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Machulin AV, Abramov VM, Kosarev IV, Deryusheva EI, Priputnevich TV, Panin AN, Manoyan AM, Chikileva IO, Abashina TN, Blumenkrants DA, Ivanova OE, Papazyan TT, Nikonov IN, Suzina NE, Melnikov VG, Khlebnikov VS, Sakulin VK, Samoilenko VA, Gordeev AB, Sukhikh GT, Uversky VN, Karlyshev AV. A Novel Bifidobacterium longum Subsp. longum T1 Strain from Cow's Milk: Homeostatic and Antibacterial Activity against ESBL-Producing Escherichia coli. Antibiotics (Basel) 2024; 13:924. [PMID: 39452191 DOI: 10.3390/antibiotics13100924] [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: 08/28/2024] [Revised: 09/20/2024] [Accepted: 09/25/2024] [Indexed: 10/26/2024] Open
Abstract
Background/Objectives: The global emergence of antibiotic-resistant zooanthroponotic Escherichia coli strains, producing extended-spectrum beta-lactamases (ESBL-E) and persisting in the intestines of farm animals, has now led to the development of a pandemic of extra-intestinal infectious diseases in humans. The search for innovative probiotic microorganisms that eliminate ESBL-E from the intestines of humans and animals is relevant. Previously, we received three isolates of bifidobacteria: from milk of a calved cow (BLLT1), feces of a newborn calf (BLLT2) and feces of a three-year-old child who received fresh milk from this calved cow (BLLT3). Our goal was to evaluate the genetic identity of BLLT1, BLLT2, BLLT3 isolates using genomic DNA fingerprinting (GDF), to study the tolerance, adhesion, homeostatic and antibacterial activity of BLLT1 against ESBL-E. Methods: We used a complex of microbiological, molecular biological, and immunological methods, including next generation sequencing (NGS). Results: GDF showed that DNA fragments of BLLT2 and BLLT3 isolates were identical in number and size to DNA fragments of BLLT1. These data show for the first time the possibility of natural horizontal transmission of BLLT1 through with the milk of a calved cow into the intestines of a calf and the intestines of a child. BLLT1 was resistant to gastric and intestinal stresses and exhibited high adhesive activity to calf, pig, chicken, and human enterocytes. This indicates the unique ability of BLLT1 to inhabit the intestines of animals and humans. We are the first to show that BLLT1 has antibacterial activity against ESBL-E strains that persist in humans and animals. BLLT1 produced 145 ± 8 mM of acetic acid, which reduced the pH of the nutrient medium from 6.8 to 5.2. This had an antibacterial effect on ESBL-E. The genome of BLLT1 contains ABC-type carbohydrate transporter gene clusters responsible for the synthesis of acetic acid with its antibacterial activity against ESBL-E. BLLT1 inhibited TLR4 mRNA expression induced by ESBL-E in HT-29 enterocytes, and protected the enterocyte monolayers used in this study as a bio-model of the intestinal barrier. BLLT1 increased intestinal alkaline phosphatase (IAP) as one of the main molecular factors providing intestinal homeostasis. Conclusions: BLLT1 shows promise for the creation of innovative functional nutritional products for humans and feed additives for farm animals that will reduce the spread of ESBL-E strains in the food chain.
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Affiliation(s)
- Andrey V Machulin
- Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) Federal State Budgetary Institution "The Russian State Center for Animal Feed and Drug Standardization and Quality" (FGBU VGNKI), 123022 Moscow, Russia
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Science", Russian Academy of Science, 142290 Pushchino, Russia
| | - Vyacheslav M Abramov
- Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) Federal State Budgetary Institution "The Russian State Center for Animal Feed and Drug Standardization and Quality" (FGBU VGNKI), 123022 Moscow, Russia
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Health, 117997 Moscow, Russia
| | - Igor V Kosarev
- Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) Federal State Budgetary Institution "The Russian State Center for Animal Feed and Drug Standardization and Quality" (FGBU VGNKI), 123022 Moscow, Russia
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Health, 117997 Moscow, Russia
| | - Evgenia I Deryusheva
- Institute for Biological Instrumentation, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Science", Russian Academy of Science, 142290 Pushchino, Russia
| | - Tatiana V Priputnevich
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Health, 117997 Moscow, Russia
| | - Alexander N Panin
- Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) Federal State Budgetary Institution "The Russian State Center for Animal Feed and Drug Standardization and Quality" (FGBU VGNKI), 123022 Moscow, Russia
| | - Ashot M Manoyan
- Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) Federal State Budgetary Institution "The Russian State Center for Animal Feed and Drug Standardization and Quality" (FGBU VGNKI), 123022 Moscow, Russia
| | - Irina O Chikileva
- Blokhin National Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia
| | - Tatiana N Abashina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Science", Russian Academy of Science, 142290 Pushchino, Russia
| | - Dmitriy A Blumenkrants
- Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) Federal State Budgetary Institution "The Russian State Center for Animal Feed and Drug Standardization and Quality" (FGBU VGNKI), 123022 Moscow, Russia
| | - Olga E Ivanova
- Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) Federal State Budgetary Institution "The Russian State Center for Animal Feed and Drug Standardization and Quality" (FGBU VGNKI), 123022 Moscow, Russia
| | | | - Ilia N Nikonov
- Federal State Budgetary Educational Institution of Higher Education, St. Petersburg State University of Veterinary Medicine, 196084 Saint Petersburg, Russia
| | - Nataliya E Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Science", Russian Academy of Science, 142290 Pushchino, Russia
| | - Vyacheslav G Melnikov
- Gabrichevsky Research Institute for Epidemiology and Microbiology, 125212 Moscow, Russia
| | | | - Vadim K Sakulin
- Institute of Immunological Engineering, 142380 Lyubuchany, Russia
| | - Vladimir A Samoilenko
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Science", Russian Academy of Science, 142290 Pushchino, Russia
| | - Alexey B Gordeev
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Health, 117997 Moscow, Russia
| | - Gennady T Sukhikh
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Health, 117997 Moscow, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Andrey V Karlyshev
- Department of Biomolecular Sciences, School of Life Sciences, Chemistry and Pharmacy, Faculty of Health, Science, Social Care and Education, Kingston University London, Kingston upon Thames KT1 2EE, UK
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Gelalcha BD, Mohamed RI, Gelgie AE, Kerro Dego O. Molecular epidemiology of extended-spectrum beta-lactamase-producing- Klebsiella species in East Tennessee dairy cattle farms. Front Microbiol 2024; 15:1439363. [PMID: 39380685 PMCID: PMC11458399 DOI: 10.3389/fmicb.2024.1439363] [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: 05/27/2024] [Accepted: 07/30/2024] [Indexed: 10/10/2024] Open
Abstract
Introduction The rising prevalence of Extended-Spectrum Beta-Lactamase (ESBL)-producing Klebsiella species (spp.) poses a significant threat to human and animal health and environmental safety. To address this pressing issue, a comprehensive study was undertaken to elucidate the burden and dissemination mechanisms of ESBL-Klebsiella spp. in dairy cattle farms. Methods Fifty-seven Klebsiella species were isolated on CHROMagar™ ESBL plates and confirmed with MADLI-TOF MS and whole genome sequenced from 14 dairy farms. Results and discussion Six families of beta-lactamase (bla) (bla CTX-M, bla SHV, bla TEM, bla OXY, bla OXA, and bla SED) were detected in ESBL-Klebsiella spp. genomes. Most (73%) of isolates had the first three types of beta-lactamase genes, with bla SHV being the most frequent, followed by bla CTX-M. Most (93%) isolates harbored two or more bla genes. The isolates were genotypically MDR, with 26 distinct types of antibiotic resistance genes (ARGs) and point mutations in gyrA, gyrB, and parC genes. The genomes also harbored 22 different plasmid replicon types, including three novel IncFII. The IncFII and Col440I plasmids were the most frequent and were associated with bla CTXM-27 and qnrB19 genes, respectively. Eighteen distinct sequence types (STs), including eight isolates with novel STs of K. pneumoniae, were detected. The most frequently occurring STs were ST353 (n = 8), ST469 (n = 6), and the novel ST7501 (n = 6). Clusters of ESBL-Klebsiella strains with identical STs, plasmids, and ARGs were detected in multiple farms, suggesting possible clonal expansion. The same ESBL variant was linked to identical plasmids in different Klebsiella STs in some farms, suggesting horizontal spread of the resistance gene. The high burden and dual spread mechanism of ESBL genes in Klebsiella species, combined with the emergence of novel sequence types, could swiftly increase the prevalence of ESBL-Klebsiella spp., posing significant risks to human, animal, and environmental health. Immediate action is needed to implement rigorous surveillance and control measures to mitigate this risk.
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Affiliation(s)
- Benti D. Gelalcha
- Department of Animal Science, The University of Tennessee, Knoxville, TN, United States
| | - Ruwaa I. Mohamed
- Department of Genome Science and Technology, The University of Tennessee, Knoxville, TN, United States
| | - Aga Edema Gelgie
- Department of Animal Science, The University of Tennessee, Knoxville, TN, United States
| | - Oudessa Kerro Dego
- Department of Animal Science, The University of Tennessee, Knoxville, TN, United States
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Gatti M, Cojutti PG, Pea F. Piperacillin-tazobactam vs. carbapenems for treating hospitalized patients with ESBL-producing Enterobacterales bloodstream infections: A systematic review and meta-analysis. J Glob Antimicrob Resist 2024; 39:27-36. [PMID: 39173739 DOI: 10.1016/j.jgar.2024.08.002] [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: 06/26/2024] [Revised: 08/01/2024] [Accepted: 08/11/2024] [Indexed: 08/24/2024] Open
Abstract
OBJECTIVES To meta-analyse the clinical efficacy of piperacillin-tazobactam vs. carbapenems for treating hospitalized patients affected by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales bloodstream infections (BSIs). METHODS Two authors independently searched PubMed-MEDLINE and Scopus database up to January 17, 2024, to retrieve randomized controlled trials (RCTs) or observational studies comparing piperacillin-tazobactam vs. carbapenems for the management of hospitalized patients with ESBL-BSIs. Data were independently extracted by the two authors, and the quality of included studies was independently assessed according to ROB 2.0 or ROBINS-I tools. Mortality rate was selected as primary outcome. Meta-analysis was performed by pooling odds ratios (ORs) retrieved from studies providing adjustment for confounders using a random-effects model with the inverse variance method. RESULTS After screening 3,418 articles, 10 studies were meta-analysed (one RCT and nine retrospective observational studies; N = 1,962). Mortality rate did not significantly differ between treatment with piperacillin-tazobactam vs. carbapenems (N = 6; OR: 1.41; 95% CI: 0.96-2.07; I² = 23.6%). The findings were consistent also in subgroup analyses assessing patients receiving empirical therapy (N = 5; OR: 1.36; 95% CI: 0.99-1.85), or patients having in ≥50% of cases urinary/biliary tract as the primary BSI source (N = 2; OR: 1.26; 95% CI: 0.84-1.89). Conversely, the mortality rate was significantly higher with piperacillin-tazobactam only among patients having in <50% of cases urinary/biliary tract as the primary source of BSI (N = 3; OR: 2.02; 95% CI: 1.00-4.07). CONCLUSIONS This meta-analysis showed that, after performing appropriate adjustments for confounders, mortality and clinical outcome in patients having ESBL-producing Enterobacterales BSIs did not significantly differ among those receiving piperacillin-tazobactam compared to those receiving carbapenems.
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Affiliation(s)
- Milo Gatti
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy; Clinical Pharmacology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
| | - Pier Giorgio Cojutti
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy; Clinical Pharmacology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Federico Pea
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy; Clinical Pharmacology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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Eddair Y, Belouad E, Benaissa E, Abassor T, Bsaibiss F, Maleb A, Elouennass M. Phenotypic and genotypic characterization of extended-spectrum beta-lactamase-producing Enterobacteriaceae in a Moroccan hospital. Access Microbiol 2024; 6:000822.v3. [PMID: 39070755 PMCID: PMC11282464 DOI: 10.1099/acmi.0.000822.v3] [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: 03/26/2024] [Accepted: 06/05/2024] [Indexed: 07/30/2024] Open
Abstract
Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) is a major public health problem in hospitals and in the community. The objective of this work was to describe the epidemiology of ESBL-E, to study their resistance profile and to determine the genes encoding the ESBL phenotype. This is a retrospective study conducted in the bacteriology laboratory of the Mohamed V Military Training Hospital in Rabat, and covering all isolates of Enterobacteriaceae from 1 January 2018 to 31 December 2020. The molecular study of ESBL genes involved a representative sample of all ESBL isolates. The overall prevalence of ESBLs in isolated Enterobacteriaceae (1402/10268) is 13.65 %. The urinary tract was the main site of isolation of ESBL (61 %). The bacterial species most concerned are Escherichia coli (41.9 %), Klebsiella pneumoniae (42.2 %) and Enterobacter cloacae (11.9 %). The study of antibiotic susceptibility showed a resistant profile marked mainly by 100 % resistance to first generation cephalosporins (1GC) and third generation cephalosporins (3GC), 55 % to piperacillin-tazobactam, 16 % to imipenem, and 87 % to fluoroquinolones. Molecular typing of ESBL strains showed a prevalence of CTX-M (95 %), SHV (50 %) and TEM (56 %). The CTX-M-1 and the CTX-M-9 groups were the most common (96.19 % and 7.62 % respectively), and CTX-M15 was found in 78.10 % of CTX-M-1 ESBL positive isolates. Most strains had more than two coexisting resistance genes. The prevalence rate of ESBL-E is critical, and preventive action at different levels (prescriber, biologist, hospital, patient, etc.) are necessary in order to limit their spread and to manage a better therapeutic strategy.
