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Sabtcheva S, Stoikov I, Ivanov IN, Donchev D, Lesseva M, Georgieva S, Teneva D, Dobreva E, Christova I. Genomic Characterization of Carbapenemase-Producing Enterobacter hormaechei, Serratia marcescens, Citrobacter freundii, Providencia stuartii, and Morganella morganii Clinical Isolates from Bulgaria. Antibiotics (Basel) 2024; 13:455. [PMID: 38786183 PMCID: PMC11117914 DOI: 10.3390/antibiotics13050455] [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: 04/25/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Carbapenemase-producing Enterobacter spp. Serratia marcescens, Citrobacter freundii, Providencia spp., and Morganella morganii (CP-ESCPM) are increasingly identified as causative agents of nosocomial infections but are still not under systematic genomic surveillance. In this study, using a combination of whole-genome sequencing and conjugation experiments, we sought to elucidate the genomic characteristics and transferability of resistance genes in clinical CP-ESCPM isolates from Bulgaria. Among the 36 sequenced isolates, NDM-1 (12/36), VIM-4 (11/36), VIM-86 (8/36), and OXA-48 (7/36) carbapenemases were identified; two isolates carried both NDM-1 and VIM-86. The majority of carbapenemase genes were found on self-conjugative plasmids. IncL plasmids were responsible for the spread of OXA-48 among E. hormaechei, C. freundii, and S. marcescens. IncM2 plasmids were generally associated with the spread of NDM-1 in C. freundii and S. marcescens, and also of VIM-4 in C. freundii. IncC plasmids were involved in the spread of the recently described VIM-86 in P. stuartii isolates. IncC plasmids carrying blaNDM-1 and blaVIM-86 were observed too. blaNDM-1 was also detected on IncX3 in S. marcescens and on IncT plasmid in M. morganii. The significant resistance transfer rates we observed highlight the role of the ESCPM group as a reservoir of resistance determinants and stress the need for strengthening infection control measures.
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Affiliation(s)
- Stefana Sabtcheva
- Laboratory for Clinical Microbiology, National Oncology Center, 1797 Sofia, Bulgaria; (I.S.); (S.G.)
| | - Ivan Stoikov
- Laboratory for Clinical Microbiology, National Oncology Center, 1797 Sofia, Bulgaria; (I.S.); (S.G.)
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Ivan N. Ivanov
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Deyan Donchev
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Magdalena Lesseva
- Department of Microbiology, University Multiprofile Hospital for Active Treatment and Emergency Medicine “N. I. Pirogov”, 1606 Sofia, Bulgaria;
| | - Sylvia Georgieva
- Laboratory for Clinical Microbiology, National Oncology Center, 1797 Sofia, Bulgaria; (I.S.); (S.G.)
| | - Deana Teneva
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Elina Dobreva
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Iva Christova
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
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Abioye OE, Nontongana N, Osunla CA, Okoh AI. Antibiotic resistance and virulence genes profiling of Vibrio cholerae and Vibrio mimicus isolates from some seafood collected at the aquatic environment and wet markets in Eastern Cape Province, South Africa. PLoS One 2023; 18:e0290356. [PMID: 37616193 PMCID: PMC10449182 DOI: 10.1371/journal.pone.0290356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
The current study determines the density of Vibrio spp. and isolates V. cholerae and Vibrio mimicus from fish-anatomical-sites, prawn, crab and mussel samples recovered from fish markets, freshwater and brackish water. Virulence and antibiotic resistance profiling of isolates were carried out using standard molecular and microbiology techniques. Vibrio spp. was detected in more than 90% of samples [134/144] and its density was significantly more in fish than in other samples. Vibrio. cholerae and V. mimicus were isolated in at least one sample of each sample type with higher isolation frequency in fish samples. All the V. cholerae isolates belong to non-O1/non-O139 serogroup. One or more V. cholerae isolates exhibited intermediate or resistance against each of the eighteen panels of antibiotics used but 100% of the V. mimicus were susceptible to amikacin, gentamycin and chloramphenicol. Vibrio cholerae exhibited relatively high resistance against polymyxin, ampicillin and amoxicillin/clavulanate while V. mimicus isolates exhibited relatively high resistance against nitrofurantoin, ampicillin and polymixin. The multiple-antibiotic-resistance-index [MARI] for isolates ranges between 0 and 0.67 and 48% of the isolates have MARI that is >0.2 while 55% of the isolates exhibit MultiDrug Resistance Phenotypes. The percentage detection of acc, ant, drf18, sul1, mcr-1, blasvh, blaoxa, blatem, blaoxa48, gyrA, gyrB and parC resistance-associated genes were 2%, 9%, 14%, 7%, 2%, 25%, 7%, 2%, 2%, 32%, 25% and 27% respectively while that for virulence-associated genes in increasing other was ace [2%], tcp [11%], vpi [16%], ompU [34%], toxR [43%], rtxC [70%], rtxA [73%] and hyla [77%]. The study confirmed the potential of environmental non-O1/non-O139 V. cholerae and V. mimicus to cause cholera-like infection and other vibriosis which could be difficult to manage with commonly recommended antibiotics. Thus, regular monitoring of the environment to create necessary awareness for this kind of pathogens is important in the interest of public health.
