence of human intestinal pathogens in C-I lineage. To better understand the features of C-I strains and their infections, extensive surveillance and larger population studies of C-I strains are needed. The C-I-specific detection system developed in this study will be a powerful tool for screening and identifying C-I strains.
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Affiliation(s)
- Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Yoko Arimizu
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
- Department of Infectious Disease, National Hospital Organization Kyushu Medical Center, Fukuoka, 810-0065, Japan
| | - Seina Miyahara
- Department of Microbiology, Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, 889-2155, Japan
| | - Yuki Wakabayashi
- Division of Microbiology, Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shuji Yoshino
- Department of Microbiology, Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, 889-2155, Japan
| | - Tetsuya Harada
- Division of Microbiology, Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Kazuko Seto
- Division of Planning, Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Takeshi Yamamoto
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan.
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14
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Ma W, Zhu B, Wang W, Wang Q, Cui X, Wang Y, Dong X, Li X, Ma J, Cheng F, Shi X, Chen L, Niu S, Hao M. Genetic and enzymatic characterization of two novel bla NDM-36, -37 variants in Escherichia coli strains. Eur J Clin Microbiol Infect Dis 2023; 42:471-480. [PMID: 36810726 PMCID: PMC9998317 DOI: 10.1007/s10096-023-04576-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023]
Abstract
The widespread of different NDM variants in clinical Enterobacterales isolates poses a serious public health concern, which requires continuous monitoring. In this study, three E. coli strains carrying two novel blaNDM variants of blaNDM-36, -37 were identified from a patient with refractory urinary tract infection (UTI) in China. We conducted antimicrobial susceptibility testing (AST), enzyme kinetics analysis, conjugation experiment, whole-genome sequencing (WGS), and bioinformatics analysis to characterize the blaNDM-36, -37 enzymes and their carrying strains. The blaNDM-36, -37 harboring E. coli isolates belonged to ST227, O9:H10 serotype and exhibited intermediate or resistance to all β-lactams tested except aztreonam and aztreonam/avibactam. The genes of blaNDM-36, -37 were located on a conjugative IncHI2-type plasmid. NDM-37 differed from NDM-5 by a single amino acid substitution (His261Tyr). NDM-36 differed from NDM-37 by an additional missense mutation (Ala233Val). NDM-36 had increased hydrolytic activity toward ampicillin and cefotaxime relative to NDM-37 and NDM-5, while NDM-37 and NDM-36 had lower catalytic activity toward imipenem but higher activity against meropenem in comparison to NDM-5. This is the first report of co-occurrence of two novel blaNDM variants in E. coli isolated from the same patient. The work provides insights into the enzymatic function and demonstrates the ongoing evolution of NDM enzymes.
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Affiliation(s)
- Wanshan Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Bo Zhu
- Xiamen Key Laboratory of Genetic Testing, Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Wen Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, No. 1 Friendship Road, Yuzhong District, Chongqing, China
| | - Qian Wang
- Department of Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xiaodi Cui
- School of Clinical Medicine, Jining Medical University, Jining, China
| | - Yujiao Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Xiutao Dong
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Xiaofeng Li
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Jianping Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Fang Cheng
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Xiaohong Shi
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Siqiang Niu
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, No. 1 Friendship Road, Yuzhong District, Chongqing, China.
| | - Mingju Hao
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China.