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Affiliation(s)
- Yassine Eddair
- Laboratory of Bacteriology, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Elmehdi Belouad
- Laboratory of Bacteriology, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Elmostafa Benaissa
- Laboratory of Bacteriology, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
- Research Team of Epidemiology and Bacterial Resistance, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Tilila Abassor
- Laboratory of Bacteriology, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Fatna Bsaibiss
- Laboratory of Bacteriology, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Adil Maleb
- Laboratory of Microbiology, Mohammed VI University Hospital, Faculty of Medicine and Pharmacy, University Mohammed the First, Oujda, Morocco
| | - Mostafa Elouennass
- Laboratory of Bacteriology, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
- Research Team of Epidemiology and Bacterial Resistance, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
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Miyagi K, Shimoji N. Rapid discrimination methods for clinical and environmental strains of Aeromonas hydrophila and A. veronii biovar sobria using the N-terminal sequence of the flaA gene and investigation of antimicrobial resistance. Lett Appl Microbiol 2024; 77:ovae052. [PMID: 38830808 DOI: 10.1093/lambio/ovae052] [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: 10/30/2023] [Revised: 05/27/2024] [Accepted: 06/01/2024] [Indexed: 06/05/2024]
Abstract
Although the genus Aeromonas inhabits the natural environment, it has also been isolated from hospital patient specimens as a causative agent of Aeromonas infections. However, it is not known whether clinical strains live in the natural environment, and if these strains have acquired antimicrobial resistance. In this study, we performed the typing of flagellin A gene (flaA) of clinical and environmental strains of Aeromonas hydrophila and A. veronii biovar sobria using Polymerase Chain Reaction (PCR) assay with newly designed primers. Detection rates of the clinical and environmental flaA types of A. hydrophila were 66.7% and 88.2%, and the corresponding rates for A. veronii biovar sobria were 66.7% and 90.9%. The PCR assays could significantly discriminate between clinical and environmental strains of both species in approximately 4 h. Also, among the 63 clinical Aeromonas strains used, only one extended-spectrum β-lactamase-producing bacteria, no plasmid-mediated quinolone resistance bacteria, and only four multidrug-resistant bacteria were detected. Therefore, the PCR assays could be useful for the rapid diagnosis of these Aeromonas infections and the monitoring of clinical strain invasion into water-related facilities and environments. Also, the frequency of drug-resistant Aeromonas in clinical isolates from Okinawa Prefecture, Japan, appeared to be low.
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Affiliation(s)
- Kazufumi Miyagi
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa 903-0215, Japan
| | - Noriaki Shimoji
- Department of Clinical Laboratory, Urasoe General Hospital, 4-16-1 Iso, Urasoe-shi, Okinawa 901-2132, Japan
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Yus C, Gámez E, Arruebo M. Expert opinion on antimicrobial therapies: is there enough scientific evidence to state that targeted therapies outperform non-targeted ones? Expert Opin Drug Deliv 2024; 21:593-609. [PMID: 38619078 DOI: 10.1080/17425247.2024.2340661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/04/2024] [Indexed: 04/16/2024]
Abstract
INTRODUCTION Different active and passive strategies have been developed to fight against pathogenic bacteria. Those actions are undertaken to reduce the bacterial burden while minimizing the possibilities to develop not only antimicrobial resistance but also antimicrobial side-effects such as allergic or hypersensitivity reactions. AREAS COVERED We have reviewed preclinical results that evidence that targeted antimicrobial therapies outperform non-targeted ones. Active selective targeting against pathogenic bacteria has been achieved through the functionalization of antimicrobials, either alone or encapsulated within micro- or nanocarriers, with various recognition moieties. These moieties include peptides, aptamers, antibodies, carbohydrates, extracellular vesicles, cell membranes, infective agents, and other affinity ligands with specific bacterial tropism. Those selective ligands increase retention and enhance effectiveness reducing the side-effects and the required dose to exert the antimicrobial action at the site of infection. EXPERT OPINION When using targeted antimicrobial therapies not only reduced side-effects are observed, but also, compared to the administration of equivalent doses of the non-targeted drugs, a superior efficacy has been demonstrated against planktonic, sessile, and intracellular pathogenic bacterial persisters. The translation of those targeted therapies to subsequent phases of clinical development still requires the demonstration of a reduction in the probabilities for the pathogen to develop resistance when using targeted approaches.
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Affiliation(s)
- Cristina Yus
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza, Spain
- Department of Chemical and Environmental Engineering, University of Zaragoza, Zaragoza, Spain
| | - Enrique Gámez
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza, Spain
- Department of Chemical and Environmental Engineering, University of Zaragoza, Zaragoza, Spain
| | - Manuel Arruebo
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza, Spain
- Department of Chemical and Environmental Engineering, University of Zaragoza, Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragon), Zaragoza, Spain
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Chen C, Wang W, Zhang J, Zhang L, Zhao J, Deng J, Li W, Li X, Zhuo W, Huang L, Chen J. Genomic characteristics of two strains of ESBL-producing Klebsiella pneumoniae ST268 isolated from different samples of one patient. J Glob Antimicrob Resist 2024; 36:319-325. [PMID: 38266958 DOI: 10.1016/j.jgar.2024.01.007] [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: 05/29/2023] [Revised: 11/20/2023] [Accepted: 01/13/2024] [Indexed: 01/26/2024] Open
Abstract
OBJECTIVES This study reports the whole-genome sequences of two strains of extended-spectrum beta-lactamase (ESBL)-producing and multidrug-resistant (MDR) K. pneumoniae ST268 and explores their acquired antibiotic resistance genes (ARGs) and the mobile genetic elements (MGEs). METHODS Two strains of K. pneumoniae ST268 were isolated from different samples of one patient. Assessment of antimicrobial susceptibility was performed, and then whole-genome sequencing was conducted. Acquired ARGs, insertion sequences, and transposons harboured by the two strains of K. pneumoniae ST268 were identified, and then the genetic contexts associated with the ARGs were analysed systematically. RESULTS Two strains of K. pneumoniae ST268 were found to carry the 118.6-kb hybrid IncFIIK:IncQ1:repBR1701 plasmid. All the acquired ARGs carried by the IncF plasmid were found to be situated on the 25.3-kb MDR region bracketed by ISKpn19 and IS26, which was widely present in the plasmids in 14 STs of strains in K. pneumoniae but also in IncF plasmids from Shigella flexneri and Klebsiella quasipneumoniae. Notably, the IncF plasmids harbouring the 25.3-kb MDR region were geographically distributed mainly in China, and the pKP161637-1/pKP160802-1 in our study was the first report on the IncF plasmid carrying the 25.3-kb MDR region bracketed in K. pneumoniae ST268. CONCLUSIONS Two strains of ESBL-producing K. pneumoniae ST268 with a MDR IncF plasmid were identified in a hospital in China. The ARGs were identified on the 25.3-kb MDR region, bracketed by ISKpn19 and IS26, of the IncF plasmids, which were present not only in the K. pneumoniae but also in the S. flexneri and K. quasipneumoniae.
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Affiliation(s)
- Chao Chen
- Department of Neurology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Wei Wang
- Department of Pulmonary and Critical Care Medicine, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Jiechang Zhang
- Department of Cardiology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Limei Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Jianhua Zhao
- Department of Neurosurgery, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Jinming Deng
- Department of Neurology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Wang Li
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Xiaobin Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Wenyan Zhuo
- Department of Neurology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China.
| | - Lian Huang
- Department of Neurology, The First Affiliated Hospital of Jinan University, Guangzhou, China.
| | - Jing Chen
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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Dinda V, Kimang’a AN, Kariuki D, Sifuna AW, O’Brien TJ, Welch M, Reva ON. Whole genome sequencing and genotyping Klebsiella pneumoniae multi-drug resistant hospital isolates from Western Kenya. Access Microbiol 2024; 6:000667.v4. [PMID: 38361654 PMCID: PMC10866029 DOI: 10.1099/acmi.0.000667.v4] [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: 06/13/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024] Open
Abstract
Objectives Klebsiella pneumoniae are a frequent cause of nosocomial infections worldwide. Sequence type 147 (ST147) has been reported as a major circulating high-risk lineage in many countries, and appears to be a formidable platform for the dissemination of antimicrobial resistance (AMR) determinants. However, the distribution of this pathogen in Western African hospitals has been scarcely studied. The main objective of this work was to perform whole genome sequencing of K. pneumoniae isolates from a referral hospital in Kakamega (Kenya) for genotyping and identification of AMR and virulence determinants. Methods In total, 15 K. pneumoniae isolates showing a broad spectrum antimicrobial resistance were selected for whole genome sequencing by Illumina HiSeq 2500 platform. Results ST147 was the dominant lineage among the highly-resistant K. pneumoniae isolates that we sequenced. ST147 was associated with both community- and the hospital-acquired infections, and with different infection sites, whereas other STs were predominantly uropathogens. Multiple antibiotic resistance and virulence determinants were detected in the genomes including extended-spectrum β-lactamases (ESBL) and carbapenemases. Many of these genes were plasmid-borne. Conclusions Our data suggest that the evolutionary success of ST147 may be linked with the acquisition of broad host-range plasmids, and their propensity to accrue AMR and virulence determinants. Although ST147 is a dominant lineage in many countries worldwide, it has not been previously reported as prevalent in Africa. Our data suggest an influx of new nosocomial pathogens with new virulence genes into African hospitals from other continents.
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Affiliation(s)
- Victor Dinda
- Department of Medical Laboratory Science, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Andrew Nyerere Kimang’a
- Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Daniel Kariuki
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Anthony Wawire Sifuna
- Department of Medical Biochemistry, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Thomas James O’Brien
- Department of Biochemistry, University of Cambridge, Hopkins Building, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Hopkins Building, Cambridge, UK
| | - Oleg N. Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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Gatti M, Bonazzetti C, Pascale R, Giannella M, Viale P, Pea F. Real-Time TDM-Guided Optimal Joint PK/PD Target Attainment of Continuous Infusion Piperacillin-Tazobactam Monotherapy Is an Effective Carbapenem-Sparing Strategy for Treating Non-Severe ESBL-Producing Enterobacterales Secondary Bloodstream Infections: Findings from a Prospective Pilot Study. Microorganisms 2024; 12:151. [PMID: 38257978 PMCID: PMC10819442 DOI: 10.3390/microorganisms12010151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
(1) Objectives: To assess the impact of optimal joint pharmacokinetic/pharmacodynamic (PK/PD) target attainment of continuous infusion (CI) piperacillin-tazobactam monotherapy on the microbiological outcome of documented ESBL-producing Enterobacterlaes secondary bloodstream infections (BSIs). (2) Methods: Patients hospitalized in the period January 2022-October 2023, having a documented secondary BSI caused by ESBL-producing Enterobacterales, and being eligible for definitive targeted CI piperacillin-tazobactam monotherapy according to specific pre-defined inclusion criteria (i.e., absence of septic shock at onset; favorable clinical evolution in the first 48 h after starting treatment; low-intermediate risk primary infection source) were prospectively enrolled. A real-time therapeutic drug monitoring (TDM)-guided expert clinical pharmacological advice (ECPA) program was adopted for optimizing (PK/PD) target attainment of CI piperacillin-tazobactam monotherapy. Steady-state plasma concentrations (Css) of both piperacillin and tazobactam were measured, and the free fractions (f) were calculated based on theoretical protein binding. The joint PK/PD target attainment was considered optimal whenever the piperacillin fCss/MIC ratio was >4 and the tazobactam fCss/target concentration (CT) ratio was >1 (quasi-optimal or suboptimal if only one or neither of the two thresholds were achieved, respectively). Univariate analysis was carried out for assessing variables potentially associated with failure in achieving the optimal joint PK/PD target of piperacillin-tazobactam and microbiological eradication. (3) Results: Overall, 35 patients (median age 79 years; male 51.4%) were prospectively included. Secondary BSIs resulted from urinary tract infections as a primary source in 77.2% of cases. The joint PK/PD target attainment was optimal in as many as 97.1% of patients (34/35). Microbiological eradication occurred in 91.4% of cases (32/35). Attaining the quasi-optimal/suboptimal joint PK/PD target of CI piperacillin-tazobactam showed a trend toward a higher risk of microbiological failure (33.3% vs. 0.0%; p = 0.08) (4) Conclusions: Real-time TDM-guided optimal joint PK/PD target attainment of CI piperacillin-tazobactam monotherapy may represent a valuable and effective carbapenem-sparing strategy when dealing with non-severe ESBL-producing Enterobacterales secondary BSIs.
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Affiliation(s)
- Milo Gatti
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; (M.G.); (C.B.); (R.P.); (M.G.); (P.V.)
- Clinical Pharmacology Unit, Department for Integrated Infectious Risk Management, IRCCS Azienda Ospedaliero-Universitaria of Bologna, 40138 Bologna, Italy
| | - Cecilia Bonazzetti
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; (M.G.); (C.B.); (R.P.); (M.G.); (P.V.)
- Infectious Disease Unit, Department for Integrated Infectious Risk Management, IRCCS Azienda Ospedaliero-Universitaria of Bologna, 40138 Bologna, Italy
| | - Renato Pascale
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; (M.G.); (C.B.); (R.P.); (M.G.); (P.V.)
- Infectious Disease Unit, Department for Integrated Infectious Risk Management, IRCCS Azienda Ospedaliero-Universitaria of Bologna, 40138 Bologna, Italy
| | - Maddalena Giannella
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; (M.G.); (C.B.); (R.P.); (M.G.); (P.V.)
- Infectious Disease Unit, Department for Integrated Infectious Risk Management, IRCCS Azienda Ospedaliero-Universitaria of Bologna, 40138 Bologna, Italy
| | - Pierluigi Viale
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; (M.G.); (C.B.); (R.P.); (M.G.); (P.V.)
- Infectious Disease Unit, Department for Integrated Infectious Risk Management, IRCCS Azienda Ospedaliero-Universitaria of Bologna, 40138 Bologna, Italy
| | - Federico Pea
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; (M.G.); (C.B.); (R.P.); (M.G.); (P.V.)
- Clinical Pharmacology Unit, Department for Integrated Infectious Risk Management, IRCCS Azienda Ospedaliero-Universitaria of Bologna, 40138 Bologna, Italy
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Valadbeigi M, Mahmoudifard M, Ganji SM, Mehrabian S. Study on the antibacterial effect of CuO nanoparticles on Klebsiella pneumonia bacteria: Efficient treatment for colorectal cancer. Biotechnol Appl Biochem 2023; 70:1785-1793. [PMID: 37264727 DOI: 10.1002/bab.2481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Colorectal cancer (CRC) is a widespread type of cancer across the world. One efficient therapy approach is the use of antibiotic agents, but one of the main issues related to treating CRC is microbial resistance to antibiotics. As microbes are becoming more resistant to antibiotics and other traditional antimicrobial agents, nanobiotechnology has made it possible to employ nanomaterials with the aim of creating a new generation of antimicrobial agents. In the present study, we have assessed the antimicrobial potential of CuO nanoparticles (NPs) against gram-negative bacteria like Klebsiella pneumoniae carrying PKS genes responsible for encoding colibactin as the key factor for CRC development. For this purpose, the antibacterial effects of conventional antibacterial agents, including erythromycin, piperacillin, and ampicillin, as well as CuONPs, were compared on isolated strains from cancerous candidates. The obtained results revealed that isolates (K. pneumoniae) showed resistance toward the mentioned conventional antibiotics, but CuONPs showed efficient antibacterial properties against K. pneumonia with a MIC = 62 μg/mL. On the other hand, a synergistic antibacterial effect was obtained when CuONPs were used in combination with conventional antibiotics, which are ineffective when used alone. Therefore, CuONPs can be introduced as an excellent antimicrobial agent against K. pneumoniae bacteria in CRC, especially when they are combined with other antibiotics since they can activate the antimicrobial activity of the conventional antibiotics.
