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Maina JW, Mutua JM, Musyoki AM. Carbapenem-resistant gram-negative bacterial infections and risk factors for acquisition in a Kenyan intensive care unit. BMC Infect Dis 2024; 24:522. [PMID: 38783175 PMCID: PMC11118991 DOI: 10.1186/s12879-024-09256-6] [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: 12/18/2023] [Accepted: 03/26/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Carbapenem-resistant Gram-negative bacteria (CR-GNB) are a critical public health threat globally; however, there are inadequate surveillance data, especially in intensive care units (ICU), to inform infection prevention and control in many resource-constrained settings. Here, we assessed the prevalence of CR-GNB infections and risk factors for acquisition in a Kenyan ICU. METHODS A hospital-based cross-sectional study design was adopted, recruiting 162 patients clinically presenting with bacterial infection after 48 h of ICU admission, from January to October 2022 at the Nairobi West Hospital, Kenya. Demographics and clinical data were collected by case report form. The type of sample collected, including blood, tracheal aspirate, ascitic tap, urine, stool, and sputum depended on the patient's clinical presentation and were transported to the hospital Microbiology laboratory in a cool box for processing within 2 h. The samples were analyzed by cultured and BD Phoenix system used for isolates' identity and antimicrobial susceptibility. RESULTS CR-GNB infections prevalence was 25.9% (42/162), with Klebsiella pneumoniae (35.7%, 15/42) and Pseudomonas aeruginosa (26.2%, 11/42) predominating. All isolates were multidrug-resistant (MDR). P. aeruginosa and A. baumannii were 100% colistin-resistant, while K. pneumoniae (33.3%) was tigecycline-resistant. History of antibiotics (aOR = 3.40, p = 0.005) and nasogastric tube (NGT) use (aOR = 5.84, p = < 0.001) were the risk factors for infection. CONCLUSION Our study highlights high MDR- and CR-GNB infections in ICU, with prior antibiotic exposure and NGT use as risk factors, and diminishing clinical value of colistin and tigecycline. In this study setting and beyond, strict implementation of antimicrobial stewardship programs and adherence to infection prevention and control through monitoring, evaluation and feedback are warranted to curb CR-GNB infections, especially among the risk groups.
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Affiliation(s)
- Jane Wairimu Maina
- Department of Medical Laboratory, The Nairobi West Hospital, Nairobi, P.O BOX 43375-00100, Kenya
| | - Jeniffer Munyiva Mutua
- Department of Laboratory Medicine, Kenyatta National Hospital, Nairobi, P.O Box 20723-00202, Kenya
| | - Abednego Moki Musyoki
- Department of Medical Laboratory Sciences, Kenyatta University, Nairobi, P.O BOX 43844-00100, Kenya.
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Ofosu-Appiah F, Acquah EE, Mohammed J, Sakyi Addo C, Agbodzi B, Ofosu DAS, Myers CJ, Mohktar Q, Ampomah OW, Ablordey A, Amissah NA. Klebsiella pneumoniae ST147 harboring blaNDM-1, multidrug resistance and hypervirulence plasmids. Microbiol Spectr 2024; 12:e0301723. [PMID: 38315028 PMCID: PMC10913492 DOI: 10.1128/spectrum.03017-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/17/2023] [Indexed: 02/07/2024] Open
Abstract
The spread of hypervirulent (hv) and carbapenem-/multidrug-resistant Klebsiella pneumoniae is an emerging problem in healthcare settings. The New Delhi metallo-β-lactamase-1 (blaNDM-1) is found in Enterobacteriaceae including K. pneumoniae. The blaNDM-1 is capable of hydrolyzing β-lactam antibiotics which are used for treatment of severe infections caused by multidrug-resistant Gram-negative bacteria. This is associated with the unacceptably high mortality rate in immunocompromised burn injury patients. This study reports on the characterization of blaNDM-1 gene and virulence factors in hv carbapenem-/multidrug-resistant K. pneumoniae ST147 in the burns unit of a tertiary teaching hospital during routine surveillance. Two K. pneumoniae strains were obtained from wounds of burn-infected patients from May 2020 to July 2021. The hypervirulence genes and genetic context of the blaNDM-1 gene and mobile genetic elements potentially involved in the transposition of the gene were analyzed. We identified a conserved genetic background and an IS26 and open reading frame flanking the blaNDM-1 gene that could suggest its involvement in the mobilization of the gene. The plasmid harbored additional antibiotic resistance predicted regions that were responsible for resistance to almost all the routinely used antibiotics. To ensure the identification of potential outbreak strains during routine surveillance, investigations on resistance genes and their environment in relation to evolution are necessary for molecular epidemiology.IMPORTANCEData obtained from this study will aid in the prompt identification of disease outbreaks including evolving resistance and virulence of the outbreak bacteria. This will help establish and implement antimicrobial stewardship programs and infection prevention protocols in fragile health systems in countries with limited resources. Integration of molecular surveillance and translation of whole-genome sequencing in routine diagnosis will provide valuable data for control of infection. This study reports for the first time a high-risk clone K. pneumoniae ST147 with hypervirulence and multidrug-resistance features in Ghana.