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15
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Chicken Production and Human Clinical Escherichia coli Isolates Differ in Their Carriage of Antimicrobial Resistance and Virulence Factors. Appl Environ Microbiol 2023; 89:e0116722. [PMID: 36651726 PMCID: PMC9973021 DOI: 10.1128/aem.01167-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Contamination of food animal products by Escherichia coli is a leading cause of foodborne disease outbreaks, hospitalizations, and deaths in humans. Chicken is the most consumed meat both in the United States and across the globe according to the U.S. Department of Agriculture. Although E. coli is a ubiquitous commensal bacterium of the guts of humans and animals, its ability to acquire antimicrobial resistance (AMR) genes and virulence factors (VFs) can lead to the emergence of pathogenic strains that are resistant to critically important antibiotics. Thus, it is important to identify the genetic factors that contribute to the virulence and AMR of E. coli. In this study, we performed in-depth genomic evaluation of AMR genes and VFs of E. coli genomes available through the National Antimicrobial Resistance Monitoring System GenomeTrackr database. Our objective was to determine the genetic relatedness of chicken production isolates and human clinical isolates. To achieve this aim, we first developed a massively parallel analytical pipeline (Reads2Resistome) to accurately characterize the resistome of each E. coli genome, including the AMR genes and VFs harbored. We used random forests and hierarchical clustering to show that AMR genes and VFs are sufficient to classify isolates into different pathogenic phylogroups and host origin. We found that the presence of key type III secretion system and AMR genes differentiated human clinical isolates from chicken production isolates. These results further improve our understanding of the interconnected role AMR genes and VFs play in shaping the evolution of pathogenic E. coli strains. IMPORTANCE Pathogenic Escherichia coli causes disease in both humans and food-producing animals. E. coli pathogenesis is dependent on a repertoire of virulence factors and antimicrobial resistance genes. Food-borne outbreaks are highly associated with the consumption of undercooked and contaminated food products. This association highlights the need to understand the genetic factors that make E. coli virulent and pathogenic in humans and poultry. This research shows that E. coli isolates originating from human clinical settings and chicken production harbor different antimicrobial resistance genes and virulence factors that can be used to classify them into phylogroups and host origins. In addition, to aid in the repeatability and reproducibility of the results presented in this study, we have made a public repository of the Reads2Resistome pipeline and have provided the accession numbers associated with the E. coli genomes analyzed.
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Calvo PA, Mateo-Cáceres V, Díaz-Arco S, Redrejo-Rodríguez M, de Vega M. The enterohemorrhagic Escherichia coli insertion sequence-excision enhancer protein is a DNA polymerase with microhomology-mediated end-joining activity. Nucleic Acids Res 2023; 51:1189-1207. [PMID: 36715333 PMCID: PMC9943667 DOI: 10.1093/nar/gkad017] [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: 10/31/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/31/2023] Open
Abstract
Bacterial genomes contain an abundance of transposable insertion sequence (IS) elements that are essential for genome evolution and fitness. Among them, IS629 is present in most strains of enterohemorrhagic Escherichia coli O157 and accounts for many polymorphisms associated with gene inactivation and/or genomic deletions. The excision of IS629 from the genome is promoted by IS-excision enhancer (IEE) protein. Despite IEE has been identified in the most pathogenic serotypes of E. coli, its biochemical features that could explain its role in IS excision are not yet understood. We show that IEE is present in >30% of all available E. coli genome assemblies, and is highly conserved and very abundant within enterohemorrhagic, enteropathogenic and enterotoxigenic genomes. In vitro analysis of the recombinant protein from E. coli O157:H7 revealed the presence of a Mn2+-dependent error-prone DNA polymerase activity in its N-terminal archaeo-eukaryotic primase (AEP) domain able to promote dislocations of the primer and template strands. Importantly, IEE could efficiently perform in vitro an end-joining reaction of 3'-single-strand DNA overhangs with ≥4 bp of homology requiring both the N-terminal AEP and C-terminal helicase domains. The proposed role for IEE in the novel IS excision mechanism is discussed.
