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Almas S, Carpenter RE, Rowan C, Tamrakar VK, Bishop J, Sharma R. Advantage of precision metagenomics for urinary tract infection diagnostics. Front Cell Infect Microbiol 2023; 13:1221289. [PMID: 37469596 PMCID: PMC10352793 DOI: 10.3389/fcimb.2023.1221289] [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: 05/12/2023] [Accepted: 06/15/2023] [Indexed: 07/21/2023] Open
Abstract
Background Urinary tract infections (UTIs) remain a diagnostic challenge and often promote antibiotic overuse. Despite urine culture being the gold standard for UTI diagnosis, some uropathogens may lead to false-negative or inconclusive results. Although PCR testing is fast and highly sensitive, its diagnostic yield is limited to targeted microorganisms. Metagenomic next-generation sequencing (mNGS) is a hypothesis-free approach with potential of deciphering the urobiome. However, clinically relevant information is often buried in the enormous amount of sequencing data. Methods Precision metagenomics (PM) is a hybridization capture-based method with potential of enhanced discovery power and better diagnostic yield without diluting clinically relevant information. We collected 47 urine samples of clinically suspected UTI and in parallel tested each sample by microbial culture, PCR, and PM; then, we comparatively analyzed the results. Next, we phenotypically classified the cumulative microbial population using the Explify® data analysis platform for potential pathogenicity. Results Results revealed 100% positive predictive agreement (PPA) with culture results, which identified only 13 different microorganisms, compared to 19 and 62 organisms identified by PCR and PM, respectively. All identified organisms were classified into phenotypic groups (0-3) with increasing pathogenic potential and clinical relevance. This PM can simultaneously quantify and phenotypically classify the organisms readily through bioinformatic platforms like Explify®, essentially providing dissected and quantitative results for timely and accurate empiric UTI treatment. Conclusion PM offers potential for building effective diagnostic models beyond usual care testing in complex UTI diseases. Future studies should assess the impact of PM-guided UTI management on clinical outcomes.
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Affiliation(s)
- Sadia Almas
- Department of Research, Advanta Genetics, Tyler, TX, United States
| | - Rob E. Carpenter
- Department of Research, Advanta Genetics, Tyler, TX, United States
- Soules College of Business, University of Texas at Tyler, Tyler, TX, United States
| | - Chase Rowan
- Department of Research, Advanta Genetics, Tyler, TX, United States
| | - Vaibhav K. Tamrakar
- Divison of Communicable Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
- Department of Research, RetroBioTech LLC, Coppell, TX, United States
| | - Joseph Bishop
- Department of Research, Advanta Genetics, Tyler, TX, United States
| | - Rahul Sharma
- Department of Research, Advanta Genetics, Tyler, TX, United States
- Department of Research, RetroBioTech LLC, Coppell, TX, United States
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Buberg ML, Wasteson Y, Lindstedt BA, Witsø IL. In vitro digestion of ESC-resistant Escherichia coli from poultry meat and evaluation of human health risk. Front Microbiol 2023; 14:1050143. [PMID: 36846779 PMCID: PMC9947789 DOI: 10.3389/fmicb.2023.1050143] [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: 09/21/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction The spread of antimicrobial resistance (AMR) has become a threat against human and animal health. Third and fourth generation cephalosporins have been defined as critically important antimicrobials by The World Health Organization. Exposure to Extended spectrum cephalosporin-resistant E. coli may result in consumers becoming carriers if these bacteria colonize the human gut or their resistance genes spread to other bacteria in the gut microbiota. In the case that these resistant bacteria at later occasions cause disease, their resistance characteristics may lead to failure of treatment and increased mortality. We hypothesized that ESC-resistant E. coli from poultry can survive digestion and thereby cause infections and/or spread their respective resistance traits within the gastro-intestinal tract. Methods In this study, a selection of 31 ESC-resistant E. coli isolates from retail chicken meat was exposed to a static in vitro digestion model (INFOGEST). Their survival, alteration of colonizing characteristics in addition to conjugational abilities were investigated before and after digestion. Whole genome data from all isolates were screened through a custom-made virulence database of over 1100 genes for virulence- and colonizing factors. Results and discussion All isolates were able to survive digestion. Most of the isolates (24/31) were able to transfer their bla CMY2-containing plasmid to E. coli DH5-á, with a general decline in conjugation frequency of digested isolates compared to non-digested. Overall, the isolates showed a higher degree of cell adhesion than cell invasion, with a slight increase after digestion compared non-digested, except for three isolates that displayed a major increase of invasion. These isolates also harbored genes facilitating invasion. In the virulence-associated gene analysis two isolates were categorized as UPEC, and one isolate was considered a hybrid pathogen. Altogether the pathogenic potential of these isolates is highly dependent on the individual isolate and its characteristics. Poultry meat may represent a reservoir and be a vehicle for dissemination of potential human pathogens and resistance determinants, and the ESC-resistance may complicate treatment in the case of an infection.