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Affiliation(s)
- Frederick Ofosu-Appiah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Ezra E. Acquah
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Jibril Mohammed
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Comfort Sakyi Addo
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Bright Agbodzi
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorcas A. S. Ofosu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Charles J. Myers
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Quaneeta Mohktar
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Opoku-Ware Ampomah
- The Burns Unit, Reconstructive Plastic Surgery and Burns Unit, Korle Bu Teaching Hospital, Accra, Ghana
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Nana Ama Amissah
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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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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Ali MG, Almoneim ZA, Kareem SM. Evaluated gene expressions of Metallo beta lactamase genes GIM and , VIM, SPM in Pseudomonas aeruginosa clinical isolates. Mol Biol Rep 2023; 50:10111-10120. [PMID: 37917414 DOI: 10.1007/s11033-023-08883-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/03/2023] [Indexed: 11/04/2023]
Abstract
Pseudomonas aeruginosa is considered as one of the human health care problems, P. aeruginosa's carbapenem resistance emerges by several different mechanisms, some of which include carbapenems genes. P. aeruginosa's carbapenem resistance is a significant health concern, So this study aims to evaluate MBL gene expressions. The study was conducted at the Department of Microbiology, AL-Mahmoodia Hospital, over one year from January to December 2022. The samples were collected from patients with different clinical sources (Burn, Urine, Wound, Sputum, Ear, and Blood), from different ages while. Samples were collected from three hospitals in Baghdad including Al-Yarmouk Teaching Hospital, AL-Mahmmodiya Hospital, and Child's Central Teaching Hospital. A study analyzed 55 P. aeruginosa strains from various clinical sources, the study utilizes the chemical characterization, VITEK 2 system, 16s rRNA, antibiogram sensitivity tests, antibiotic susceptibility using eight antibiotics, including Amikacin, Ciprofloxacin, Levofloxacin, Imipenem Meropenem, Piperacillin, Cefepim and Aztreonam. The test of bacterial susceptibility revealed that each isolate was highly resistant to piperacillin, which are 96.36%, and lower resistance to Ciprofloxacin, which are 32%. Phenotypic screening carbapenem resistance methods combined the disk synergy test and conventional PCR that were used to detect isolates by using 16 S rRNA. This proves that the bacteria is P. aeruginosa and computed by measuring gene expression of the target genes (GIM, VIM, SPM) by using the real-time PCR, which is employed for twenty-five isolates. The result indicates that the expression level of the VIM gene is highly regulated in carbapenem-resistance isolates compared to control isolates that is 1.00. While the expression level of gene GIM and SPM is downregulated in carbapenem-resistance isolates compared to control isolates that is 6. The carbapenem VIM and GIM, SPM (class B) genes are essential for resistance in P. aeruginosa induced by chromosomal changes that modify membrane permeability efflux pump overexpression for genes. As a result, many studies require for discovering new strategies to reduce the threat to public health through preventing the spread of these isolates via tight infections, control measures, and the reduction of the danger to public health.