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Affiliation(s)
- Maria Valadbeigi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Matin Mahmoudifard
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Shahla Mohammad Ganji
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Sedigheh Mehrabian
- Department of Microbiology, Faculty of Life Sciences, Azad Islamic University, North Tehran Branch, Tehran, Iran
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Kumari K, Sharma PK, Shikha S, Singh RP. Molecular characterization and in-depth genome analysis of Enterobacter sp. S-16. Funct Integr Genomics 2023; 23:245. [PMID: 37460717 DOI: 10.1007/s10142-023-01161-6] [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: 03/14/2023] [Revised: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
Enterobacter species are considered to be an opportunistic human pathogen owing to the existence of antibiotic-resistant strains and drug resides; however, the detailed analysis of the antibiotic resistance and virulence features in environmental isolates is poorly characterized. Here, in the study, we characterized the biochemical characteristics, and genome, pan-genome, and comparative genome analyses of an environmental isolate Enterobacter sp. S-16. The strain was identified as Enterobacter spp. by using 16S rRNA gene sequencing. To unravel genomic features, whole genome of Enterobacter sp. S-16 was sequenced using a hybrid assembly approach and genome assembly was performed using the Unicycler tool. The assembled genome contained the single conting size 5.3 Mbp, GC content 55.43%, and 4500 protein-coding genes. The genome analysis revealed the various gene clusters associated with virulence, antibiotic resistance, type VI secretion system (T6SS), and many stress tolerant genes, which may provide important insight for adapting to changing environment conditions. Moreover, different metabolic pathways were identified that potentially contribute to environmental survival. Various hydrolytic enzymes and motility functions equipped the strain S-16 as an active colonizer. The genome analysis confirms the presence of carbohydrate-active enzymes (CAZymes), and non-enzymatic carbohydrate-binding modules (CBMs) involved in the hydrolysis of complex carbohydrate polymers. Moreover, the pan-genome analysis provides detailed information about the core genes and shared genes with the closest related Enterobacter species. The present study is the first report showing the presence of YdhE/NorM in Enterobacter spp. Thus, the elucidation of genome sequencing will increase our understanding of the pathogenic nature of environmental isolate, supporting the One Health Concept.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, Pin 835215, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Shweta Shikha
- Shyama Prasad Mukherjee University, Ranchi, Jharkhand, India
| | - Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, Pin 835215, India.
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India.
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12
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Awoke T, Teka B, Aseffa A, Seman A, Sebre S, Yitayew B, Yeshitela B, Abebe T, Mihret A. Magnitude and Molecular Characterization of Extended-Spectrum β-Lactamase Genes among Klebsiella pneumoniae Isolates in a Large Tertiary Hospital in Ethiopia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1370:91-102. [PMID: 36318402 DOI: 10.1007/5584_2022_739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Background Extended-spectrum β-lactamases (ESBLs)-producing Klebsiella pneumoniae is reported worldwide increasingly. However, studies on ESBLs are still scarce in Ethiopia. Therefore, the current study aimed to determine the magnitude and resistance patterns of ESBL-producing K. pneumoniae as well as the frequency of ESBL-encoding genes.Methods A cross-sectional study was conducted from September 2018 to February 2019 at Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia among a total of 132 non-duplicate K. pneumoniae isolates. Phenotypic detection of ESBL production was done using Combined Disc Test. ESBL-encoding genes of blaCTX-M, blaTEM, and blaSHV were detected through multiplex PCR.Results The magnitude of ESBL production was 102/132 (77.3%). ESBL positive isolates were 100% resistant to ceftriaxone, cefotaxime, and cefuroxime. Co-resistance of ESBL-positive isolates to other non β-lactam antimicrobials was high to trimethoprim-sulfamethoxazole (96.1%) followed by tetracycline (75.5%) and gentamicin (73.5%). However, these isolates showed high susceptibility to amikacin (96.1%) and meropenem (89.2%). From the total ESBL-positive isolates, 82.6%, 73.5%, and 75% carried blaCTX-M, blaTEM, and blaSHV genes, respectively. The majority 78/102 (76.5%) of ESBL-positive isolates harbored all three types of ESBL genes simultaneously.Conclusions The magnitude of ESBL-producing K. pneumoniae isolates was very alarming in the study area. The co-occurrence of blaCTX-M, blaTEM, and blaSHV genes is high, demanding large-scale studies to evaluate the presence of antimicrobial resistance super-clones. ESBL-producing isolates showed high resistance to most of the antimicrobials, needing phenotypic detection of ESBL regularly for better management of patients.
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Affiliation(s)
- Tewachew Awoke
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Brhanu Teka
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Aminu Seman
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Shemse Sebre
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Berhanu Yitayew
- College of Medicine, Institute of Health Sciences, Debre Berhan University, Debre Berhan, Ethiopia
| | | | - Tamrat Abebe
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adane Mihret
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
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Resistance to Some New Drugs and Prevalence of ESBL- and MBL-Producing Enterobacteriaceae Uropathogens Isolated from Diabetic Patients. Life (Basel) 2022; 12:life12122125. [PMID: 36556490 PMCID: PMC9788504 DOI: 10.3390/life12122125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Diabetes is a leading non-communicable disease and a risk factor for relapsing infections. The current study was aimed at investigating the prevalence and antibiotic susceptibility of carbapenem-resistant (CR) uropathogens of the family Enterobacteriaceae in diabetic patients. The data of 910 bacterial isolates was collected from diagnostic laboratories during January 2018 to December 2018. The bacterial isolates were identified using traditional methods including colonial characteristics, biochemical tests, and API (20E). Antimicrobial susceptibility and phenotypic characterization of ESBL, MBLs, and KPC was determined by utilizing CLSI recommended methods. The phenotypically positive isolates were further analyzed for resistance-encoding genes by manual PCR and Check-MDR CT103XL microarray. Susceptibility to colistin and cefiderocol was tested in accordance with CLSI guidelines. The data revealed that most of the patients were suffering from type 2 diabetes for a duration of more than a year and with uncontrolled blood sugar levels. Escherichia coli and Klebsiella pneumoniae were the most frequently encountered pathogens, followed by Enterobacter cloacae and Proteus mirabilis. More than 50% of the isolates showed resistance to 22 antibiotics, with the highest resistance (>80%) against tetracycline, ampicillin, and cefazolin. The uropathogens showed less resistance to non-β-lactam antibiotics, including amikacin, fosfomycin, and nitrofurantoin. In the phenotypic assays, 495 (54.3%) isolates were found to be ESBL producers, while ESBL-TEM and -PER were the most prevalent ESBL types. The resistance to carbapenems was slightly less (250; 27.5%) than ESBL producers, yet more common amongst E. coli isolates. MBL production was a common feature in carbapenem-resistant isolates (71.2%); genotypic characterization also validated this trend. The isolates were found to be sensitive against the new drugs, cefiderocol and eravacycline. with 7−28% resistance, except for P. mirabilis which had 100% resistance against eravacycline. This study concludes that a few types of ESBL and carbapenemases are common in the uropathogens isolated from the diabetic patients, and antibiotic stewardship programs need to be revisited, particularly to cure UTIs in diabetic patients.
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14
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Dai P, Hu D. The making of hypervirulent Klebsiella pneumoniae. J Clin Lab Anal 2022; 36:e24743. [PMID: 36347819 PMCID: PMC9757020 DOI: 10.1002/jcla.24743] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/01/2022] [Accepted: 10/09/2022] [Indexed: 10/08/2023] Open
Abstract
Klebsiella pneumoniae is a notorious bacterium in clinical practice. Virulence, carbapenem-resistance and their convergence among K. pneumoniae are extensively discussed in this article. Hypervirulent K. pneumoniae (HvKP) has spread from the Asian Pacific Rim to the world, inducing various invasive infections, such as pyogenic liver abscess, endophthalmitis, and meningitis. Furthermore, HvKP has acquired more and more drug resistance. Among multidrug-resistant HvKP, hypervirulent carbapenem-resistant K. pneumoniae (Hv-CRKP), and carbapenem-resistant hypervirulent K. pneumoniae (CR-HvKP) are both devastating for their extreme drug resistance and virulence. The hypervirulence of HvKP is primarily attributed to hypercapsule, macromolecular exopolysaccharides, or excessive siderophores, although it has many other factors, for example, lipopolysaccharides, fimbriae, and porins. In contrast with classical determination of HvKP, that is, animal lethality test, molecular determination could be an optional and practical method after improvement. HvKP, including Hv-CRKP and CR-HvKP, has been progressing. R-M and CRISPR-Cas systems may play pivotal roles in such evolutions. Hv-CRKP and CR-HvKP, in particular the former, should be of severe concern due to their being more and more prevalent.
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Affiliation(s)
- Piaopiao Dai
- Department of Laboratory MedicineTaizhou Municipal HospitalTaizhouChina
| | - Dakang Hu
- Department of Laboratory MedicineTaizhou Municipal HospitalTaizhouChina
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15
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Bastidas-Caldes C, Romero-Alvarez D, Valdez-Vélez V, Morales RD, Montalvo-Hernández A, Gomes-Dias C, Calvopiña M. Extended-Spectrum Beta-Lactamases Producing Escherichia coli in South America: A Systematic Review with a One Health Perspective. Infect Drug Resist 2022; 15:5759-5779. [PMID: 36204394 PMCID: PMC9531622 DOI: 10.2147/idr.s371845] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Carlos Bastidas-Caldes
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
- Doctoral Program in Public and Animal Health, Faculty of Veterinary Medicine, University of Extremadura, Cáceres, Spain
- Correspondence: Carlos Bastidas-Caldes, One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, 170124, Ecuador, Tel +593 983 174949, Email
| | - Daniel Romero-Alvarez
- One Health Reserch Group, Faculty of Medicine, Universidad de las Américas, Quito, Ecuador
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, The University of Kansas, Lawrence, KS, USA
| | - Victor Valdez-Vélez
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
| | - Roberto D Morales
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
| | - Andrés Montalvo-Hernández
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
| | - Cicero Gomes-Dias
- Department of Basic Health Sciences, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Manuel Calvopiña
- One Health Reserch Group, Faculty of Medicine, Universidad de las Américas, Quito, Ecuador
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Chandrakar C, Shakya S, Patyal A, Jain A, Ali SL, Mishra OP. ERIC-PCR based molecular typing of multidrug resistant Escherichia coli isolated from houseflies (Musca domestica) in the environment of milk and meat shops. Lett Appl Microbiol 2022; 75:1549-1558. [PMID: 36038146 DOI: 10.1111/lam.13821] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 12/01/2022]
Abstract
The emergence and spread of antimicrobial resistance has become a major global public health concern. A component of this problem is the spread of the antibiotic resistant bacteria. Flies move freely between habitats of food-producing animals and human beings and thus have great potential for dissemination of antimicrobial resistant bacteria from a contaminated environment to milk and meat markets, posing potential hazards for the consumers. During the present study, a total of 150 houseflies were captured from milk and meat shops located in Durg and Raipur city of Chhattisgarh, India. The E. coli were isolated from houseflies and characterized on the basis of cultural and molecular tests. Further, the isolates were subjected to antimicrobial susceptibility testing against frequently used antibiotics using disk diffusion method. The antibiotic resistance genes and int1 gene were detected using polymerase chain reaction (PCR). A total of 45 E. coli isolates were obtained from the fly samples with overall prevalence rate of 30.0%. Antibiogram results confirmed that E. coli isolates were resistant to multiple antibiotics. Out of the (45) isolates of E. coli, 17 (37.8%) isolates were extended spectrum beta-lactamase (ESBL) producer and multi-drug resistant (MDR). Out of the ESBL and MDR E.coli isolates, blaCTX-M (24.4%), blaTEM (11.1%), tetA (28.8%), tetB (26.7%), gyrA (26.7%), parC (31. 1%) and int1 genes (15.5%) were detected but none of the isolates were found positive for blaSHV gene. Findings of the present study confirm that MDR E. coli are widely distributed in houseflies and play an important role in transmission of antibiotic-resistant bacteria from contaminated environment to milk and meat shop environment.