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Affiliation(s)
| | - Nolonwabo Nontongana
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
| | - Charles A. Osunla
- Department of Microbiology, Adekunle Ajasin University, Akungba Akoko, Nigeria
| | - Anthony I. Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
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Abordo AMS, Carascal MB, Remenyi R, Dalisay DS, Saludes JP. Clinically Isolated β-Lactam-Resistant Gram-Negative Bacilli in a Philippine Tertiary Care Hospital Harbor Multi-Class β-Lactamase Genes. Pathogens 2023; 12:1019. [PMID: 37623979 PMCID: PMC10459468 DOI: 10.3390/pathogens12081019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
In the Philippines, data are scarce on the co-occurrence of multiple β-lactamases (BLs) in clinically isolated Gram-negative bacilli. To investigate this phenomenon, we characterized BLs from various β-lactam-resistant Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa isolated from a Philippine tertiary care hospital. The selected Gram-negative bacilli (n = 29) were resistant to either third-generation cephalosporins (resistance category 1 (RC1)), cephalosporins and penicillin-β-lactamase inhibitors (RC2), or carbapenems (RC3). Isolates resistant to other classes of antibiotics but susceptible to early-generation β-lactams were also selected (RC4). All isolates underwent antibiotic susceptibility testing, disk-diffusion-based BL detection assays, and PCR with sequence analysis of extended-spectrum BLs (ESBLs), metallo-BLs, AmpC BLs, and oxacillinases. Among the study isolates, 26/29 harbored multi-class BLs. All RC1 isolates produced ESBLs, with blaCTX-M as the dominant (19/29) gene. RC2 isolates produced ESBLs, four of which harbored blaTEM plus blaOXA-1 or other ESBL genes. RC3 isolates carried blaNDM and blaIMP, particularly in three of the metallo-BL producers. RC4 Enterobacteriaceae carried blaCTX-M, blaTEM, and blaOXA-24-like, while A. baumannii and P. aeruginosa in this category carried either blaIMP or blaOXA-24. Genotypic profiling, in complement with phenotypic characterization, revealed multi-class BLs and cryptic metallo-BLs among β-lactam-resistant Gram-negative bacilli.
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Affiliation(s)
- Alecks Megxel S. Abordo
- Clinical and Translational Research Institute, The Medical City, Pasig 1605, Philippines or (A.M.S.A.); (M.B.C.); (R.R.)
| | - Mark B. Carascal
- Clinical and Translational Research Institute, The Medical City, Pasig 1605, Philippines or (A.M.S.A.); (M.B.C.); (R.R.)
| | - Roland Remenyi
- Clinical and Translational Research Institute, The Medical City, Pasig 1605, Philippines or (A.M.S.A.); (M.B.C.); (R.R.)