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Affiliation(s)
- Marwa Ghalib Ali
- Department of Medical Laboratory, AL-Mahmmodiya Hospital, Ministry of Health, Baghdad, Iraq
| | | | - Sawsan M Kareem
- Branch of Biotechnology, Department of Biology, College of Science, Mustansiriyah University, POX 10244, Baghdad, Iraq.
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Arowolo MT, Orababa OQ, Olaitan MO, Osibeluwo BV, Essiet UU, Batholomew OH, Ogunrinde OG, Lagoke OA, Soriwei JD, Ishola OD, Ezeani OM, Onishile AO, Olumodeji E. Prevalence of carbapenem resistance in Acinetobacter baumannii and Pseudomonas aeruginosa in sub-Saharan Africa: A systematic review and meta-analysis. PLoS One 2023; 18:e0287762. [PMID: 38015906 PMCID: PMC10684001 DOI: 10.1371/journal.pone.0287762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 06/13/2023] [Indexed: 11/30/2023] Open
Abstract
Carbapenems are effective drugs against bacterial pathogens and resistance to them is considered a great public health threat, especially in notorious nosocomial pathogens like Acinetobacter baumannii and Pseudomonas aeruginosa. In this study, we aimed to determine the prevalence of carbapenem resistance in A. baumannii and P. aeruginosa infections in Sub-Saharan Africa. Databases (PubMed, Scopus, Web of Science, and African Journal Online) were systematically searched following the Preferred Reporting Items for Systematic review and meta-analysis protocols (PRISMA-P) 2020 statements for articles reporting carbapenem-resistant Acinetobacter baumannii (CRAB) and carbapenem-resistant Pseudomonas aeruginosa (CRPA) prevalence between 2012 and 2022. Pooled prevalence was determined with the random effect model and funnel plots were used to determine heterogeneity in R. A total of 47 articles were scanned for eligibility, among which 25 (14 for carbapenem-resistant A. baumannii and 11 for carbapenem-resistant P. aeruginosa) were included in the study after fulfilling the eligibility criteria. The pooled prevalence of CRPA in the present study was estimated at 8% (95% CI; 0.02-0.17; I2 = 98%; P <0.01). There was high heterogeneity (Q = 591.71, I2 = 98.9%; P<0.0001). In addition, this study's pooled prevalence of CRAB was estimated at 20% (95% CI; 0.04-0.43; I2 = 99%; P <0.01). There was high heterogeneity (Q = 1452.57, I2 = 99%; P<0.0001). Also, a funnel plot analysis of the studies showed high degree of heterogeneity. The carbapenemase genes commonly isolated from A. baumannii in this study include blaOXA23, blaOXA48, blaGES., blaNDM, blaVIM, blaOXA24, blaOXA58, blaOXA51, blaSIM-1, blaOXA40, blaOXA66, blaOXA69, blaOXA91, with blaOXA23 and blaVIM being the most common. On the other hand, blaNDM, blaVIM, blaIMP, blaOXA48, blaOXA51, blaSIM-1, blaOXA181, blaKPC, blaOXA23, blaOXA50 were the commonly isolated carbapenemase genes in P. aeruginosa, among which blaVIM and blaNDM genes were the most frequently isolated. Surveillance of drug-resistant pathogens in Sub-Saharan Africa is essential in reducing the region's disease burden. This study has shown that the region has significantly high multidrug-resistant pathogen prevalence. This is a wake-up call for policymakers to put in place measures to reduce the spread of these critical priority pathogens.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jeffrey Difiye Soriwei
- Department of Public Health in Microbiology, University of Bedfordshire, Luton, United Kingdom
| | | | | | - Aminat Oyeronke Onishile
- Faculty of Health Studies, School of Nursing and Healthcare Leadership, University of Bradford, West Yorkshire, England, United Kingdom
| | - Elizabeth Olumodeji
- Department of Biology, Texas Women University, Denton, TX, United States of America