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Affiliation(s)
- Choodamani Chandrakar
- Department of Veterinary Public Health and Epidemiology, Dau Shri Vasudev Chandrakar Kamdhenu Vishwavidyalaya, Durg, 491001, India
| | - Sanjay Shakya
- Department of Veterinary Public Health and Epidemiology, Dau Shri Vasudev Chandrakar Kamdhenu Vishwavidyalaya, Durg, 491001, India
| | - Anil Patyal
- Department of Veterinary Public Health and Epidemiology, Dau Shri Vasudev Chandrakar Kamdhenu Vishwavidyalaya, Durg, 491001, India
| | - Asit Jain
- Department of Animal Genetics and Breeding, Dau Shri Vasudev Chandrakar Kamdhenu Vishwavidyalaya, Durg, 491001, India
| | - Syed L Ali
- Department of Veterinary Medicine, Dau Shri Vasudev Chandrakar Kamdhenu Vishwavidyalaya, Durg, 491001, India
| | - O P Mishra
- Department of Veterinary Physiology and Biochemistry, Dau Shri Vasudev Chandrakar Kamdhenu Vishwavidyalaya, Durg, 491001, India
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Conserved FimK Truncation Coincides with Increased Expression of Type 3 Fimbriae and Cultured Bladder Epithelial Cell Association in Klebsiella quasipneumoniae. J Bacteriol 2022; 204:e0017222. [PMID: 36005809 PMCID: PMC9487511 DOI: 10.1128/jb.00172-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella spp. commonly cause both uncomplicated urinary tract infection (UTI) and recurrent UTI (rUTI). Klebsiella quasipneumoniae, a relatively newly defined species of Klebsiella, has been shown to be metabolically distinct from Klebsiella pneumoniae, but its type 1 and type 3 fimbriae have not been studied. K. pneumoniae uses both type 1 and type 3 fimbriae to attach to host epithelial cells. The type 1 fimbrial operon is well conserved between Escherichia coli and K. pneumoniae apart from fimK, which is unique to Klebsiella spp. FimK contains an N-terminal DNA binding domain and a C-terminal phosphodiesterase (PDE) domain that has been hypothesized to cross-regulate type 3 fimbriae expression via modulation of cellular levels of cyclic di-GMP. Here, we find that a conserved premature stop codon in K. quasipneumoniae fimK results in truncation of the C-terminal PDE domain and that K quasipneumoniae strain KqPF9 cultured bladder epithelial cell association and invasion are dependent on type 3 but not type 1 fimbriae. Further, we show that basal expression of both type 1 and type 3 fimbrial operons as well as cultured bladder epithelial cell association is elevated in KqPF9 relative to uropathogenic K. pneumoniae TOP52. Finally, we show that complementation of KqPF9ΔfimK with the TOP52 fimK allele reduced type 3 fimbrial expression and cultured bladder epithelial cell attachment. Taken together these data suggest that the C-terminal PDE of FimK can modulate type 3 fimbrial expression in K. pneumoniae and its absence in K. quasipneumoniae may lead to a loss of type 3 fimbrial cross-regulation. IMPORTANCE K. quasipneumoniae is often indicated as the cause of opportunistic infections, including urinary tract infection, which affects >50% of women worldwide. However, the virulence factors of K. quasipneumoniae remain uninvestigated. Prior to this work, K. quasipneumoniae and K. pneumoniae had only been distinguished phenotypically by metabolic differences. This work contributes to the understanding of K. quasipneumoniae by evaluating the contribution of type 1 and type 3 fimbriae, which are critical colonization factors encoded by all Klebsiella spp., to K. quasipneumoniae bladder epithelial cell attachment in vitro. We observe clear differences in bladder epithelial cell attachment and regulation of type 3 fimbriae between uropathogenic K. pneumoniae and K. quasipneumoniae that coincide with a structural difference in the fimbrial regulatory gene fimK.
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Avci FG, Tastekil I, Jaisi A, Ozbek Sarica P, Sariyar Akbulut B. A review on the mechanistic details of OXA enzymes of ESKAPE pathogens. Pathog Glob Health 2022; 117:219-234. [PMID: 35758005 PMCID: PMC10081068 DOI: 10.1080/20477724.2022.2088496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The production of β-lactamases is a prevalent mechanism that poses serious pressure on the control of bacterial resistance. Furthermore, the unavoidable and alarming increase in the transmission of bacteria producing extended-spectrum β-lactamases complicates treatment alternatives with existing drugs and/or approaches. Class D β-lactamases, designated as OXA enzymes, are characterized by their activity specifically towards oxacillins. They are widely distributed among the ESKAPE bugs that are associated with antibiotic resistance and life-threatening hospital infections. The inadequacy of current β-lactamase inhibitors for conventional treatments of 'OXA' mediated infections confirms the necessity of new approaches. Here, the focus is on the mechanistic details of OXA-10, OXA-23, and OXA-48, commonly found in highly virulent and antibiotic-resistant pathogens Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter spp. to describe their similarities and differences. Furthermore, this review contains a specific emphasis on structural and computational perspectives, which will be valuable to guide efforts in the design/discovery of a common single-molecule drug against ESKAPE pathogens.
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Affiliation(s)
- Fatma Gizem Avci
- Bioengineering Department, Uskudar University, Uskudar, 34662, Turkey
| | - Ilgaz Tastekil
- Bioengineering Department, Marmara University, Kadikoy, 34722, Turkey
| | - Amit Jaisi
- Drug and Cosmetics Excellence Center, School of Pharmacy, Walailak University, 80160, Nakhon Si Thammarat, Thailand
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Wang X, Zhang Y, Li C, Li G, Wu D, Li T, Qu Y, Deng W, He Y, Penttinen P, Zhang H, Huang Y, Zhao K, Zou L. Antimicrobial resistance of Escherichia coli, Enterobacter spp., Klebsiella pneumoniae and Enterococcus spp. isolated from the feces of giant panda. BMC Microbiol 2022; 22:102. [PMID: 35421931 PMCID: PMC9008915 DOI: 10.1186/s12866-022-02514-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/01/2022] [Indexed: 11/26/2022] Open
Abstract
Background Escherichia coli, Enterobacter spp., Klebsiella pneumoniae and Enterococcus spp., common gut bacteria in giant pandas, include opportunistic pathogens. The giant panda is an endangered species, classified as vulnerable by the World Wildlife Foundation. Continuous monitoring for the emergence of antimicrobial resistance (AMR) among bacterial isolates from giant pandas is vital not only for their protection but also for public health. Results A total of 166 E. coli, 68 Enterobacter spp., 116 K. pneumoniae and 117 Enterococcus spp. isolates were collected from fecal samples of 166 giant pandas. In the antimicrobial susceptibility tests, 144 E. coli isolates, 66 Enterobacter spp. isolates, 110 K. pneumoniae isolates and 43 Enterococcus spp. isolates were resistant to at least one antimicrobial. The resistant isolates carried antimicrobial resistance genes (ARGs), including sul3, blaTEM, blaSHV and tetA. The differences in the prevalence of the bla types implied that the genetic basis for β-lactam resistance among the E. coli, Enterobacter spp. and K. pneumoniae isolates was different. The strain K. pneumoniae K85 that was resistant to sixteen antimicrobials was selected for whole genome sequencing. The genome contained Col440I, IncFIBK and IncFIIK plasmids and altogether 258 ARGs were predicted in the genome; 179 of the predicted ARGs were efflux pump genes. The genetic environment of the β-lactamase genes blaCTX-M-3 and blaTEM-1 in the K. pneumoniae K85 genome was relatively similar to those in other sequenced K. pneumoniae genomes. In comparing the giant panda age groups, the differences in the resistance rates among E. coli, K. pneumoniae and Enterobacter spp. isolates suggested that the infections in giant pandas of different age should be treated differently. Conclusions Antimicrobial resistance was prevalent in the bacterial isolates from the giant pandas, implying that the gut bacteria may pose serious health risks for captive giant pandas. The resistance genes in the genome of K. pneumoniae K85 were associated with insertion sequences and integron-integrase genes, implying a potential for the further spread of the antimicrobial resistance. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02514-0.
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Surveillance Study of Klebsiella pneumoniae in the Giant Panda Revealed High Genetic Diversity and Antibiotic Therapy Challenge. Antibiotics (Basel) 2022; 11:antibiotics11040473. [PMID: 35453225 PMCID: PMC9030629 DOI: 10.3390/antibiotics11040473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 01/02/2023] Open
Abstract
Klebsiella pneumoniae is not only a worldwide human pathogen, it also effects wildlife, such as the giant panda (Ailuropoda melanoleuca), in which it has recently been evidenced to result in diarrhea, organ failure, and even death. A K. pneumoniae investigation was carried out at the Chengdu Research Base of Giant Panda Breeding in 2018. As part of the investigation, the pulsed-field gel electrophoresis (PFGE) typing, multilocus-sequence typing (MLST), antibiotic resistance profiles (ARPs), and antibiotic resistance genes (ARGs) were studied based on all isolates. Fecal samples were collected from 72 A. melanoleuca from May to December 2018, and a total of 90 K. pneumoniae were isolated from 153 fecal samples. The genotyping results showed that the isolates had high diversity, of which 84 clusters were obtained by PFGE and 57 STs by MLST. The overall trend of the similarity of isolates was the first sample period > second sample period > third sample period, which showed the increasement of genome variability of K. pneumoniae. In addition, 90 isolates showed high resistance to ampicillin, rifampicin, and compound sulfamethoxazole. Of the obtained isolates, 50% carried 6~8 ARPs, and the carrying volume increased during three sample periods, in which we found two isolates carrying 12 and 13 ARPs during the third sample period, respectively. Moreover, a total of 65 ARGs were detected (90.28%, 65/72) in 90 K. pneumoniae samples. Almost all bacteria sampled contained 17 ARGs that belonged to the β-lactamase, Multidrug, MGEs, Aminoglycoside, and Tetracycline, which may be the basis of ARPs of K. pneumoniae. Moreover, the types of Multidrug and MGEs had a greater impact on antibiotic susceptivity of K. pneumoniae. Our results showed that K. pneumoniae has a serious risk of transmission in A. melanoleuca and K. pneumoniae had a high possibility of genome diversity and the risk of drugs tolerance under the large antibiotic usage.
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Discrimination between Carbapenem-Resistant and Carbapenem-Sensitive Klebsiella pneumoniae Strains through Computational Analysis of Surface-Enhanced Raman Spectra: a Pilot Study. Microbiol Spectr 2022; 10:e0240921. [PMID: 35107359 PMCID: PMC8809336 DOI: 10.1128/spectrum.02409-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In clinical settings, rapid and accurate diagnosis of antibiotic resistance is essential for the efficient treatment of bacterial infections. Conventional methods for antibiotic resistance testing are time consuming, while molecular methods such as PCR-based testing might not accurately reflect phenotypic resistance. Thus, fast and accurate methods for the analysis of bacterial antibiotic resistance are in high demand for clinical applications. In this pilot study, we isolated 7 carbapenem-sensitive Klebsiella pneumoniae (CSKP) strains and 8 carbapenem-resistant Klebsiella pneumoniae (CRKP) strains from clinical samples. Surface-enhanced Raman spectroscopy (SERS) as a label-free and noninvasive method was employed for discriminating CSKP strains from CRKP strains through computational analysis. Eight supervised machine learning algorithms were applied for sample analysis. According to the results, all supervised machine learning methods could successfully predict carbapenem sensitivity and resistance in K. pneumoniae, with a convolutional neural network (CNN) algorithm on top of all other methods. Taken together, this pilot study confirmed the application potentials of surface-enhanced Raman spectroscopy in fast and accurate discrimination of Klebsiella pneumoniae strains with different antibiotic resistance profiles. IMPORTANCE With the low-cost, label-free, and nondestructive features, Raman spectroscopy is becoming an attractive technique with great potential to discriminate bacterial infections. In this pilot study, we analyzed surfaced-enhanced Raman spectroscopy (SERS) spectra via supervised machine learning algorithms, through which we confirmed the application potentials of the SERS technique in rapid and accurate discrimination of Klebsiella pneumoniae strains with different antibiotic resistance profiles.
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Maseda E, de la Rica AS. Controversies in the management of ESBL-producing Enterabacterales. Clinical Implications. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2022; 35 Suppl 3:41-45. [PMID: 36285857 PMCID: PMC9717462 DOI: 10.37201/req/s03.10.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Extended-spectrum β-lactamases (ESBL)-producing organisms currently represent a major health problem. Although recently published guidelines still consider carbapenems as the treatment of choice for ESBL-producing infections, it is necessary to find non-carbapenem β-lactams as alternatives to reduce the effects associated with their overutilization. In this review we focus on these alternatives to carbepenem use. It is possible that piperacillin-tazobactam may be an alternative in clinical settings with "low inoculum" infections like urinary tract infections. Newer β-lactam-β-lactamase inhibitors (BLBLIs) are potential options too. The current available data support the efficacy of both ceftazidime-avibactam and ceftolozane-tazobactam against susceptible ESBL-producing Enterobacterales (ESBL-E). We are waiting for the results of MERINO-3 study to confirm whether ceftolozane-tazobactam is a good option versus meropenem for treating bloodstream infections caused by ESBL- or AmpC-producing Enterobacterales.
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Affiliation(s)
- Emilio Maseda
- Hospital La Paz. Hospital Quirón Torrejón. Madrid, Spain,Correspondence: Emilio Maseda Hospital La Paz. Madrid, Spain E-mail:
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Studies on molecular epidemiology of ESβL-producing Klebsiella pneumoniae isolated from patients hospitalized in a specialist hospital in southern Poland. POSTEP HIG MED DOSW 2021. [DOI: 10.2478/ahem-2021-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Introduction. Extended-spectrum β-lactamase (ESβL)-producing Klebsiella pneumoniae is currently one of the most common causes of nosocomial infections worldwide. The study aimed to characterize antibiotic resistance profile, the prevalence of selected genes encoding ESβLs, virulence, and the genetic relationship in 139 K. pneumoniae isolates identified in John Paul II Specialist Hospital in Southern Poland, collected in 2016.
Materials/Methods. Bacterial identification and the preliminary antibiotic susceptibilities was performed using the VI-TEK® 2 Compact automated system. Genes encoding ESβLs were amplified by CTX-Mplex PCR and PCR reactions. The presence of nine genes encoding virulence factors was studied by multiplex PCR. Clonality was investigated by PFGE after digestion with SpeI endonuclease.
Results. K. pneumoniae were mostly recovered from the respiratory tract (40.3%), urine (32.4%), wound swabs (19.4%) and blood (5%). In summary, 82.7% of strains were classified as multidrug resistant (MDR). All isolates were confirmed as ESβL producers and carried bla
CTX-M-type (85.6%), bla
SHV (82%), bla
TEM (77.7%), bla
CTX-M-9 (75.6%) and bla
CTX-M-1 (1.4%) in various combinations. Moreover, triple bla genes were observed in 72% of isolates. The most common virulence-as-sociated genes found among the isolates were entB (91.4%), ybtS (55.4%), iutA (55.4%), magA (53.2%), kfu (14.4%), K2 (11.5%), mrkD (10.1%), rmpA (7.9%) and allS (5%). The PFGE analysis identified 4 major clusters (A–D) comprising 61% of the entire collection.
Conclusions. Our results indicate that the presence of a wide variety of MDR K. pneumoniae harbor ESβLs and virulence genes. Studies on molecular epidemiology of ESβL-producing K. pneumoniae isolates are needed, particularly for epidemiological surveillance in the hospital environment.