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Affiliation(s)
- May Linn Buberg
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Yngvild Wasteson
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Bjørn Arne Lindstedt
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Ingun Lund Witsø
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway,*Correspondence: Ingun Lund Witsø ✉
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Zhang S, Yang G, Jiang Y. Antibiotic and metal resistance of Stenotrophomonas maltophilia isolates from Eboling permafrost of the Tibetan Plateau. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:11798-11810. [PMID: 36097311 DOI: 10.1007/s11356-022-22888-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Whole-genome sequencing of pathogenic bacteria Stenotrophomonas maltophilia from a less polluted environment of permafrost can help understand the intrinsic resistome of both antibiotics and metals. This study aimed to examine the maximum minimum inhibitory concentration (MIC) of both antibiotics and metals, as well as antibiotic resistance genes and metal resistance genes annotated from whole-genome sequences. The permafrost S. maltophilia was sensitive to ciprofloxacin, tetracycline, streptomycin, and bacitracin, and resistant to chloramphenicol, trimethoprim-sulfamethoxazole, erythromycin, Zn2+, Ni2+, Cu2+, and Cr6+, with a lower maximum MIC, compared with clinical S. maltophilia. The former strain belonged to the lower antibiotic resistance gene (ARG) and metal resistance gene (MRG) clusters compared with the latter ones. The permafrost strain contained no or only one kind of ARG or MRG on a single genomic island, which explained the aforementioned lower maximum MIC and less diversity of ARGs or MRGs. The result indicated that the co-occurrence of antibiotic and metal resistance was due to a certain innate ability of S. maltophilia. The continuous human use of antibiotics or metals induced selective pressure, resulting in higher MIC and more diverse ARGs and MRGs in human-impacted environments.
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Affiliation(s)
- Shuhong Zhang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China.
| | - Guangli Yang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Yali Jiang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
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Aguirre-Sánchez JR, Valdez-Torres JB, Del Campo NC, Martínez-Urtaza J, Del Campo NC, Lee BG, Quiñones B, Chaidez-Quiroz C. Phylogenetic group and virulence profile classification in Escherichia coli from distinct isolation sources in Mexico. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 106:105380. [PMID: 36283634 DOI: 10.1016/j.meegid.2022.105380] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022]
Abstract
Escherichia coli is a leading cause of human enteric diseases worldwide. The rapid and accurate causal agent identification to a particular source represents a crucial step in the establishment of safety and health measures in the affected human populations and would thus provide insights into the relationship of traits that may contribute for pathogen persistence in a particular reservoir. The objective of the present study was to characterize over two hundred E. coli strains from different isolation sources in Mexico by conducting a correspondence analysis to explore associations with the detected phylogenetic groups. The results indicated that E. coli strains, recovered from distinct sources in Mexico, were classified into phylogroups B1 (35.8%), A (27.8%), and D (12.3%) and were clustered to particular clades according to the predicted phylogroups. The results from correspondence analysis showed that E. coli populations from distinct sources in Mexico, belonging to different phylogroups, were not dispersed randomly and were associated with a particular isolation source. Phylogroup A was strongly associated with human sources, and the phylogroup B1 showed a significant relationship with food sources. Additionally, phylogroup D was also related to human sources. Phylogroup B2 was associated with herbivorous and omnivorous mammals. Moreover, common virulence genes in the examined E. coli strains, assigned to all phylogroups, were identified as essential markers for survival and invasion in the host. Although virulence profiles varied among the detected phylogroups, E. coli strains belonging to phylogroup D, associated with humans, were found to contain the largest virulence gene repertoire conferring for persistence and survival in the host. In summary, these findings provide fundamental information for a better characterization of pathogenic E. coli, recovered from distinct isolation sources in Mexico and would assist in the development of better tools for identifying potential transmission routes of contamination.
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Affiliation(s)
- José R Aguirre-Sánchez
- Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, 80110 Culiacán, Sinaloa, Mexico
| | - José B Valdez-Torres
- Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, 80110 Culiacán, Sinaloa, Mexico
| | - Nohemí Castro Del Campo
- Facultad de Medicina Veterinaria y Zootecnia de la Universidad Autónoma de Sinaloa, 80260 Culiacán, Sinaloa, Mexico
| | - Jaime Martínez-Urtaza
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Nohelia Castro Del Campo
- Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, 80110 Culiacán, Sinaloa, Mexico
| | - Bertram G Lee
- U.S. Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA 94710, United States
| | - Beatriz Quiñones
- U.S. Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA 94710, United States
| | - Cristóbal Chaidez-Quiroz
- Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, 80110 Culiacán, Sinaloa, Mexico.