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Affiliation(s)
- Patricia A Calvo
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Nicolás Cabrera 1, Madrid 28049, Spain
| | - Víctor Mateo-Cáceres
- Department of Biochemistry, School of Medicine, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas Alberto Sols (Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Silvia Díaz-Arco
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Nicolás Cabrera 1, Madrid 28049, Spain
| | - Modesto Redrejo-Rodríguez
- Department of Biochemistry, School of Medicine, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas Alberto Sols (Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Miguel de Vega
- To whom correspondence should be addressed. Tel: +34 911964717; Fax: +34 911964420;
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Mariotti A, Ezzraimi AE, Camoin-Jau L. Effect of antiplatelet agents on Escherichia coli sepsis mechanisms: A review. Front Microbiol 2022; 13:1043334. [PMID: 36569083 PMCID: PMC9780297 DOI: 10.3389/fmicb.2022.1043334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/07/2022] [Indexed: 12/13/2022] Open
Abstract
Despite ever-increasing improvements in the prognosis of sepsis, this condition remains a frequent cause of hospitalization and mortality in Western countries. Sepsis exposes the patient to multiple complications, including thrombotic complications, due to the ability of circulating bacteria to activate platelets. One of the bacteria most frequently implicated in sepsis, Escherichia coli, a Gram-negative bacillus, has been described as being capable of inducing platelet activation during sepsis. However, to date, the mechanisms involved in this activation have not been clearly established, due to their multiple characteristics. Many signaling pathways are thought to be involved. At the same time, reports on the use of antiplatelet agents in sepsis to reduce platelet activation have been published, with variable results. To date, their use in sepsis remains controversial. The aim of this review is to summarize the currently available knowledge on the mechanisms of platelet activation secondary to Escherichia coli sepsis, as well as to provide an update on the effects of antiplatelet agents in these pathological circumstances.
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Affiliation(s)
- Antoine Mariotti
- Aix Marseille Univ., IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France,IHU Méditerranée Infection, Marseille, France,Haematology Laboratory, Hôpital de la Timone, APHM, Marseille, France
| | - Amina Ezzeroug Ezzraimi
- Aix Marseille Univ., IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France,IHU Méditerranée Infection, Marseille, France
| | - Laurence Camoin-Jau
- Aix Marseille Univ., IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France,IHU Méditerranée Infection, Marseille, France,Haematology Laboratory, Hôpital de la Timone, APHM, Marseille, France,*Correspondence: Laurence Camoin-Jau,
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Bumunang EW, Zaheer R, Stanford K, Laing C, Niu D, Guan LL, Chui L, Tarr GAM, McAllister TA. Genomic Analysis of Shiga Toxin-Producing E. coli O157 Cattle and Clinical Isolates from Alberta, Canada. Toxins (Basel) 2022; 14:toxins14090603. [PMID: 36136541 PMCID: PMC9505746 DOI: 10.3390/toxins14090603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 12/02/2022] Open
Abstract
Shiga toxin (stx) is the principal virulence factor of the foodborne pathogen, Shiga toxin-producing Escherichia coli (STEC) O157:H7 and is associated with various lambdoid bacterio (phages). A comparative genomic analysis was performed on STEC O157 isolates from cattle (n = 125) and clinical (n = 127) samples to characterize virulence genes, stx-phage insertion sites and antimicrobial resistance genes that may segregate strains circulating in the same geographic region. In silico analyses revealed that O157 isolates harboured the toxin subtypes stx1a and stx2a. Most cattle (76.0%) and clinical (76.4%) isolates carried the virulence gene combination of stx1, stx2, eae and hlyA. Characterization of stx1 and stx2-carrying phages in assembled contigs revealed that they were associated with mlrA and wrbA insertion sites, respectively. In cattle isolates, mlrA and wrbA insertion sites were occupied more often (77% and 79% isolates respectively) than in clinical isolates (38% and 1.6% isolates, respectively). Profiling of antimicrobial resistance genes (ARGs) in the assembled contigs revealed that 8.8% of cattle (11/125) and 8.7% of clinical (11/127) isolates harboured ARGs. Eight antimicrobial resistance genes cassettes (ARCs) were identified in 14 isolates (cattle, n = 8 and clinical, n = 6) with streptomycin (aadA1, aadA2, ant(3’’)-Ia and aph(3’’)-Ib) being the most prevalent gene in ARCs. The profound disparity between the cattle and clinical strains in occupancy of the wrbA locus suggests that this trait may serve to differentiate cattle from human clinical STEC O157:H7. These findings are important for stx screening and stx-phage insertion site genotyping as well as monitoring ARGs in isolates from cattle and clinical samples.