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Antimicrobial Susceptibility and Frequency of bla and qnr Genes in Salmonella enterica Isolated from Slaughtered Pigs. Antibiotics (Basel) 2021; 10:antibiotics10121442. [PMID: 34943653 PMCID: PMC8698178 DOI: 10.3390/antibiotics10121442] [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: 10/10/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 12/03/2022] Open
Abstract
Salmonella enterica is known as one of the most common foodborne pathogens worldwide. While salmonellosis is usually self-limiting, severe infections may require antimicrobial therapy. However, increasing resistance of Salmonella to antimicrobials, particularly fluoroquinolones and cephalosporins, is of utmost concern. The present study aimed to investigate the antimicrobial susceptibility of S. enterica isolated from pork, the major product in Philippine livestock production. Our results show that both the qnrS and the blaTEM antimicrobial resistance genes were present in 61.2% of the isolates. While qnrA (12.9%) and qnrB (39.3%) were found less frequently, co-carriage of blaTEM and one to three qnr subtypes was observed in 45.5% of the isolates. Co-carriage of blaTEM and blaCTX-M was also observed in 3.9% of the isolates. Antimicrobial susceptibility testing revealed that the majority of isolates were non-susceptible to ampicillin and trimethoprim/sulfamethoxazole, and 13.5% of the isolates were multidrug-resistant (MDR). MDR isolates belonged to either O:3,10, O:4, or an unidentified serogroup. High numbers of S. enterica carrying antimicrobial resistance genes (ARG), specifically the presence of isolates co-carrying resistance to both β-lactams and fluoroquinolones, raise a concern on antimicrobial use in the Philippine hog industry and on possible transmission of ARG to other bacteria.
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Outbreak of CTX-M-15 Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae ST394 in a French Intensive Care Unit Dedicated to COVID-19. Pathogens 2021; 10:pathogens10111426. [PMID: 34832582 PMCID: PMC8618658 DOI: 10.3390/pathogens10111426] [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] [Received: 10/08/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
Infections caused by extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-KP) are constantly rising worldwide and are often reported as causative agent of outbreaks in intensive care units (ICUs). During the first wave of the COVID-19 pandemic, bacterial cross-transmission was thought unlikely to occur due to the reinforcement of hygiene measures and prevention control. However, we report here an ESBL-producing K. pneumoniae (ST394) isolate responsible for a nosocomial outbreak in an ICU dedicated to COVID-19 patients.
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Abdelrahim SS, Fouad M, Abdallah N, Ahmed RF, Zaki S. Comparative Study of CTX-M-15 Producing Escherichia coli ST131 Clone Isolated from Urinary Tract Infections and Acute Diarrhoea. Infect Drug Resist 2021; 14:4027-4038. [PMID: 34616160 PMCID: PMC8487868 DOI: 10.2147/idr.s325669] [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: 06/22/2021] [Accepted: 09/02/2021] [Indexed: 11/23/2022] Open
Abstract
Background and Purpose The alarming increase in the prevalence of CTX-M-15 extended-spectrum β-lactamase (ESBL) producing E. coli has been significantly linked to the clonal expansion of emerging sequence type (ST131). This study aimed to screen for the O16/O25-ST131 clones among different phylogenetic types of E. coli strains isolated from urinary and diarrhoeal samples. Methods A total of 205 E. coli strains isolated from patients with UTI and acute diarrhoea were investigated by phenotypic and genotypic methods for ESBL identification. Molecular methods were used for identification of O25/O16-ST131 clone and phylogenetic typing of E. coli isolates. Results O25-ST131 clone was detected in 89/105 (84.8%) and 47/100 (47%) of urinary and intestinal E. coli isolates, respectively, with a significant difference (P-value<0.001). There was a significant high rate of occurrence of ESBLs, MDR, and antibiotic resistance to most antibiotic classes among O25-ST131 than non-O25-ST131 isolates. CTX-M-15 gene was detected in 64/71 (90%) of ESBLs producing intestinal isolates and 54/79 (68.4%) of urinary ESBLs producing isolates. The O25-ST131 clone was reported among all phylogenetic groups. The O16-ST131 clone serotype was not detected in the study isolates. Conclusion High prevalence of the O25-ST131 clone was reported among extraintestinal and intestinal E. coli isolates. First detection of the O25-ST131 clone among phylogenetic groups other than group B2 draws attention of the ability of this clone to transfer among commensal groups. An increasing in the prevalence of CTX-M-15 among E. coli strains especially of intestinal origin is alarming as the intestine is the main reservoir for ExPEC strains causing UTI.
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Affiliation(s)
- Soha S Abdelrahim
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, Egypt
| | - Magdy Fouad
- Tropical Medicine Department, Gastroenterology Unit, Faculty of Medicine, Minia University, Minia, Egypt
| | - Nilly Abdallah
- Internal Medicine Department, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Rasha F Ahmed
- Department of Medical Biochemistry, Faculty of Medicine, Minia University, Minia, Egypt
| | - Shaimaa Zaki
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, Egypt
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Dadashpour R, Moghaddam MJM, Salehi Z. Prevalence of non-extended spectrum β-lactamases SHV-1 and TEM-1 or -2 types in multidrug-resistant Enterobacteriaceae in northern Iran. Biol Futur 2021; 71:419-426. [PMID: 34554461 DOI: 10.1007/s42977-020-00044-2] [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: 12/11/2019] [Accepted: 09/02/2020] [Indexed: 11/24/2022]
Abstract
The present study aimed to evaluate TEM-1 or -2 and SHV-1 β-lactamases frequency in multidrug-resistant (MDR) Enterobacteriaceae isolated from patients' urine in northern Iran. The resistance pattern to 20 antibiotics and ESBL production in 200 MDR Enterobacteriaceae was detected using the disk diffusion test and double-disk synergy test (DDST), respectively. Multiplex PCR was applied to detect blaTEM-1 or -2 and blaSHV genes in isolates. DDST findings were inconsistent with multiplex PCR results. The distribution of each of blaTEM-1 or -2 and blaSHV genes, either alone or in combination, in the ESBL-producing isolates was higher than the non-ESBL-producing isolates. There was a significant effect of the presence of blaTEM-1 or -2 gene on resistance to cephalotin at the p < 0.01 level and cefepime, tetracycline, and streptomycin at the P < 0.05 level, and the presence of blaSHV-1 gene on resistance to fosfomycin at the P < 0.05 level as well as the presence both blaTEM-1 or -2 and blaSHV-1 genes on resistance to cephalotin and fosfomycin at the P < 0.01 level. In all isolates, ESBL production, except for cephalotin resistance, did not improve resistance to other antibiotics used and even non-ESBL-producing isolates showed higher resistance to antibiotics compared to ESBL-producing isolates. It seems that mechanisms other than production of ESBL to be involved as part of the resistance mechanisms of the studied isolates against the used antibiotics. For epidemiological studies, both phenotypic and molecular tests must be included to identify the blaTEM-1 or -2 and blaSHV-1 genotypes to ensure infection prevention and control.
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Affiliation(s)
| | | | - Zivar Salehi
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
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Antibiotic-resistant bacteria, antibiotic resistance genes, and antibiotic residues in wastewater from a poultry slaughterhouse after conventional and advanced treatments. Sci Rep 2021; 11:16622. [PMID: 34404868 PMCID: PMC8371126 DOI: 10.1038/s41598-021-96169-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Slaughterhouse wastewater is considered a reservoir for antibiotic-resistant bacteria and antibiotic residues, which are not sufficiently removed by conventional treatment processes. This study focuses on the occurrence of ESKAPE bacteria (Enterococcus spp., S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, Enterobacter spp.), ESBL (extended-spectrum β-lactamase)-producing E. coli, antibiotic resistance genes (ARGs) and antibiotic residues in wastewater from a poultry slaughterhouse. The efficacy of conventional and advanced treatments (i.e., ozonation) of the in-house wastewater treatment plant regarding their removal was also evaluated. Target culturable bacteria were detected only in the influent and effluent after conventional treatment. High abundances of genes (e.g., blaTEM, blaCTX-M-15, blaCTX-M-32, blaOXA-48, blaCMY and mcr-1) of up to 1.48 × 106 copies/100 mL were detected in raw influent. All of them were already significantly reduced by 1–4.2 log units after conventional treatment. Following ozonation, mcr-1 and blaCTX-M-32 were further reduced below the limit of detection. Antibiotic residues were detected in 55.6% (n = 10/18) of the wastewater samples. Despite the significant reduction through conventional and advanced treatments, effluents still exhibited high concentrations of some ARGs (e.g., sul1, ermB and blaOXA-48), ranging from 1.75 × 102 to 3.44 × 103 copies/100 mL. Thus, a combination of oxidative, adsorptive and membrane-based technologies should be considered.
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Mbyemeire H, Ssekatawa K, Kato CD, Wampande EM. Molecular characterization and distribution of cephalosporin resistance determinants in Escherichia coli and Klebsiella pneumoniae isolated from patients attending Kampala International University Teaching Hospital in Bushenyi, Western Uganda. ALEXANDRIA JOURNAL OF MEDICINE 2021. [DOI: 10.1080/20905068.2021.1952821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Herbert Mbyemeire
- Department of Biochemistry, Faculty of Biomedical Sciences, Kampala International University-Western, Bushenyi, Uganda
- African Center of Excellence in Materials Product Development and Nanotechnology (MAPRONANO ACE, College of Engineering Design Art and Technology Makerere University, Kampala, Uganda, Africa
| | - Kenneth Ssekatawa
- Department of Biochemistry, Faculty of Biomedical Sciences, Kampala International University-Western, Bushenyi, Uganda
- African Center of Excellence in Materials Product Development and Nanotechnology (MAPRONANO ACE, College of Engineering Design Art and Technology Makerere University, Kampala, Uganda, Africa
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Charles D. Kato
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
- Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University-Western Campus, Bushenyi, Uganda
| | - Eddie M. Wampande
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
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Adwan G, Omar G. Phenotypic and molecular characterization of fluoroquinolone resistant Pseudomonas aeruginosa isolates in Palestine. BRAZ J BIOL 2021; 82:e239868. [PMID: 34190800 DOI: 10.1590/1519-6984.239868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/23/2020] [Indexed: 11/21/2022] Open
Abstract
Fluoroquinolones are important antimicrobial agents for the treatment of Pseudomonas infections. A total of 11 isolates of P. aeruginosa were collected from different clinical samples from different medical centers in the North West Bank-Palestine during 2017. In this study, resistance to fluoroquinolones and secretions of β-lactamases were detected by phenotypic methods, while presence of β-lactamase gene sequences and other virulence factors were detected by PCR technique. PCR product for gyrA, parC and parE genes were sequenced for further analyses. The phylogenetic analyses, population diversity indices and haplotypes determination were conducted using computer programs MEGA version 6, DnaSP 5.1001 and median-joining algorithm in the program Network 5, respectively. Results of this study showed that the MIC for ciprofloxacin and norfloxacin had a range of 32-256 µg/ml. In addition, all isolates carried either exoT or exoT and exoY genes, different β-lactamase genes and 82% of these isolates harbored class 1 integrons. Analyses of the gyrA, parC and parE sequences were found to be polymorphic, had high haplotype diversity (0.945-0.982), low nucleotide diversity (0.01225-0.02001) and number of haplotypes were 9 for each gyrA and parE genes and 10 haplotypes for parC gene. The founder haplotypes being Hap-1 (18%), Hap-2 (27.3%) and Hap-6 (9.1%) for gyrA, parC and parE genes, respectively. Two of ParE haplotypes were detected as indel haplotypes. The Median-joining- (MJ) networks constructed from haplotypes of these genes showed a star-like expansion. The neutrality tests (Tajima's D test and Fu's Fs test) for these genes showed negative values. Palestinian fluoroquinolone resistant P. aeruginosa strains showed high MIC level for fluoroquinolones, β-lactamase producers, carried type III secretion exotoxin-encoding genes, most of them had integrase I gene and had high level of mutations in QRDR regions in gyrA, parC and parE genes. All these factors may play an important role in the invasiveness of these strains and make them difficult to treat. Isolation of these strains from different medical centers, indicate the need for a strict application of infection control measures in Medical centers in the North West Bank-Palestine that aim to reduce expense and damage caused by P. aeruginosa infections. Molecular analyses showed that Palestinian fluoroquinolone resistant P. aeruginosa haplotypes are not genetically differentiated; however, more mutations may exist in these strains.
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Affiliation(s)
- G Adwan
- An-Najah National University, Department of Biology and Biotechnology, Nablus, Palestine
| | - G Omar
- An-Najah National University, Department of Biology and Biotechnology, Nablus, Palestine
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Recent strategies for inhibiting multidrug-resistant and β-lactamase producing bacteria: A review. Colloids Surf B Biointerfaces 2021; 205:111901. [PMID: 34116398 DOI: 10.1016/j.colsurfb.2021.111901] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/24/2021] [Accepted: 06/01/2021] [Indexed: 12/26/2022]
Abstract
β-lactam antibiotics are one of the most commonly used drugs for treating bacterial infections, but their clinical effectiveness has been severely affected with bacteria developing resistance against their action. Production of β-lactamase enzymes by bacteria that can degrade β-lactams is the most common mechanism of acquiring such resistance, leading to the emergence of multiple-drug resistance in them. Therefore, the development of efficient approaches to combat infections caused by β-lactamase producing and multidrug-resistant bacteria is the need of the hour. The present review attempts to understand such recent strategies that are in line for development as potential alternatives to conventional antibiotics. We find that apart from efforts being made to develop new antibiotics, several other approaches are being explored, which can help tackle infections caused by resistant bacteria. This includes the development of plant-based drugs, antimicrobial peptides, nano-formulations, bacteriophage therapy, use of CRISPR-Cas9, RNA silencing and antibiotic conjugates with nanoparticles of antimicrobial peptides. The mechanism of action of these novel approaches and potential issues limiting their translation from laboratory to clinics is also discussed. The review is important from an interesting knowledge base which can be useful for researchers working in this domain.