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Tapia-Arreola AK, Ruiz-Garcia DA, Rodulfo H, Sharma A, De Donato M. High Frequency of Antibiotic Resistance Genes (ARGs) in the Lerma River Basin, Mexico. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192113988. [PMID: 36360888 PMCID: PMC9657182 DOI: 10.3390/ijerph192113988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 05/31/2023]
Abstract
The spread of beta-lactamase-producing bacteria is of great concern and the environment has been found to be a main source of contamination. Herein, it was proposed to determine the frequency of antimicrobial-resistant-Gram-negative bacteria throughout the Lerma River basin using phenotypic and molecular methods. Resistant bacteria were isolated with chromogenic media and antimicrobial susceptibility tests were used to characterize their resistance. ARGs for beta-lactams, aminoglycosides, and quinolones were detected by PCR. Species were identified by Sanger sequencing the 16S rRNA gene and the representative genomes of MDR strains were sequenced by NGS. A high variation in the number of isolates was observed in the 20 sampled sites, while observing a low diversity among the resistant bacteria. Of the 12 identified bacterial groups, C. freundii, E. coli, and S. marcescens were more predominant. A high frequency of resistance to beta-lactams, quinolones, and aminoglycosides was evidenced, where the blaCTX,qnrB, qnrS y, and aac(6')lb-cr genes were the most prevalent. C. freundii showed the highest frequency of MDR strains. Whole genome sequencing revealed that S. marcescens and K. pneumoniae showed a high number of shared virulence and antimicrobial resistance genes, while E. coli showed the highest number of unique genes. The contamination of the Lerma River with MDR strains carrying various ARGs should raise awareness among environmental authorities to assess the risks and regulations regarding the optimal hygienic and sanitary conditions for this important river that supports economic activities in the different communities in Mexico.
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Zhang L, Huang W, Zhang S, Li Q, Wang Y, Chen T, Jiang H, Kong D, Lv Q, Zheng Y, Ren Y, Liu P, Jiang Y, Chen Y. Rapid Detection of Bacterial Pathogens and Antimicrobial Resistance Genes in Clinical Urine Samples With Urinary Tract Infection by Metagenomic Nanopore Sequencing. Front Microbiol 2022; 13:858777. [PMID: 35655992 PMCID: PMC9152355 DOI: 10.3389/fmicb.2022.858777] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/11/2022] [Indexed: 12/24/2022] Open
Abstract
Urinary tract infections (UTIs) are among the most common acquired bacterial infections in humans. The current gold standard method for identification of uropathogens in clinical laboratories is cultivation. However, culture-based assays have substantial drawbacks, including long turnaround time and limited culturability of many potential pathogens. Nanopore sequencing technology can overcome these limitations and detect pathogens while also providing reliable predictions of drug susceptibility in clinical samples. Here, we optimized a metagenomic nanopore sequencing (mNPS) test for pathogen detection and identification in urine samples of 76 patients with acute uncomplicated UTIs. We first used twenty of these samples to show that library preparation by the PCR Barcoding Kit (PBK) led to the highest agreement of positive results with gold standard clinical culture tests, and enabled antibiotic resistance detection in downstream analyses. We then compared the detection results of mNPS with those of culture-based diagnostics and found that mNPS sensitivity and specificity of detection were 86.7% [95% confidence interval (CI), 73.5-94.1%] and 96.8% (95% CI, 82.4-99.9%), respectively, indicating that the mNPS method is a valid approach for rapid and specific detection of UTI pathogens. The mNPS results also performed well at predicting antibiotic susceptibility phenotypes. These results demonstrate that our workflow can accurately diagnose UTI-causative pathogens and enable successful prediction of drug-resistant phenotypes within 6 h of sample receipt. Rapid mNPS testing is thus a promising clinical diagnostic tool for infectious diseases, based on clinical urine samples from UTI patients, and shows considerable potential for application in other clinical infections.