| | - Doralyn S. Dalisay
- Center for Chemical Biology and Biotechnology (C2B2) and Department of Biology, University of San Agustin, Iloilo 5000, Philippines;
- Balik Scientist Program, Philippine Council for Health Research and Development, Department of Science and Technology, Taguig 1631, Philippines
| | - Jonel P. Saludes
- Balik Scientist Program, Philippine Council for Health Research and Development, Department of Science and Technology, Taguig 1631, Philippines
- Center for Natural Drug Discovery and Development (CND3) and Department of Chemistry, University of San Agustin, Iloilo 5000, Philippines
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Chen H, Li B, Shi S, Zhou T, Wang X, Wang Z, Zhou X, Wang M, Shi W, Ren L. Au-Fe 3O 4 nanozyme coupled with CRISPR-Cas12a for sensitive and visual antibiotic resistance diagnosing. Anal Chim Acta 2023; 1251:341014. [PMID: 36925313 DOI: 10.1016/j.aca.2023.341014] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 02/27/2023]
Abstract
The accumulation and spread of antibiotic resistance bacteria (ARB) in the environment may accelerate the formation of superbugs and seriously threaten the health of all living beings. The timeliness and accurate diagnosing of antibiotic resistance is essential to controlling the propagation of superbugs in the environment and formulating effective public health management programs. Herein, we developed a speedy, sensitive, accurate, and user-friendly colorimetric assay for antibiotic resistance, via a synergistic combination of the peroxidase-like property of the Au-Fe3O4 nanozyme and the specific gene identification capability of the CRISPR-Cas12a. Once the CRISPR-Cas12a system recognizes a target resistance gene, it activates its trans-cleavage activity and subsequently releases the Au-Fe3O4 nanozymes, which oxidizes the 3,3,5,5-tetramethylbenzidine (TMB) with color change from transparent to blue. The diagnosing signals could be captured and analyzed by a smartphone. This method detected kanamycin-resistance genes, ampicillin-resistance genes, and chloramphenicol-resistance genes by simple operation steps with high sensitivity (<0.1 CFU μL-1) and speediness (<1 h). This approach may prove easy for the accurate and sensitive diagnosis of the ARGs or ARB in the field, thus surveilling and controlling the microbial water quality flexibly and efficiently.
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Affiliation(s)
- Haoxiang Chen
- Department of Biomaterials, The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, College of Materials, Xiamen University, Xiamen, 361005, PR China
| | - Bangying Li
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, PR China
| | - Shangyi Shi
- State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, PR China; School of Computer Science and Technology, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Tao Zhou
- Department of Biomaterials, The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, College of Materials, Xiamen University, Xiamen, 361005, PR China
| | - Xiumin Wang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, PR China
| | - Zuyong Wang
- College of Materials Science and Engineering, Hunan University, Changsha, 410072, PR China
| | - Xi Zhou
- Department of Biomaterials, The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, College of Materials, Xiamen University, Xiamen, 361005, PR China
| | - Miao Wang
- Department of Biomaterials, The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, College of Materials, Xiamen University, Xiamen, 361005, PR China
| | - Wei Shi
- Department of Biomaterials, The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, College of Materials, Xiamen University, Xiamen, 361005, PR China.
| | - Lei Ren
- Department of Biomaterials, The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, College of Materials, Xiamen University, Xiamen, 361005, PR China; State Key Lab of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, 361005, PR China.
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Schmidt J, Zdarska V, Kolar M, Mlynarcik P. Analysis of BlaEC family class C beta-lactamase. FEMS Microbiol Lett 2023; 370:fnad097. [PMID: 37757475 PMCID: PMC10563145 DOI: 10.1093/femsle/fnad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 09/29/2023] Open
Abstract
Recent years have witnessed an increased prevalence of intrinsic and acquired beta-lactamase-producing bacteria, severely limiting human and veterinary medicine therapeutic options. The present study aimed to design specific oligonucleotides for rapid PCR detection of the cephalosporinase-encoding gene blaEC (BlaEC family class C beta-lactamase). A total of three primers were designed to detect 2281 variants of the blaEC gene and two sets of primer pairs were also tested against DNA from 11 strains. The study indicates that the proposed primers should be able to detect 100% of all described blaEC genes in different bacterial strains and monitor their spread. After comparing the amino acid sequences, a phylogenetic tree was created based on the presence of conserved amino acids and homologous motifs. More than 24 760 mutations in BlaEC enzymes have been identified. The mutations involving 371 amino acid positions and these hotspots can change the structure and activity of the monitored enzymes. We predicted several BlaEC enzymes with a broadened substrate activity against higher-generation cephalosporins.