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Affiliation(s)
- Emmanuel W. Bumunang
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Kim Stanford
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 1M4, Canada
| | - Chad Laing
- National Centre for Animal Disease Canadian Food Inspection Agency, Lethbridge, AB T1J 0P3, Canada
| | - Dongyan Niu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P9, Canada
| | - Linda Chui
- Alberta Precisions Laboratory, Alberta Public Health, Edmonton, AB T6G 2J2, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Gillian A. M. Tarr
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
- Correspondence:
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Kromann S, Baig S, Stegger M, Olsen RH, Bojesen AM, Jensen HE, Thøfner I. Longitudinal study on background lesions in broiler breeder flocks and their progeny, and genomic characterisation of Escherichia coli. Vet Res 2022; 53:52. [PMID: 35799204 PMCID: PMC9264609 DOI: 10.1186/s13567-022-01064-7] [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: 02/01/2022] [Accepted: 04/21/2022] [Indexed: 12/02/2022] Open
Abstract
In broiler breeders, background mortality is rarely addressed, however, it represents the death of a vast number of birds, a constant productivity loss, welfare concerns and it might affect chick quality. The study aimed to unveil lesions leading to mortality in a study population perceived as healthy, combined with whole-genome sequencing (WGS) of Escherichia coli, a well-known contributor to disease problems in poultry. Broiler breeders (n = 340) originating from three distinct, putative healthy flocks and their progeny (n = 154) were subjected to a comprehensive post-mortem examination, bacteriological sampling, and sequencing of 77 E. coli isolates. Productivity data confirmed an exemplary health status of the enrolled flocks, and post-mortem examination further verified the absence of general disease problems. Among the submitted broiler breeders, exudative peritonitis (31.2%) was the most frequent lesion linked to infectious disease, whereas airsacculitis, pericarditis, perihepatitis, and salpingitis occurred in 18.5%, 3.5%, 3.8% and 17%, respectively. Yolksacculitis occurred in 15.6% of the broilers, whilst pericarditis, perihepatitis and peritonitis were diagnosed in 9.7%, 7.1% and 9.1%, respectively. WGS revealed a diverse population where ST95 dominated the population retrieved from broiler breeders, whereas ST10 was highly prevalent among broilers. Both lineages could be isolated from extraintestinal sites of birds without lesions indicative of infection. In general, the genetic diversity within flocks was comparable to the diversity between farms, and the overall occurrence of resistance markers was low. In conclusion, a comprehensive insight into lesions associated with background mortality is presented, together with a vast diversity of E. coli isolated from extraintestinal sites during a non-outbreak situation.
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Affiliation(s)
- Sofie Kromann
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark. .,DanHatch Denmark A/S, Rugerivej 26, 9760, Vrå, Denmark.
| | - Sharmin Baig
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Rikke Heidemann Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Anders Miki Bojesen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Henrik Elvang Jensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Ida Thøfner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
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Ezzeroug Ezzraimi A, Hannachi N, Mariotti A, Rolland C, Levasseur A, Baron SA, Rolain JM, Camoin-Jau L. The Antibacterial Effect of Platelets on Escherichia coli Strains. Biomedicines 2022; 10:biomedicines10071533. [PMID: 35884840 PMCID: PMC9313237 DOI: 10.3390/biomedicines10071533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 01/02/2023] Open
Abstract
Platelets play an important role in defense against pathogens; however, the interaction between Escherichia coli and platelets has not been well described and detailed. Our goal was to study the interaction between platelets and selected strains of E. coli in order to evaluate the antibacterial effect of platelets and to assess bacterial effects on platelet activation. Washed platelets and supernatants of pre-activated platelets were incubated with five clinical colistin-resistant and five laboratory colistin-sensitive strains of E. coli in order to study bacterial growth. Platelet activation was measured with flow cytometry by evaluating CD62P expression. To identify the difference in strain behavior toward platelets, a pangenome analysis using Roary and O-antigen serotyping was carried out. Both whole platelets and the supernatant of activated platelets inhibited growth of three laboratory colistin-sensitive strains. In contrast, platelets promoted growth of the other strains. There was a negative correlation between platelet activation and bacterial growth. The Roary results showed no logical clustering to explain the mechanism of platelet resistance. The diversity of the responses might be due to strains of different types of O-antigen. Our results show a bidirectional interaction between platelets and E. coli whose expression is dependent on the bacterial strain involved.