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Affiliation(s)
- Lei Zhang
- College of Life Science, Yantai University, Yantai, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Shengwei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,Department of Clinical Laboratory, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Qian Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ye Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ting Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Qingyu Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuhao Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ying Chen
- College of Life Science, Yantai University, Yantai, China
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Teixeira P, Pinto N, Henriques I, Tacão M. KPC-3-, GES-5-, and VIM-1-Producing Enterobacterales Isolated from Urban Ponds. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19105848. [PMID: 35627386 PMCID: PMC9141432 DOI: 10.3390/ijerph19105848] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 01/27/2023]
Abstract
Carbapenems are antibiotics of pivotal importance in human medicine, the efficacy of which is threatened by the increasing prevalence of carbapenem-resistant Enterobacterales (CRE). Urban ponds may be reservoirs of CRE, although this hypothesis has been poorly explored. We assessed the proportion of CRE in urban ponds over a one-year period and retrieved 23 isolates. These were submitted to BOX-PCR, PFGE, 16S rDNA sequencing, antibiotic susceptibility tests, detection of carbapenemase-encoding genes, and conjugation assays. Isolates were affiliated with Klebsiella (n = 1), Raoultella (n = 11), Citrobacter (n = 8), and Enterobacter (n = 3). Carbapenemase-encoding genes were detected in 21 isolates: blaKPC (n = 20), blaGES-5 (n = 6), and blaVIM (n = 1), with 7 isolates carrying two carbapenemase genes. Clonal isolates were collected from different ponds and in different campaigns. Citrobacter F6, Raoultella N9, and Enterobacter N10 were predicted as pathogens from whole-genome sequence analysis, which also revealed the presence of several resistance genes and mobile genetic elements. We found that blaKPC-3 was located on Tn4401b (Citrobacter F6 and Enterobacter N10) or Tn4401d (Raoultella N9). The former was part of an IncFIA-FII pBK30683-like plasmid. In addition, blaGES-5 was in a class 3 integron, either chromosomal (Raoultella N9) or plasmidic (Enterobacter N10). Our findings confirmed the role of urban ponds as reservoirs and dispersal sites for CRE.
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Affiliation(s)
- Pedro Teixeira
- CESAM (Centre for Marine and Environmental Studies), University of Aveiro, 3810-193 Aveiro, Portugal; (P.T.); (M.T.)
- Biology Department, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Nuno Pinto
- Biology Department, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Isabel Henriques
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3004-531 Coimbra, Portugal
- Correspondence:
| | - Marta Tacão
- CESAM (Centre for Marine and Environmental Studies), University of Aveiro, 3810-193 Aveiro, Portugal; (P.T.); (M.T.)
- Biology Department, University of Aveiro, 3810-193 Aveiro, Portugal;
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Richter L, du Plessis EM, Duvenage S, Allam M, Ismail A, Korsten L. Whole Genome Sequencing of Extended-Spectrum- and AmpC- β-Lactamase-Positive Enterobacterales Isolated From Spinach Production in Gauteng Province, South Africa. Front Microbiol 2021; 12:734649. [PMID: 34659162 PMCID: PMC8517129 DOI: 10.3389/fmicb.2021.734649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase- (AmpC) producing Enterobacterales in irrigation water and associated irrigated fresh produce represents risks related to the environment, food safety, and public health. In South Africa, information about the presence of ESBL/AmpC-producing Enterobacterales from non-clinical sources is limited, particularly in the water-plant-food interface. This study aimed to characterize 19 selected MDR ESBL/AmpC-producing Escherichia coli (n=3), Klebsiella pneumoniae (n=5), Serratia fonticola (n=10), and Salmonella enterica (n=1) isolates from spinach and associated irrigation water samples from two commercial spinach production systems within South Africa, using whole genome sequencing (WGS). Antibiotic resistance genes potentially encoding resistance to eight different classes were present, with bla CTX-M-15 being the dominant ESBL encoding gene and bla ACT-types being the dominant AmpC encoding gene detected. A greater number of resistance genes across more antibiotic classes were seen in all the K. pneumoniae strains, compared to the other genera tested. From one farm, bla CTX-M-15-positive K. pneumoniae strains of the same sequence type 985 (ST 985) were present in spinach at harvest and retail samples after processing, suggesting successful persistence of these MDR strains. In addition, ESBL-producing K. pneumoniae ST15, an emerging high-risk clone causing nosocomical outbreaks worldwide, was isolated from irrigation water. Known resistance plasmid replicon types of Enterobacterales including IncFIB, IncFIA, IncFII, IncB/O, and IncHI1B were observed in all strains following analysis with PlasmidFinder. However, bla CTX-M-15 was the only β-lactamase resistance gene associated with plasmids (IncFII and IncFIB) in K. pneumoniae (n=4) strains. In one E. coli and five K. pneumoniae strains, integron In191 was observed. Relevant similarities to human pathogens were predicted with PathogenFinder for all 19 strains, with a confidence of 0.635-0.721 in S. fonticola, 0.852-0.931 in E. coli, 0.796-0.899 in K. pneumoniae, and 0.939 in the S. enterica strain. The presence of MDR ESBL/AmpC-producing E. coli, K. pneumoniae, S. fonticola, and S. enterica with similarities to human pathogens in the agricultural production systems reflects environmental and food contamination mediated by anthropogenic activities, contributing to the spread of antibiotic resistance genes.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Erika M. du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
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