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Affiliation(s)
- Jiri Schmidt
- Department of Biotechnology, Faculty of Science, Palacky University Olomouc, 17. listopadu 1192/12, 779 00 Olomouc, Czechia
| | - Veronika Zdarska
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 779 00 Olomouc, Czechia
| | - Milan Kolar
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 779 00 Olomouc, Czechia
| | - Patrik Mlynarcik
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 779 00 Olomouc, Czechia
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Zhang T, Li J, Wang N, Wang H, Yu L. Metagenomic analysis reveals microbiome and resistome in the seawater and sediments of Kongsfjorden (Svalbard, High Arctic). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151937. [PMID: 34838907 DOI: 10.1016/j.scitotenv.2021.151937] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/02/2021] [Accepted: 11/20/2021] [Indexed: 06/13/2023]
Abstract
Kongsfjorden in the high Arctic, a typical Arctic fjord, experienced long-time input of nutrients and pollutants from the remote and local resources, providing a platform for characterizing the diversity and distribution of antibiotic resistance genes (ARGs). However, the microbiome and antibiotic resistome in this pristine marine system have not been well documented. The present study aimed to characterize the diversity and distribution of bacterial communities and associated ARGs in seawater (12 samples) and sediments (13 samples) of Kongsfjorden via metagenomic analysis. In terms of both bacterial community compositions and ARG profiles, the seawater was significantly distinct from sediment. Only 29 ARG subtypes were detected in the Arctic seawater and sediments. Furthermore, three geochemical factors (i.e., longitude, depth, and PO43-) greatly influenced the bacterial communities in sediment samples, while longitude, depth, and latitude were crucial geochemical factors influencing the ARG profiles in sediment samples. Procrustes analysis revealed a significant correlation between bacterial community compositions and ARG profiles in seawater and sediment samples. Further analysis revealed the metagenome-assembled genomes (MAGs) with ARG subtypes. Overall, our study provides insights into the microbiome and resistome in a pristine Arctic fjord, thereby providing vital information for environmental management.
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Affiliation(s)
- Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China.
| | - Jun Li
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Nengfei Wang
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, PR China
| | - Hao Wang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Liyan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China.
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Pandey D, Singhal N, Kumar M. Investigating the OXA Variants of ESKAPE Pathogens. Antibiotics (Basel) 2021; 10:antibiotics10121539. [PMID: 34943751 PMCID: PMC8699015 DOI: 10.3390/antibiotics10121539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
ESKAPE pathogens are the leading cause of nosocomial infections. The Global Priority List of WHO has categorized ESKAPE as priority 1 and 2 pathogens. Even though several mechanisms contribute to antimicrobial resistance, OXA β-lactamase has emerged as a new threat in combating nosocomial infections. In the present study we have investigated the presence of OXA and their variants, copy number, distribution on chromosomes/plasmids, subfamilies, phylogenetic relationships, amino acid identities and variabilities in ESKAPE pathogens. Our results revealed that a total of 929 OXA were present in 2258 completely assembled genomes, which could be further subdivided into 16 sub-families. Among all the ESKAPE pathogens, OXA were highly prevalent in A. baumannii, followed by P. aeruginosa and K. pneumoniae but completely absent in E. faecium and S. aureus while, only a few copies were found in Enterobacter spp. Most of the OXA variants belonged to the OXA-51-like subfamily (200 proteins), followed by OXA-50-like subfamily (189 proteins), OXA-23-like subfamily (156 proteins) and OXA-1-like subfamily (154 proteins). OXA-51-like, OXA-213-like, OXA-134-like, OXA-58-like, OXA-24-like and OXA-20-like subfamilies were present exclusively in A. baumannii. Phylogenetic tree of the subfamilies revealed that OXA-1-like and OXA-33-like, OXA-51-like and OXA-213-like and, OXA-5-like and OXA-10-like belonged to the same branches with amino acid identities as 100%, 97.10% and 80.90% respectively. This indicates that the members of these subfamily-pairs might have evolved from the same ancestor or have recently diverged. Thus, a judicious use of carbapenems is warranted to curtail the rise of new OXA enzymes and preserve them. This is the first detailed report about the OXA of ESKAPE pathogens.
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Insights into the Resistome and Phylogenomics of a ST195 Multidrug-Resistant Acinetobacter baumannii Clinical Isolate from the Czech Republic. Life (Basel) 2021; 11:life11101079. [PMID: 34685451 PMCID: PMC8537504 DOI: 10.3390/life11101079] [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: 06/04/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 11/17/2022] Open
Abstract
Increasing antimicrobial resistance in nosocomial pathogens, such as Acinetobacter baumannii, is becoming a serious threat to public health. It is necessary to detect β-lactamase-producing microorganisms in clinical settings to be able to control the spread of carbapenem resistance. This study was conducted to evaluate the presence of β-lactamases in a selected clinical isolate of A. baumannii of ST2P/ST195Ox and to characterize possible enzymes, as well as its β-lactam resistome, using PCR and whole-genome sequencing analysis. PCR and sequencing confirmed that the isolate harbored five bla gene alleles, namely, blaADC-73, blaTEM-1, blaOXA-23, blaOXA-58 and blaOXA-66, as well as aminoglycosides, macrolides, sulfonamides and tetracyclines resistance determinants, which were either chromosomally and/or plasmid located. Furthermore, a gene order comparison using MAUVE alignment showed multiple changes compared with the clinical isolate of Malaysian A. baumannii AC30 genome and 76 regions with high homology. This study suggests that resistance to β-lactams in this A. baumannii isolate is mainly due to an overproduction of β-lactamases in combination with other resistance mechanism (efflux pump system).