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Selvakumar V, Kannan K, Panneerselvam A, Suresh M, Nooruddin T, Pal K, Elkodous MA, Nada HG, El-Bastawisy HS, Tolba MM, Noureldeen A, Darwish H, Fayad E, Khairy WA, Nasser HA, El-Sayyad GS. Molecular identification of extended spectrum β-lactamases (ESBLs)-producing strains in clinical specimens from Tiruchirappalli, India. APPLIED NANOSCIENCE 2021. [DOI: 10.1007/s13204-021-01886-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Khalifa SM, Abd El-Aziz AM, Hassan R, Abdelmegeed ES. β-lactam resistance associated with β-lactamase production and porin alteration in clinical isolates of E. coli and K. pneumoniae. PLoS One 2021; 16:e0251594. [PMID: 34014957 PMCID: PMC8136739 DOI: 10.1371/journal.pone.0251594] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/28/2021] [Indexed: 12/23/2022] Open
Abstract
β-lactam resistance represents a worldwide problem and a serious challenge for antimicrobial treatment. Hence this research was conducted to recognize several mechanisms mediating β-lactam resistance in E. coli and K. pneumoniae clinical isolates collected from Mansoura University hospitals, Egypt. A total of 80 isolates, 45 E. coli and 35 K. pneumoniae isolates, were collected and their antibiotic susceptibility was determined by the Disc diffusion method followed by phenotypic and genotypic detection of extended-spectrum β-lactamases (ESBLs), AmpC β-lactamase, carbapenemase enzymes. The outer membrane protein porins of all isolates were analyzed and their genes were examined using gene amplification and sequencing. Also, the resistance to complement-mediated serum killing was estimated. A significant percentage of isolates (93.8%) were multidrug resistance and showed an elevated resistance to β-lactam antibiotics. The presence of either ESBL or AmpC enzymes was high among isolates (83.75%). Also, 60% of the isolated strains were carbapenemase producers. The most frequently detected gene of ESBL among all tested isolates was blaCTX-M-15 (86.3%) followed by blaTEM-1 (81.3%) and blaSHV-1 (35%) while the Amp-C gene was present in 83.75%. For carbapenemase-producing isolates, blaNDM1 was the most common (60%) followed by blaVIM-1 (35%) and blaOXA-48 (13.8%). Besides, 73.3% and 40% of E. coli and K. pneumoniae isolates respectively were serum resistant. Outer membrane protein analysis showed that 93.3% of E. coli and 95.7% of K. pneumoniae isolates lost their porins or showed modified porins. Furthermore, sequence analysis of tested porin genes in some isolates revealed the presence of frameshift mutations that produced truncated proteins of smaller size. β-lactam resistance in K. pneumoniae and E. coli isolates in our hospitals is due to a combination of β-lactamase activity and porin loss/alteration. Hence more restrictions should be applied on β-lactams usage to decrease the emergence of resistant strains.
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Affiliation(s)
- Sara M. Khalifa
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Abeer M. Abd El-Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
- * E-mail: ,
| | - Ramadan Hassan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Eman S. Abdelmegeed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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Yang B, Fang D, Lv Q, Wang Z, Liu Y. Targeted Therapeutic Strategies in the Battle Against Pathogenic Bacteria. Front Pharmacol 2021; 12:673239. [PMID: 34054548 PMCID: PMC8149751 DOI: 10.3389/fphar.2021.673239] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/23/2021] [Indexed: 12/14/2022] Open
Abstract
The emergence and rapid spread of antibiotic resistance in pathogenic bacteria constitute a global threat for public health. Despite ongoing efforts to confront this crisis, the pace of finding new potent antimicrobials is far slower than the evolution of drug resistance. The abuse of broad-spectrum antibiotics not only accelerates the formation of resistance but also imposes a burden on the intestinal microbiota, which acts a critical role in human homeostasis. As such, innovative therapeutic strategies with precision are pressingly warranted and highly anticipated. Recently, target therapies have achieved some breakthroughs by the aid of modern technology. In this review, we provide an insightful illustration of current and future medical targeted strategies, including narrow-spectrum agents, engineered probiotics, nanotechnology, phage therapy, and CRISPR-Cas9 technology. We discuss the recent advances and potential hurdles of these strategies. Meanwhile, the possibilities to mitigate the spread of resistance in these approaches are also mentioned. Altogether, a better understanding of the advantages, disadvantages, and mechanisms of action of these targeted therapies will be conducive to broadening our horizons and optimizing the existing antibacterial approaches.
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Affiliation(s)
- Bingqing Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Dan Fang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Qingyan Lv
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
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Dolatyar Dehkharghani A, Haghighat S, Rahnamaye Farzami M, Douraghi M, Rahbar M. Subtyping β-lactamase-producing Escherichia coli strains isolated from patients with UTI by MLVA and PFGE methods. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:437-443. [PMID: 34094024 PMCID: PMC8143711 DOI: 10.22038/ijbms.2021.49790.11372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 03/07/2021] [Indexed: 12/03/2022]
Abstract
OBJECTIVES Strain subtyping is an important epidemiological tool to trace contamination, determine clonal relationships between different strains, and the cause of outbreaks. Current subtyping methods, however, yield less than optimal subtype discrimination. Pulsed-field gel electrophoresis is the gold standard method for Escherichia coli and Multiple-Locus Variable-number tandem repeat Analysis is a rapid PCR-based method. The purpose of this study was to evaluate MLVA and PFGE methods for subtyping β -lactamase-producing E. coli strains isolated from urinary tract infections. MATERIALS AND METHODS Overall, 230 E. coli isolates from patients with urinary tract infections were examined for antimicrobial susceptibility testing. 10-loci and 7-loci MLVA and PFGE methods were used for molecular typing of β -lactamase-producing E. coli isolates. RESULTS Out of 230 isolates, 130 (56.5%) β -lactamase-producing E. coli isolates were found in this study. The diversity indices of the VNTR loci showed an average diversity of 0.48 and 0.54 for 7-loci and 10-loci MLVA, respectively. The discriminatory power of PFGE showed a value of 0.87. The discordance between the methods was high. CONCLUSION Our study showed that PFGE is more discriminatory than MVLA. MLVA is a PCR- based method and can generate unmistakable data, in contrast to PFGE. Optimization of polymorphic VNTR is essential to improve the discriminatory power of MLVA based on geographical region.
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Affiliation(s)
- Alireza Dolatyar Dehkharghani
- Department of Microbiology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Setareh Haghighat
- Department of Microbiology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Marjan Rahnamaye Farzami
- Department of Microbiology, Research Center of Reference Health Laboratory, Ministry of Health and Medical Education, Tehran, Iran
| | - Masoumeh Douraghi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Rahbar
- Department of Microbiology, Research Center of Reference Health Laboratory, Ministry of Health and Medical Education, Tehran, Iran
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Calderón VV, Bonnelly R, Del Rosario C, Duarte A, Baraúna R, Ramos RT, Perdomo OP, Rodriguez de Francisco LE, Franco EF. Distribution of Beta-Lactamase Producing Gram-Negative Bacterial Isolates in Isabela River of Santo Domingo, Dominican Republic. Front Microbiol 2021; 11:519169. [PMID: 33519720 PMCID: PMC7838461 DOI: 10.3389/fmicb.2020.519169] [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: 12/11/2019] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
Bacteria carrying antibiotic resistance genes (ARGs) are naturally prevalent in lotic ecosystems such as rivers. Their ability to spread in anthropogenic waters could lead to the emergence of multidrug-resistant bacteria of clinical importance. For this study, three regions of the Isabela river, an important urban river in the city of Santo Domingo, were evaluated for the presence of ARGs. The Isabela river is surrounded by communities that do not have access to proper sewage systems; furthermore, water from this river is consumed daily for many activities, including recreation and sanitation. To assess the state of antibiotic resistance dissemination in the Isabela river, nine samples were collected from these three bluedistinct sites in June 2019 and isolates obtained from these sites were selected based on resistance to beta-lactams. Physico-chemical and microbiological parameters were in accordance with the Dominican legislation. Matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses of ribosomal protein composition revealed a total of 8 different genera. Most common genera were as follows: Acinetobacter (44.6%) and Escherichia (18%). Twenty clinically important bacterial isolates were identified from urban regions of the river; these belonged to genera Escherichia (n = 9), Acinetobacter (n = 8), Enterobacter (n = 2), and Klebsiella (n = 1). Clinically important multi-resistant isolates were not obtained from rural areas. Fifteen isolates were selected for genome sequencing and analysis. Most isolates were resistant to at least three different families of antibiotics. Among beta-lactamase genes encountered, we found the presence of blaTEM, blaOXA, blaSHV, and blaKPC through both deep sequencing and PCR amplification. Bacteria found from genus Klebsiella and Enterobacter demonstrated ample repertoire of antibiotic resistance genes, including resistance from a family of last resort antibiotics reserved for dire infections: carbapenems. Some of the alleles found were KPC-3, OXA-1, OXA-72, OXA-132, CTX-M-55, CTX-M-15, and TEM-1.
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Affiliation(s)
- Víctor V. Calderón
- Instituto Tecnológico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
| | - Roberto Bonnelly
- Instituto Tecnológico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
| | - Camila Del Rosario
- Instituto Tecnológico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
| | - Albert Duarte
- Instituto Tecnológico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
| | - Rafael Baraúna
- Institute of Biological Sciences, Federal University of Pará-UFPA, Belem, Brazil
| | - Rommel T. Ramos
- Institute of Biological Sciences, Federal University of Pará-UFPA, Belem, Brazil
| | - Omar P. Perdomo
- Instituto Tecnológico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
| | | | - Edian F. Franco
- Instituto Tecnológico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
- Institute of Biological Sciences, Federal University of Pará-UFPA, Belem, Brazil
- Instituto de Innovación en Biotecnología e Industria (IIBI), Santo Domingo, Dominican Republic
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Cooper AL, Carter C, McLeod H, Wright M, Sritharan P, Tamber S, Wong A, Carrillo CD, Blais BW. Detection of carbapenem-resistance genes in bacteria isolated from wastewater in Ontario. Facets (Ott) 2021. [DOI: 10.1139/facets-2020-0101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bacterial carbapenem resistance is a major public health concern since these antimicrobials are often the last resort to treat serious human infections. To evaluate methodologies for detection of carbapenem resistance, carbapenem-tolerant bacteria were isolated from wastewater treatment plants in Toronto, Ottawa, and Arnprior, Ontario. A total of 135 carbapenem-tolerant bacteria were recovered. Polymerase chain reaction (PCR) indicated the presence of carbapenem hydrolysing enzymes KPC ( n = 10), GES ( n = 5), VIM ( n = 7), and IMP ( n = 1), and β-lactamases TEM ( n = 7), PER ( n = 1), and OXA-variants ( n = 16). A subset of 46 isolates were sequenced and analysed using ResFinder and CARD-RGI. Both programs detected carbapenem resistance genes in 35 sequenced isolates and antimicrobial resistance genes (ARGs) conferring resistance to multiple class of other antibiotics. Where β-lactamase resistance genes were not initially identified, lowering the thresholds for ARG detection enabled identification of closely related β-lactamases. However, no known carbapenem resistance genes were found in seven sequenced Pseudomonas spp. isolates. Also of note was a multi-drug-resistant Klebsiella pneumoniae isolate from Ottawa, which harboured resistance to seven antimicrobial classes including β-lactams. These results highlight the diversity of genes encoding carbapenem resistance in Ontario and the utility of whole genome sequencing over PCR for ARG detection where resistance may result from an assortment of genes.
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Affiliation(s)
- Ashley L. Cooper
- Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1A 0Y9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Cassandra Carter
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Hana McLeod
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Marie Wright
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Prithika Sritharan
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Sandeep Tamber
- Microbiology Research Division, Bureau of Microbial Hazards, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Catherine D. Carrillo
- Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1A 0Y9, Canada
| | - Burton W. Blais
- Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1A 0Y9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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ElBaradei A, Maharem DA, Kader O, Ghareeb MK, Naga IS. Fecal carriage of ESBL-producing Escherichia coli in Egyptian patients admitted to the Medical Research Institute hospital, Alexandria University. AIMS Microbiol 2020; 6:422-433. [PMID: 33364536 PMCID: PMC7755583 DOI: 10.3934/microbiol.2020025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/29/2020] [Indexed: 01/11/2023] Open
Abstract
Commensal ESBL-producing E. coli represent a reservoir for resistance genes therefore, their detection is crucial to restrain the spread of beta-lactam resistance. Hence, the aim of the present study was phenotypic and genotypic characterization of commensal ESBL-producing E. coli obtained from the stool of patients at the time of admission and at the time of discharge from the Medical Research Institute hospital. A total of 70 E. coli isolates were collected from 35 patients and were categorized into Group A (samples obtained on admission) and Group B (samples obtained at the time of discharge). Phenotypically, 30 isolates were ESBL producers (40% of E. coli isolates collected on admission and 45.7% of the strains obtained at the time of discharge were ESBL producers). Most of them harbored one to three plasmids with sizes ranging from one kbp to ten kbp. Upon genotypic investigation, blaCTX-M was the most detected gene in 80% of ESBL strains, followed by blaTEM in 53.3% and the least detected was blaSHV in only 13.3%. By comparing group A and group B, ten patients were found to carry commensal ESBL-producing E. coli, in two patients these isolates carried ESBL genes that were identical on admission and on discharge. However, in eight patients, these isolates carried different ESBL genes, which were newly harbored during hospital stay. The high abundance of MDR commensal E. coli 48.57% together with the presence of 42.86% ESBL-producing commensal E. coli among our isolates represents an alarming threat, as they are frequently associated with the increased risk of infection, higher costs and longer hospital stay.
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Affiliation(s)
- Amira ElBaradei
- Department of Microbiology and Immunology, Faculty of Pharmacy, Pharos University in Alexandria, Alexandria, Egypt.,Alexandria University Hospital, Alexandria University, Alexandria, Egypt
| | - Dalia Ali Maharem
- Department of Internal Medicine, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Ola Kader
- Department of Microbiology, Medical Research Institute, University of Alexandria, Alexandria, Egypt
| | | | - Iman S Naga
- Department of Microbiology, Medical Research Institute, University of Alexandria, Alexandria, Egypt
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Mohamed ES, Khairy RMM, Abdelrahim SS. Prevalence and molecular characteristics of ESBL and AmpC β -lactamase producing Enterobacteriaceae strains isolated from UTIs in Egypt. Antimicrob Resist Infect Control 2020; 9:198. [PMID: 33303028 PMCID: PMC7727156 DOI: 10.1186/s13756-020-00856-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 11/18/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Infections caused by Enterobacteriaceae are mainly treated with the β-lactam antibiotics, nevertheless, the emergence of species with plasmid-borne β-lactamases has decreased the efficacy of these antibiotics. Therefore, continuing studies on the resistance pattern of different regions is important for assessment of proper antimicrobial therapy protocols. The study aimed to characterize extended-spectrum β-lactamase (ESBL) and AmpC β -lactamase (AmpC) producing Enterobacteriaceae isolated from community-acquired UTIs in Egypt. METHODS Out of 705 urine samples, 440 Enterobacteriaceae isolates were investigated to detect ESBL and AmpC β -lactamases producers by phenotypic and molecular methods. RESULTS Out of 440 Enterobacteriaceae isolates, 311 were identified as ESBL producers by phenotypic testing. ESBL genes were detected in 308 isolates. BlaCTX-M-type was the most prevalent 254 (81.6%), out of them blaCTXM-15 was the commonest (152, 48.8%) followed by blaCTX-M-1 (140, 45%), blaCTX-M-8 (72, 23.1%) and lastly blaCTX-M-2 (4, 1.3%). blaTEM gene also was detected in a high rate (189, 60.7%). Two hundred and thirty-five (75.5%) of ESBL producers harbored blaCTX-M in combination with blaTEM and/or blaSHV genes. Multiple drug resistance in the ESBL-producers was significantly (P < 0.05) higher than in non-ESBL producers. Imipenem was the most effective drug against ESBL producers. Among 35 cefoxitin resistant isolates, 18 (51.4%) identified as carrying AmpC genes by multiplex PCR. Within AmpC β -lactamase genes, DHA gene was the predominant gene (15, 42.3%). CIT and MOX genes were also present, but in a low rate (5, 14.2% and 4, 11.4%) respectively. Co-existence of multiple AmpC genes was detected exclusively in K. pneumoniae isolates. E. coli isolates harbored DHA gene only. However, FOX gene was not detected in the study isolates. Seventeen of isolates carrying AmpC genes were also positive for ESBL genes. CONCLUSION The study shows that the prevalence of ESBL producing Enterobacteriaceae spread in south Egypt is alarming, however AmpC β -lactamase production is not so high.
