<i>Acinetobacter baumannii</i> Global Clone-Specific Resistomes Explored in Clinical Isolates Recovered from Egypt
<i>Acinetobacter baumannii</i> (<i>A. baumannii</i>) is a highly problematic pathogen with an enormous capacity to acquire or upregulate antibiotic drug resistance determinants. The genomic epidemiology and resistome structure of 46 <i>A. baumannii</i> clinical is...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-07-01
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| Series: | Antibiotics |
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| Online Access: | https://www.mdpi.com/2079-6382/12/7/1149 |
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| author | Samira M. Hamed Walid F. Elkhatib Hanka Brangsch Ahmed S. Gesraha Shawky Moustafa Dalia F. Khater Mathias W. Pletz Lisa D. Sprague Heinrich Neubauer Gamal Wareth |
| author_facet | Samira M. Hamed Walid F. Elkhatib Hanka Brangsch Ahmed S. Gesraha Shawky Moustafa Dalia F. Khater Mathias W. Pletz Lisa D. Sprague Heinrich Neubauer Gamal Wareth |
| author_sort | Samira M. Hamed |
| collection | DOAJ |
| description | <i>Acinetobacter baumannii</i> (<i>A. baumannii</i>) is a highly problematic pathogen with an enormous capacity to acquire or upregulate antibiotic drug resistance determinants. The genomic epidemiology and resistome structure of 46 <i>A. baumannii</i> clinical isolates were studied using whole-genome sequencing. The isolates were chosen based on reduced susceptibility to at least three classes of antimicrobial compounds and were initially identified using MALDI-TOF/MS, followed by polymerase chain reaction amplification of <i>bla</i><sub>OXA-51-like</sub> genes. The susceptibility profiles were determined using a broth microdilution assay. Multi-, extensive-, and pan-drug resistance was shown by 34.8%, 63.0%, and 2.2% of the isolates, respectively. These were most susceptible to colistin (95.7%), amikacin, and trimethoprim/sulfamethoxazole (32.6% each), while only 26.1% of isolates were susceptible to tigecycline. In silico multi-locus sequence typing revealed 8 Pasteur and 22 Oxford sequence types (STs) including four novel STs (ST<sup>Oxf</sup> 2805, 2806, 2807, and 2808). The majority of the isolates belonged to Global Clone (GC) 2 (76.4%), GC5 (19.6%), GC4 (6.5%), GC9 (4.3%), and GC7 (2.2%) lineages. An extensive resistome potentially conferring resistance to the majority of the tested antimicrobials was identified in silico. Of all known carbapenem resistance genes, <i>bla</i><sub>OXA-23</sub> was carried by most of the isolates (69.6%), followed by IS<i>Aba1</i>-amplified <i>bla</i><sub>ADC</sub> (56.5%), <i>bla</i><sub>NDM-1</sub> and <i>bla</i><sub>GES-11</sub> (21.7% each), and <i>bla</i><sub>GES-35</sub> (2.2%) genes. A significant correlation was found between carbapenem resistance and <i>carO</i> mutations, which were evident in 35 (76.0%) isolates. A lower proportion of carbapenem resistance was noted for strains possessing both <i>bla</i><sub>OXA-23</sub>- and <i>bla</i><sub>GES-11</sub>. Amikacin resistance was most probably mediated by <i>armA</i>, <i>aac(6′)-Ib9</i>, and <i>aph(3′)-VI</i>, most commonly coexisting in GC2 isolates. No mutations were found in <i>pmrABC</i> or <i>lpxACD</i> operons in the colistin-resistant isolates. Tigecycline resistance was associated with <i>adeS</i> (N268Y) and <i>baeS</i> (A436T) mutations. While the lineage-specific distribution of some genes (e.g., <i>bla</i><sub>ADC</sub> and <i>bla</i><sub>OXA-51-like</sub> alleles) was evident, some resistance genes, such as <i>bla</i><sub>OXA-23</sub> and <i>sul1</i>, were found in all GCs. The data generated here highlight the contribution of five GCs in <i>A. baumannii</i> infections in Egypt and enable the comprehensive analysis of GC-specific resistomes, thus revealing the dissemination of the carbapenem resistance gene <i>bla</i><sub>OXA-23</sub> in isolates encompassing all GCs. |
| first_indexed | 2024-03-11T01:21:33Z |
| format | Article |
| id | doaj.art-62712e5ebc4b467f92b7a2723c48845c |
| institution | Directory Open Access Journal |
| issn | 2079-6382 |
| language | English |
| last_indexed | 2024-03-11T01:21:33Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Antibiotics |