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Affiliation(s)
- Amina Ezzeroug Ezzraimi
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
| | - Nadji Hannachi
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- Département de Pharmacie, Faculté de Médecine, Université Ferhat Abbas Sétif I, Sétif 19000, Algeria
| | - Antoine Mariotti
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
- Laboratoire d’Hématologie, Hôpital de la Timone, APHM, Boulevard Jean-Moulin, 13385 Marseille, France
| | - Clara Rolland
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
- Aix Marseille University, IRD, SSA, APHM, VITROME, IHU Méditerranée Infection, 13385 Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
- Aix Marseille University, IRD, SSA, APHM, VITROME, IHU Méditerranée Infection, 13385 Marseille, France
| | - Sophie Alexandra Baron
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
| | - Jean-Marc Rolain
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
| | - Laurence Camoin-Jau
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
- Laboratoire d’Hématologie, Hôpital de la Timone, APHM, Boulevard Jean-Moulin, 13385 Marseille, France
- Correspondence: ; Tel.: +33-4-13-73-24-01; Fax: +33-4-13-73-24-02
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Genome Informatics and Machine Learning-Based Identification of Antimicrobial Resistance-Encoding Features and Virulence Attributes in Escherichia coli Genomes Representing Globally Prevalent Lineages, Including High-Risk Clonal Complexes. mBio 2021; 13:e0379621. [PMID: 35164570 PMCID: PMC8844930 DOI: 10.1128/mbio.03796-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Escherichia coli, a ubiquitous commensal/pathogenic member from the Enterobacteriaceae family, accounts for high infection burden, morbidity, and mortality throughout the world. With emerging multidrug resistance (MDR) on a massive scale, E. coli has been listed as one of the Global Antimicrobial Resistance and Use Surveillance System (GLASS) priority pathogens. Understanding the resistance mechanisms and underlying genomic features appears to be of utmost importance to tackle further spread of these multidrug-resistant superbugs. While a few of the globally prevalent sequence types (STs) of E. coli, such as ST131, ST69, ST405, and ST648, have been previously reported to be highly virulent and harboring MDR, there is no clarity if certain ST lineages have a greater propensity to acquire MDR. In this study, large-scale comparative genomics of a total of 5,653 E. coli genomes from 19 ST lineages revealed ST-wide prevalence patterns of genomic features, such as antimicrobial resistance (AMR)-encoding genes/mutations, virulence genes, integrons, and transposons. Interpretation of the importance of these features using a Random Forest Classifier trained with 11,988 genomic features from whole-genome sequence data identified ST-specific or phylogroup-specific signature proteins mostly belonging to different protein superfamilies, including the toxin-antitoxin systems. Our study provides a comprehensive understanding of a myriad of genomic features, ST-specific proteins, and resistance mechanisms entailing different lineages of E. coli at the level of genomes; this could be of significant downstream importance in understanding the mechanisms of AMR, in clinical discovery, in epidemiology, and in devising control strategies. IMPORTANCE With the leap in whole-genome data being generated, the application of relevant methods to mine biologically significant information from microbial genomes is of utmost importance to public health genomics. Machine-learning methods have been used not only to mine, curate, or classify the data but also to identify the relevant features that could be linked to a particular class/target. This is perhaps one of the pioneering studies that has attempted to classify a large repertoire of E. coli genome data sets (5,653 genomes) belonging to 19 different STs (including well-studied as well as understudied STs) using machine learning approaches. Important features identified by these approaches have revealed ST-specific signature proteins, which could be further studied to predict possible associations with the phenotypic profiles, thereby providing a better understanding of virulence and the resistance mechanisms among different clonal lineages of E. coli.
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