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Affiliation(s)
- Ebtisam S Mohamed
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt
| | - Rasha M M Khairy
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt.
| | - Soha S Abdelrahim
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt
- Department of Biomedical Sciences, College of Medicine, King Faisal University, Al Hofuf, Saudi Arabia
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Sib E, Lenz-Plet F, Barabasch V, Klanke U, Savin M, Hembach N, Schallenberg A, Kehl K, Albert C, Gajdiss M, Zacharias N, Müller H, Schmithausen RM, Exner M, Kreyenschmidt J, Schreiber C, Schwartz T, Parčina M, Bierbaum G. Bacteria isolated from hospital, municipal and slaughterhouse wastewaters show characteristic, different resistance profiles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:140894. [PMID: 32763594 DOI: 10.1016/j.scitotenv.2020.140894] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
Multidrug-resistant bacteria cause difficult-to-treat infections and pose a risk for modern medicine. Sources of multidrug-resistant bacteria include hospital, municipal and slaughterhouse wastewaters. In this study, bacteria with resistance to 3rd generation cephalosporins were isolated from all three wastewater biotopes, including a maximum care hospital, municipal wastewaters collected separately from a city and small rural towns and the wastewaters of two pig and two poultry slaughterhouses. The resistance profiles of all isolates against clinically relevant antibiotics (including β-lactams like carbapenems, the quinolone ciprofloxacin, colistin, and trimethoprim/sulfamethoxazole) were determined at the same laboratory. The bacteria were classified according to their risk to human health using clinical criteria, with an emphasis on producers of carbapenemases, since carbapenems are prescribed for hospitalized patients with infections with multi-drug resistant bacteria. The results showed that bacteria that pose the highest risk, i. e., bacteria resistant to all β-lactams including carbapenems and ciprofloxacin, were mainly disseminated by hospitals and were present only in low amounts in municipal wastewater. The isolates from hospital wastewater also showed the highest rates of resistance against antibiotics used for treatment of carbapenemase producers and some isolates were susceptible to only one antibiotic substance. In accordance with these results, qPCR of resistance genes showed that 90% of the daily load of carbapenemase genes entering the municipal wastewater treatment plant was supplied by the clinically influenced wastewater, which constituted approximately 6% of the wastewater at this sampling point. Likewise, the signature of the clinical wastewater was still visible in the resistance profiles of the bacteria isolated at the entry into the wastewater treatment plant. Carbapenemase producers were not detected in slaughterhouse wastewater, but strains harboring the colistin resistance gene mcr-1 could be isolated. Resistances against orally available antibiotics like ciprofloxacin and trimethoprim/sulfamethoxazole were widespread in strains from all three wastewaters.
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Affiliation(s)
- Esther Sib
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany; Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Franziska Lenz-Plet
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Vanessa Barabasch
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Ursula Klanke
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Mykhailo Savin
- Institute of Animal Sciences, University of Bonn, Bonn, Germany
| | - Norman Hembach
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Microbiology/Molecular Biology Department, Karlsruhe, Germany
| | - Anna Schallenberg
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Katja Kehl
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Cathrin Albert
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Mike Gajdiss
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Nicole Zacharias
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Heike Müller
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | | | - Martin Exner
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Judith Kreyenschmidt
- Institute of Animal Sciences, University of Bonn, Bonn, Germany; Department of Fresh Produce Logistics, Hochschule Geisenheim University, Geisenheim, Germany
| | - Christiane Schreiber
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Thomas Schwartz
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Microbiology/Molecular Biology Department, Karlsruhe, Germany
| | - Marijo Parčina
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany.
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Bassetti M, Giacobbe DR, Robba C, Pelosi P, Vena A. Treatment of extended-spectrum β-lactamases infections: what is the current role of new β-lactams/β-lactamase inhibitors? Curr Opin Infect Dis 2020; 33:474-481. [PMID: 33060469 DOI: 10.1097/qco.0000000000000685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW The widespread diffusion of extended-spectrum β-lactamases (ESBLs)-producing Enterobacteriales currently represents a major threat for public health worldwide. Carbapenems are currently considered the first-line choice for serious ESBL infections. However, the dramatic global increase in ESBL prevalence has led to a significant overuse of carbapenems that has promoted the selection and spread of carbapenemases, which might further prejudicated our ability to treat infections due to multidrug-resistant pathogens. Therefore, strategies to limit the use of carbapenems should be implemented. RECENT FINDINGS Although piperacillin-tazobactam should no longer be considered an alternative to carbapenems for definitive treatment of bloodstream infections due to ESBL-producing strains, it might still represent an alternative for step-down therapy or for low-to-moderate severity infection originating from urinary or biliary sources and when piperacillin-tazobactam minimum inhibitory concentration of 4 mg/l or less. Ceftazidime-avibactam and ceftolozane-tazobactam are both carbapenem sparing agents that appear interesting alternatives for treatment of serious ESBL infections. New β-lactams/β-lactamase inhibitors (BL/BLI), including cefepime-enmetazobactam, ceftaroline fosamil-avibactam, aztreonam-avibactam and cefepime-zidebactam, are also promising agents for treatment of ESBL infections, but further clinical data are needed to establish their efficacy relative to carbapenems. The role of carbapenems/β-lactamase inhibitors remain to be clarified. SUMMARY New BL/BLI have distinctive specificities and limitations that require further investigations. Future randomized clinical trials are required to define the best strategy for their administering for ESBL infections.
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Affiliation(s)
- Matteo Bassetti
- Infectious Diseases Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences
- Department of Health Sciences (DISSAL), University of Genoa
| | - Daniele R Giacobbe
- Infectious Diseases Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences
| | - Chiara Robba
- Anesthesia and Intensive Care, San Martino Policlinico Hospital, IRCCS for Oncology and Neurosciences
| | - Paolo Pelosi
- Anesthesia and Intensive Care, San Martino Policlinico Hospital, IRCCS for Oncology and Neurosciences
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy
| | - Antonio Vena
- Infectious Diseases Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences
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Khairy RMM, Fathy ZA, Mahrous DM, Mohamed ES, Abdelrahim SS. Prevalence, phylogeny, and antimicrobial resistance of Escherichia coli pathotypes isolated from children less than 5 years old with community acquired- diarrhea in Upper Egypt. BMC Infect Dis 2020; 20:908. [PMID: 33256619 PMCID: PMC7708180 DOI: 10.1186/s12879-020-05664-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/24/2020] [Indexed: 02/04/2023] Open
Abstract
Background Diarrhoea, affecting children in developing countries, is mainly caused by diarrheagenic Escherichia coli (DEC). This study principally aimed to determine the prevalence of DEC pathotypes and Extended-spectrum β-lactamase (ESBL) genes isolated from children under 5 years old with diarrhea. Methods A total of 320 diarrhoea stool samples were investigated. E. coli isolates were investigated for genes specific for enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC) and enterohemorrhagic E. coli (EHEC) using polymerase chain reaction (PCR). Furthermore, antimicrobial susceptibility testing, detection of antibiotic resistance-genes and phylogenetic typing were performed. Results Over all, DEC were isolated from 66/320 (20.6%) of the children with diarrhoea. EAEC was the predominant (47%), followed by typical EPEC (28.8%) and atypical EPEC (16.6%). Co-infection by EPEC and EAEC was detected in (7.6%) of isolates. However, ETEC, EIEC and EHEC were not detected. Phylogroup A (47%) and B2 (43.9%) were the predominant types. Multidrug-resistance (MDR) was found in 55% of DEC isolates. Extended-spectrum β-lactamase (ESBL) genes were detected in 24 isolates (24 blaTEM and 15 blaCTX-M-15). Only one isolate harbored AmpC β-lactamase gene (DHA gene). Conclusion The study concluded that, EAEC and EPEC are important causative agents of diarrhoea in children under 5 years. MDR among DEC has the potential to be a big concern.
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Affiliation(s)
- Rasha M M Khairy
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt.
| | - Zahra Atef Fathy
- Department of Clinical Pathology, Mallawi Hospital, Mallawi, Egypt
| | | | - Ebtisam S Mohamed
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt
| | - Soha S Abdelrahim
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt
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Antibiotic Sensitivity Screening of Klebsiella spp. and Raoultella spp. Isolated from Marine Bivalve Molluscs Reveal Presence of CTX-M-Producing K. pneumoniae. Microorganisms 2020; 8:microorganisms8121909. [PMID: 33266320 PMCID: PMC7761178 DOI: 10.3390/microorganisms8121909] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 01/01/2023] Open
Abstract
Klebsiella spp. are a major cause of both nosocomial and community acquired infections, with K. pneumoniae being responsible for most human infections. Although Klebsiella spp. are present in a variety of environments, their distribution in the sea and the associated antibiotic resistance is largely unknown. In order to examine prevalence of K. pneumoniae and related species in the marine environment, we sampled 476 batches of marine bivalve molluscs collected along the Norwegian coast. From these samples, K. pneumoniae (n = 78), K. oxytoca (n = 41), K. variicola (n = 33), K. aerogenes (n = 1), Raoultella ornithinolytica (n = 38) and R. planticola (n = 13) were isolated. The number of positive samples increased with higher levels of faecal contamination. We found low prevalence of acquired resistance in all isolates, with seven K. pneumoniae isolates showing resistance to more than one antibiotic class. The complete genome sequence of cefotaxime-resistant K. pneumoniae sensu stricto isolate 2016-1400 was obtained using Oxford Nanopore and Illumina MiSeq based sequencing. The 2016-1400 genome had two contigs, one chromosome of 5,088,943 bp and one plasmid of 191,744 bp and belonged to ST1035. The β-lactamase genes blaCTX-M-3 and blaTEM-1, as well as the heavy metal resistance genes pco, ars and sil were carried on a plasmid highly similar to one found in K. pneumoniae strain C17KP0055 from South-Korea recovered from a blood stream infection. The present study demonstrates that K. pneumoniae are prevalent in the coastal marine environment and that bivalve molluscs may act as a potential reservoir of extended spectrum β-lactamase (ESBL)-producing K. pneumoniae that may be transmitted through the food chain.
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Ogunbosi BO, Moodley C, Naicker P, Nuttall J, Bamford C, Eley B. Colonisation with extended spectrum beta-lactamase-producing and carbapenem-resistant Enterobacterales in children admitted to a paediatric referral hospital in South Africa. PLoS One 2020; 15:e0241776. [PMID: 33156820 PMCID: PMC7647087 DOI: 10.1371/journal.pone.0241776] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/21/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION There are few studies describing colonisation with extended spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and carbapenem-resistant Enterobacterales (CRE) among children in sub-Saharan Africa. Colonisation often precedes infection and multi-drug-resistant Enterobacterales are important causes of invasive infection. METHODS In this prospective cross-sectional study, conducted between April and June 2017, 200 children in a tertiary academic hospital were screened by rectal swab for EBSL-PE and CRE. The resistance-conferring genes were identified using polymerase chain reaction technology. Risk factors for colonisation were also evaluated. RESULTS Overall, 48% (96/200) of the children were colonised with at least one ESBL-PE, 8.3% (8/96) of these with 2 ESBL-PE, and one other child was colonised with a CRE (0.5% (1/200)). Common colonising ESBL-PE were Klebsiella pneumoniae (62.5%, 65/104) and Escherichia coli (34.6%, 36/104). The most frequent ESBL-conferring gene was blaCTX-M in 95% (76/80) of the isolates. No resistance- conferring gene was identified in the CRE isolate (Enterobacter cloacae). Most of the Klebsiella pneumoniae isolates were susceptible to piperacillin/tazobactam (86.2%) and amikacin (63.9%). Similarly, 94.4% and 97.2% of the Escherichia coli isolates were susceptible to piperacillin/tazobactam and amikacin, respectively. Hospitalisation for more than 7 days before study enrolment was associated with ESBL-PE colonisation. CONCLUSION Approximately half of the hospitalised children in this study were colonised with ESBL-PE. This highlights the need for improved infection prevention and control practices to limit the dissemination of these microorganisms.
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Affiliation(s)
- Babatunde O. Ogunbosi
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Clinton Moodley
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Preneshni Naicker
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - James Nuttall
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Colleen Bamford
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Brian Eley
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
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PRAJAPATI BI, SOLANKI KM, DEVI SARITA, KATIRA BP, PATEL SS, RAVAL SH, MOMIN RR. Phenotypic and molecular characterization of ESBLs producing Escherichia coli in bovine faecal and milk samples of North Gujarat. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2020. [DOI: 10.56093/ijans.v90i7.106667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Extended-spectrum β-lactamases (ESBLs) producing E. coli seems to be emerging in veterinary science impacting major threat to public health due to resistance to golden age antibiotics. In this study a total of 109 samples (42 faecal and 67 mastitis milk) of bovines were collected from different regions of North Gujarat. The samples were cultured and identified by standard procedures. The screening for ESBLs production was performed by using Cefotaxime and Cefotaxime+Clavulanate (Combination disc screening method). A total of 71 E. coli isolates were recovered from 109 samples processed, out of which thirty (42.25%) isolates (17 from milk and 13 from faecal) were positive for ESBLs showing multiple resistance to the antibiotics used. The ESBL confirmed isolates were further processed for detection of blaCTX-M, blaTEM, and blaSHV genes. Major gene detected was blaTEM in 17 (23.94%) E. coli isolates. Antibiotic resistance pattern of E. coli isolates was studied against eleven commonly used antimicrobial drugs in the northern region of Gujarat. The results recorded resistance tofollowing antibiotics: tetracycline (100%), ampicillin/sulbactum (83.10%), amoxiclav and gentamicin (83.10%), chloramphenicol (57.74%), ceftriaxone (66.19%), cefoperazone (66.19%), ciprofloxacin (74.65%), amikacin (57.74%), enrofloxacin (74.65%) and, levofloxacin (74.65%).