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Mlynarcik P, Chudobova H, Zdarska V, Kolar M. In Silico Analysis of Extended-Spectrum β-Lactamases in Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10070812. [PMID: 34356733 PMCID: PMC8300632 DOI: 10.3390/antibiotics10070812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/26/2022] Open
Abstract
The growing bacterial resistance to available β-lactam antibiotics is a very serious public health problem, especially due to the production of a wide range of β-lactamases. At present, clinically important bacteria are increasingly acquiring new elements of resistance to carbapenems and polymyxins, including extended-spectrum β-lactamases (ESBLs), carbapenemases and phosphoethanolamine transferases of the MCR type. These bacterial enzymes limit therapeutic options in human and veterinary medicine. It must be emphasized that there is a real risk of losing the ability to treat serious and life-threatening infections. The present study aimed to design specific oligonucleotides for rapid PCR detection of ESBL-encoding genes and in silico analysis of selected ESBL enzymes. A total of 58 primers were designed to detect 49 types of different ESBL genes. After comparing the amino acid sequences of ESBLs (CTX-M, SHV and TEM), phylogenetic trees were created based on the presence of conserved amino acids and homologous motifs. This study indicates that the proposed primers should be able to specifically detect more than 99.8% of all described ESBL enzymes. The results suggest that the in silico tested primers could be used for PCR to detect the presence of ESBL genes in various bacteria, as well as to monitor their spread.
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Affiliation(s)
- Patrik Mlynarcik
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 77515 Olomouc, Czech Republic; (V.Z.); (M.K.)
- Correspondence:
| | - Hana Chudobova
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacky University, Šlechtitelů 27, 78371 Olomouc, Czech Republic;
| | - Veronika Zdarska
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 77515 Olomouc, Czech Republic; (V.Z.); (M.K.)
| | - Milan Kolar
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 77515 Olomouc, Czech Republic; (V.Z.); (M.K.)
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 5, 77900 Olomouc, Czech Republic
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Mlynarcik P, Dolejska M, Vagnerova I, Kutilová I, Kolar M. Detection of clinically important β-lactamases by using PCR. FEMS Microbiol Lett 2021; 368:6294906. [PMID: 34100944 DOI: 10.1093/femsle/fnab068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 06/04/2021] [Indexed: 12/14/2022] Open
Abstract
Increasing antimicrobial resistance of nosocomial pathogens is becoming a serious threat to public health. To control the spread of this resistance, it is necessary to detect β-lactamase-producing organisms in the clinical setting. The aims of the study were to design a PCR assay for rapid detection of clinically encountered β-lactamase genes described in Enterobacteriaceae and Gram-negative non-fermenting bacteria. The functionality of proposed primers was verified using eight reference strains and 17 strains from our collection, which contained 29 different β-lactamase genes. PCR products of the test strains were confirmed by Sanger sequencing. Sequence analysis was performed using bioinformatics software Geneious. Overall, 67 pairs of primers for detecting 12 members of the class C β-lactamase family, 15 members of class A β-lactamases, six gene families of subclass B1, one member each of subclasses B2, B3 and class D β-lactamases were designed, of which 43 pairs were experimentally tested in vitro. All 29 β-lactamase genes, including 10 oxacillinase subgroups, were correctly identified by PCR. The proposed set of primers should be able to specifically detect 99.7% of analyzed β-lactamase subtypes and more than 79.8% of all described β-lactamase genes.
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Affiliation(s)
- Patrik Mlynarcik
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 775 15 Olomouc, Czechia
| | - Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czechia.,Central European Institute of Technology (CEITEC), University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czechia
| | - Iva Vagnerova
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 775 15 Olomouc, Czechia
| | - Iva Kutilová
- Central European Institute of Technology (CEITEC), University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czechia
| | - Milan Kolar
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 775 15 Olomouc, Czechia.,Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 5, 779 00 Olomouc, Czechia
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