| spelling | doaj.art-62712e5ebc4b467f92b7a2723c48845c2023-11-18T18:02:56ZengMDPI AGAntibiotics2079-63822023-07-01127114910.3390/antibiotics12071149<i>Acinetobacter baumannii</i> Global Clone-Specific Resistomes Explored in Clinical Isolates Recovered from EgyptSamira M. Hamed0Walid F. Elkhatib1Hanka Brangsch2Ahmed S. Gesraha3Shawky Moustafa4Dalia F. Khater5Mathias W. Pletz6Lisa D. Sprague7Heinrich Neubauer8Gamal Wareth9Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 12451, EgyptMicrobiology and Immunology Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Cairo 11566, EgyptInstitute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, 07743 Jena, GermanyDepartment of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta 31511, EgyptFaculty of Veterinary Medicine, Benha University, Toukh 13736, EgyptTanta Laboratory, Animal Health Research Institute, Agricultural Research Center, Tanta 31511, EgyptInstitute of Infectious Diseases and Infection Control, Jena University Hospital, 07747 Jena, GermanyInstitute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, 07743 Jena, GermanyInstitute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, 07743 Jena, GermanyInstitute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, 07743 Jena, Germany<i>Acinetobacter baumannii</i> (<i>A. baumannii</i>) is a highly problematic pathogen with an enormous capacity to acquire or upregulate antibiotic drug resistance determinants. The genomic epidemiology and resistome structure of 46 <i>A. baumannii</i> clinical isolates were studied using whole-genome sequencing. The isolates were chosen based on reduced susceptibility to at least three classes of antimicrobial compounds and were initially identified using MALDI-TOF/MS, followed by polymerase chain reaction amplification of <i>bla</i><sub>OXA-51-like</sub> genes. The susceptibility profiles were determined using a broth microdilution assay. Multi-, extensive-, and pan-drug resistance was shown by 34.8%, 63.0%, and 2.2% of the isolates, respectively. These were most susceptible to colistin (95.7%), amikacin, and trimethoprim/sulfamethoxazole (32.6% each), while only 26.1% of isolates were susceptible to tigecycline. In silico multi-locus sequence typing revealed 8 Pasteur and 22 Oxford sequence types (STs) including four novel STs (ST<sup>Oxf</sup> 2805, 2806, 2807, and 2808). The majority of the isolates belonged to Global Clone (GC) 2 (76.4%), GC5 (19.6%), GC4 (6.5%), GC9 (4.3%), and GC7 (2.2%) lineages. An extensive resistome potentially conferring resistance to the majority of the tested antimicrobials was identified in silico. Of all known carbapenem resistance genes, <i>bla</i><sub>OXA-23</sub> was carried by most of the isolates (69.6%), followed by IS<i>Aba1</i>-amplified <i>bla</i><sub>ADC</sub> (56.5%), <i>bla</i><sub>NDM-1</sub> and <i>bla</i><sub>GES-11</sub> (21.7% each), and <i>bla</i><sub>GES-35</sub> (2.2%) genes. A significant correlation was found between carbapenem resistance and <i>carO</i> mutations, which were evident in 35 (76.0%) isolates. A lower proportion of carbapenem resistance was noted for strains possessing both <i>bla</i><sub>OXA-23</sub>- and <i>bla</i><sub>GES-11</sub>. Amikacin resistance was most probably mediated by <i>armA</i>, <i>aac(6′)-Ib9</i>, and <i>aph(3′)-VI</i>, most commonly coexisting in GC2 isolates. No mutations were found in <i>pmrABC</i> or <i>lpxACD</i> operons in the colistin-resistant isolates. Tigecycline resistance was associated with <i>adeS</i> (N268Y) and <i>baeS</i> (A436T) mutations. While the lineage-specific distribution of some genes (e.g., <i>bla</i><sub>ADC</sub> and <i>bla</i><sub>OXA-51-like</sub> alleles) was evident, some resistance genes, such as <i>bla</i><sub>OXA-23</sub> and <i>sul1</i>, were found in all GCs. The data generated here highlight the contribution of five GCs in <i>A. baumannii</i> infections in Egypt and enable the comprehensive analysis of GC-specific resistomes, thus revealing the dissemination of the carbapenem resistance gene <i>bla</i><sub>OXA-23</sub> in isolates encompassing all GCs.https://www.mdpi.com/2079-6382/12/7/1149<i>Acinetobacter baumannii</i>WGSglobal clonesresistanceresistomeEgypt |
| spellingShingle | Samira M. Hamed Walid F. Elkhatib Hanka Brangsch Ahmed S. Gesraha Shawky Moustafa Dalia F. Khater Mathias W. Pletz Lisa D. Sprague Heinrich Neubauer Gamal Wareth <i>Acinetobacter baumannii</i> Global Clone-Specific Resistomes Explored in Clinical Isolates Recovered from Egypt Antibiotics <i>Acinetobacter baumannii</i> WGS global clones resistance resistome Egypt |
| title | <i>Acinetobacter baumannii</i> Global Clone-Specific Resistomes Explored in Clinical Isolates Recovered from Egypt |
| title_full | <i>Acinetobacter baumannii</i> Global Clone-Specific Resistomes Explored in Clinical Isolates Recovered from Egypt |
| title_fullStr | <i>Acinetobacter baumannii</i> Global Clone-Specific Resistomes Explored in Clinical Isolates Recovered from Egypt |
| title_full_unstemmed | <i>Acinetobacter baumannii</i> Global Clone-Specific Resistomes Explored in Clinical Isolates Recovered from Egypt |
| title_short | <i>Acinetobacter baumannii</i> Global Clone-Specific Resistomes Explored in Clinical Isolates Recovered from Egypt |
| title_sort | i acinetobacter baumannii i global clone specific resistomes explored in clinical isolates recovered from egypt |
| topic | <i>Acinetobacter baumannii</i> WGS global clones resistance resistome Egypt |
| url | https://www.mdpi.com/2079-6382/12/7/1149 |
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