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Annear D, Gaida R, Myburg K, Black J, Truter I, Bamford C, Govender S. Spectrum of Bacterial Colonization in Patients Hospitalized for Treatment of Multidrug-Resistant Tuberculosis. Microb Drug Resist 2020; 27:691-697. [PMID: 33074767 DOI: 10.1089/mdr.2020.0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study investigated the bacterial colonization in patients admitted for treatment of drug-resistant tuberculosis in a specialized TB hospital. Identification and antimicrobial susceptibility testing of bacterial isolates (n = 62) from nasal, groin, and rectal swabs [patient cohort (n = 37)] were determined by the VITEK-MS system. Resistance gene analysis was by PCR and DNA sequencing. Molecular typing of Klebsiella pneumoniae isolates was by Multilocus Sequencing Typing (MLST). Patients (n = 13/37; 35%) were colonized by multidrug-resistant (MDR) bacteria (ESBL and MRSA) on admission. Of the 24 patients who were not colonized by MDR bacteria on admission, 46% (17/37) became colonized by MDR bacteria within 1 month of admission, mostly with ESBL-producing Enterobacteriales and resistance to aminoglycosides and fluoroquinolones. ESBL Escherichia coli (41/62; 66%) and K. pneumoniae (14/62; 23%) predominated. Genes encoding for ESBLs (blaCTX-M-14, blaCTX-M-15, blaSHV-28, blaOXA-1, and blaOXY-2) and plasmid-mediated quinolone resistant genes (qnrB1, qnrB4, and qnrB10) were detected. MLST revealed genetic diversity among the K. pneumoniae isolates from hospitalized patients. This study provides insight into bacterial pathogen colonization in hospitalized TB patients with the first occurrence of the qnrB4 and qnrB10 genes and co-expression of genes: qnrB4+aac(6')-lb-cr, qnrB10+aac(6')-lb-cr, qnrB4+qnrS1, and qnrB10+qnrS1 in fluoroquinolone-resistant E. coli isolates within South Africa. However, the source and colonization routes of these isolates could not be determined.
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Affiliation(s)
- Dale Annear
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa
| | - Razia Gaida
- Drug Utilization Research Unit (DURU), Department of Pharmacy, Nelson Mandela University, Port Elizabeth, South Africa
| | - Kierra Myburg
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa
| | - John Black
- Drug Utilization Research Unit (DURU), Department of Pharmacy, Nelson Mandela University, Port Elizabeth, South Africa.,Department of Medicine, Livingstone Hospital, Eastern Cape Department of Health, Port Elizabeth, South Africa
| | - Ilse Truter
- Drug Utilization Research Unit (DURU), Department of Pharmacy, Nelson Mandela University, Port Elizabeth, South Africa
| | - Colleen Bamford
- National Health Laboratory Service, Groote Schuur Hospital Microbiology Laboratory, Cape Town, South Africa.,Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Sharlene Govender
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa
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Arango-Argoty GA, Guron GKP, Garner E, Riquelme MV, Heath LS, Pruden A, Vikesland PJ, Zhang L. ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes. Bioinformatics 2020; 36:2966-2973. [PMID: 32058567 DOI: 10.1093/bioinformatics/btaa095] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 01/31/2020] [Accepted: 02/08/2020] [Indexed: 12/20/2022] Open
Affiliation(s)
| | - G K P Guron
- Department of Civil and Environmental Engineering.,Department of Food Science and Technology, Virginia Tech, Blacksburg, VA 24061 - 0217, USA
| | - E Garner
- Department of Civil and Environmental Engineering
| | - M V Riquelme
- Department of Civil and Environmental Engineering
| | | | - A Pruden
- Department of Civil and Environmental Engineering
| | | | - L Zhang
- Department of Computer Science
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48
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Meiring S, Cohen C, de Gouveia L, du Plessis M, Kularatne R, Hoosen A, Lekalakala R, Lengana S, Seetharam S, Naicker P, Quan V, Reubenson G, Tempia S, von Mollendorf C, von Gottberg A. Declining Incidence of Invasive Meningococcal Disease in South Africa: 2003-2016. Clin Infect Dis 2020; 69:495-504. [PMID: 30351372 DOI: 10.1093/cid/ciy914] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/19/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Invasive meningococcal disease (IMD) is endemic to South Africa, where vaccine use is negligible. We describe the epidemiology of IMD in South Africa. METHODS IMD cases were identified through a national, laboratory-based surveillance program, GERMS-SA, from 2003-2016. Clinical data on outcomes and human immunodeficiency virus (HIV) statuses were available from 26 sentinel hospital sites. We conducted space-time analyses to detect clusters of serogroup-specific IMD cases. RESULTS Over 14 years, 5249 IMD cases were identified. The incidence was 0.97 cases per 100 000 persons in 2003, peaked at 1.4 cases per 100 000 persons in 2006, and declined to 0.23 cases per 100 000 persons in 2016. Serogroups were confirmed in 3917 (75%) cases: serogroup A was present in 4.7% of cases, B in 23.3%, C in 9.4%; W in 49.5%; Y in 12.3%, X in 0.3%; Z in 0.1% and 0.4% of cases were non-groupable. We identified 8 serogroup-specific, geo-temporal clusters of disease. Isolate susceptibility was 100% to ceftriaxone, 95% to penicillin, and 99.9% to ciprofloxacin. The in-hospital case-fatality rate was 17% (247/1479). Of those tested, 36% (337/947) of IMD cases were HIV-coinfected. The IMD incidence in HIV-infected persons was higher for all age categories, with an age-adjusted relative risk ratio (aRRR) of 2.5 (95% confidence interval [CI] 2.2-2.8; P < .001) from 2012-2016. No patients reported previous meningococcal vaccine exposure. Patients with serogroup W were 3 times more likely to present with severe disease than those with serogroup B (aRRR 2.7, 95% CI 1.1-6.3); HIV coinfection was twice as common with W and Y diseases (aRRR W = 1.8, 95% CI 1.1-2.9; aRRR Y = 1.9, 95% CI 1.0-3.4). CONCLUSIONS In the absence of significant vaccine use, IMD in South Africa decreased by 76% from 2003-2016. HIV was associated with an increased risk of IMD, especially for serogroup W and Y diseases.
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Affiliation(s)
- Susan Meiring
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases (NICD), a Division of the National Health Laboratory Service (NHLS), Johannesburg.,School of Public Health, University of the Witwatersrand, Johannesburg
| | - Cheryl Cohen
- School of Public Health, University of the Witwatersrand, Johannesburg.,Centre for Respiratory Diseases and Meningitis, NICD, a Division of the NHLS, Johannesburg
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, NICD, a Division of the NHLS, Johannesburg
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, NICD, a Division of the NHLS, Johannesburg
| | | | | | - Ruth Lekalakala
- Department of Medical Microbiology, NHLS and University of Limpopo, Polokwane
| | - Sarona Lengana
- Centre for Respiratory Diseases and Meningitis, NICD, a Division of the NHLS, Johannesburg
| | | | - Preneshni Naicker
- Lancet Laboratories, Cape Town.,Division of Medical Microbiology, University of Cape Town
| | - Vanessa Quan
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases (NICD), a Division of the National Health Laboratory Service (NHLS), Johannesburg
| | - Gary Reubenson
- Rahima Moosa Mother & Child Hospital, Empilweni Service & Research Unit, Department of Paediatrics & Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Stefano Tempia
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia.,Influenza Program, Centres for Disease Control and Prevention, Pretoria
| | - Claire von Mollendorf
- School of Public Health, University of the Witwatersrand, Johannesburg.,Centre for Respiratory Diseases and Meningitis, NICD, a Division of the NHLS, Johannesburg
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, NICD, a Division of the NHLS, Johannesburg.,School of Pathology, University of the Witwatersrand, Johannesburg
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Savin M, Bierbaum G, Hammerl JA, Heinemann C, Parcina M, Sib E, Voigt A, Kreyenschmidt J. Antibiotic-resistant bacteria and antimicrobial residues in wastewater and process water from German pig slaughterhouses and their receiving municipal wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138788. [PMID: 32498197 DOI: 10.1016/j.scitotenv.2020.138788] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Slaughterhouse process- and wastewater are considered as a hotspot for antibiotic-resistant bacteria and antimicrobial residues and may thus play an important role for their dissemination into the environment. In this study, we investigated occurrence and characteristics of ESKAPE bacteria (E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, Enterobacter spp.) and ESBL (extended spectrum β-lactamase) -producing E. coli in water samples of different processing stages of two German pig slaughterhouses (S1/S2) as well as their municipal wastewater treatment plants (mWWTPs). Furthermore, residues of various antimicrobials were determined. A total of 103 water samples were taken in delivery and dirty areas of the slaughterhouses S1/S2 (n = 37), their in-house WWTPs (n = 30) and mWWTPs including their receiving water bodies (n = 36). The recovered isolates (n = 886) were characterized for their antimicrobial resistance pattern and its genetic basis. Targeted species were ubiquitous along the slaughtering and wastewater chains. Phenotypic and genotypic analyses revealed a broad variety of resistance phenotypes and β-lactamase genes. Carbapenemase-producing Enterobacteriaceae (CPE), vancomycin-resistant enterococci (VRE) and healthcare-associated (HA) MRSA were recovered only from mWWTPs and their preflooders. In contrast, the mcr-1 gene was exclusively detected in E. coli from S1/S2. Residues of five antimicrobials were detected in 14.9% (10/67) of S1/S2 samples in low range concentrations (≤1.30 μg/L), whereas 91.7% (33/36) of mWWTPs samples exhibited residues of 22 different antibiotics in concentrations of up to 4.20 μg/L. Target bacteria from S1/S2 and mWWTPs exhibited differences in their abundances, resistance phenotypes and genotypes as well as clonal lineages. S1/S2 samples exhibited bacteria with zoonotic potential (e.g. MRSA of CC398, E. coli of significant clones), whereas ESKAPE bacteria exhibiting resistances of clinical importance were mainly detected in mWWTPs. Municipal WWTPs seem to fail to eliminate these bacteria leading to a discharge into the preflooder and a subsequent dissemination into the surface water.
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Affiliation(s)
- Mykhailo Savin
- Institute of Animal Sciences, University of Bonn, Bonn, Germany.
| | - Gabriele Bierbaum
- Institute for Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Germany
| | - Jens Andre Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Marijo Parcina
- Institute for Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Germany
| | - Esther Sib
- Institute for Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Germany
| | - Alexander Voigt
- Institute for Hygiene and Public Health, Medical Faculty, University of Bonn, Germany
| | - Judith Kreyenschmidt
- Institute of Animal Sciences, University of Bonn, Bonn, Germany; Hochschule Geisenheim University, Department of Fresh Produce Logistics, Geisenheim, Germany
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Jean SS, Ko WC, Hsueh PR. Susceptibility of clinical isolates of meticillin-resistant Staphylococcus aureus and phenotypic non-extended-spectrum β-lactamase-producing Klebsiella pneumoniae to ceftaroline in Taiwan: Results from Antimicrobial Testing Leadership and Surveillance (ATLAS) in 2012-2018 and Surveillance of Multicentre Antimicrobial Resistance in Taiwan (SMART) in 2018-2019. Int J Antimicrob Agents 2020; 56:106016. [PMID: 32422316 DOI: 10.1016/j.ijantimicag.2020.106016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/21/2020] [Accepted: 05/03/2020] [Indexed: 02/06/2023]
Abstract
Data on ceftaroline (CPT) susceptibility amongst clinical isolates of meticillin-resistant Staphylococcus aureus (MRSA, n=1284) and phenotypic non-extended-spectrum β-lactamase-producing (non-ESBL-P) Klebsiella pneumoniae (n=466), obtained from the Antimicrobial Testing Leadership and Surveillance (ATLAS) programme from 2012 to 2018, and selected MRSA isolates from patients with bloodstream infections (BSIs) (n=95) from the Surveillance of Multicentre Antimicrobial Resistance in Taiwan (SMART) programme from 2018 to 2019 were analysed. The minimum inhibitory concentrations (MICs) of ATLAS isolates were determined using the broth microdilution method, whereas the MICs of SMART BSI-MRSA isolates were determined using the Etest and MicroScan system. The pharmacokinetic profiles and pharmacodynamic parameters of CPT were applied to explore the optimal dosage against infections caused by Taiwanese MRSA and K. pneumoniae isolates. Approximately 7.1% of ATLAS MRSA isolates were susceptible-dose dependent (S-DD) to CPT, and 19.7% of the non-ESBL-P K. pneumoniae isolates were not susceptible to CPT. Amongst the ATLAS MRSA isolates, the S-DD rates to CPT amongst isolates causing lower respiratory tract infections were 11.9% and 8.5% for isolates from intensive care units (ICUs) and general wards (GWs), and those causing skin and soft tissue infections (SSTIs) were 20% and 5.3% for isolates from ICUs and GWs, respectively (P=0.015). Of the SSTI MRSA isolates from GWs, 22.7% displayed vancomycin MICs >1 mg/L. Amongst 95 SMART BSI MRSA isolates, 28 (46.7%) isolates exhibited lower CPT MICs by the Etest compared with 60 isolates with CPT MICs of 1-2 mg/L by the MicroScan system. CPT 600 mg as a 2-h intravenous infusion every 8 h is suggested for treatment of infections caused by MRSA and phenotypic non-ESBL-P K. pneumoniae in Taiwan.
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Affiliation(s)
- Shio-Shin Jean
- Department of Emergency, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Department of Emergency Medicine, Department of Emergency and Critical Care Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Wen-Chien Ko
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Division of Infectious Diseases and Centre for Infection Control, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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