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Maina JW, Onyambu FG, Kibet PS, Musyoki AM. Multidrug-resistant Gram-negative bacterial infections and associated factors in a Kenyan intensive care unit: a cross-sectional study. Ann Clin Microbiol Antimicrob 2023; 22:85. [PMID: 37710247 PMCID: PMC10500940 DOI: 10.1186/s12941-023-00636-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/29/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Patients admitted to intensive care units (ICU) are at risk of Gram-negative bacteria (GNB) infections, especially those caused by multidrug-resistant (MDR) isolates, increasing morbidity, mortality, and healthcare costs. However, epidemiological surveillance data on MDR bacteria to inform infection prevention and control (IPCs) interventions is limited in our study setting. Here we assessed the prevalence and factors associated with GNB infections in ICU- patients admitted in our study setting. METHODS This was a hospital-based cross-sectional study among patients admitted to ICU at the Nairobi West Hospital, Kenya, between January and October 2022. Altogether, we recruited 162 patients, excluding those hospitalized for less than 48 h and declining consent, and collected demographics and clinical data by case report form. Blood, wound and throat swab, ascetic tap, stool, urine, tracheal aspirate, and sputum samples were collected cultured. Isolates identity and antimicrobial susceptibility were elucidated using the BD Phoenix system. RESULTS The prevalence of GNB infections was 55.6%, predominated by urinary tract infections (UTIs). We recovered 13 GNB types, with Escherichia coli (33.3%) and Klebsiella pneumoniae (31.1%) as the most common isolates. Factors associated with GNB infections were a history of antibiotic use (aOR = 4.23, p = 0.001), nasogastric tube use (NGT, aOR = 3.04, p = 0.013), respiratory tract (RT, aOR = 5.3, p = 0.005) and cardiovascular (CV, aOR = 5.7, p = 0.024) conditions. 92% of the isolates were MDR,predominantly Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. CONCLUSION We report a high prevalence of MDR-GNB infections, predominated by UTI, in ICU, whereby patients with a history of antibiotic use, using the NGT, and having RT and CV conditions were at increased risk. To improve the management of ICU-admitted patients, continuous education, training, monitoring, evaluation and feedback on infection prevention and control are warranted in our study setting.
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Affiliation(s)
- Jane Wairimu Maina
- Department of Medical Laboratory Science, The Nairobi West Hospital, Nairobi, Kenya.
- Department of Medical Laboratory Science, Kenyatta University, Nairobi, Kenya.
| | | | - Peter Shikuku Kibet
- Department of Medical Laboratory Science, The Nairobi West Hospital, Nairobi, Kenya
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Kigen C, Muraya A, Kyanya C, Kingwara L, Mmboyi O, Hamm T, Musila L. Enhancing capacity for national genomics surveillance of antimicrobial resistance in public health laboratories in Kenya. Microb Genom 2023; 9:mgen001098. [PMID: 37646415 PMCID: PMC10483422 DOI: 10.1099/mgen.0.001098] [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: 02/24/2023] [Accepted: 08/06/2023] [Indexed: 09/01/2023] Open
Abstract
Genomic surveillance is vital for detecting outbreaks and understanding the epidemiology and transmission of bacterial strains, yet it is not integrated into many national antimicrobial resistance (AMR) surveillance programmes. Key factors are that few scientists in the public health sector are trained in bacterial genomics, and the diverse sequencing platforms and bioinformatic tools make it challenging to generate reproducible outputs. In Kenya, these gaps were addressed by training public health scientists to conduct genomic surveillance on isolates from the national AMR surveillance repository and produce harmonized reports. The 2-week training combined theory and laboratory and bioinformatic experiences with Klebsiella pneumoniae isolates from the surveillance repository. Whole-genome sequences generated on Illumina and Nanopore sequencers were analysed using publicly available bioinformatic tools, and a harmonized report was generated using the HAMRonization tool. Pre- and post-training tests and self-assessments were used to assess the effectiveness of the training. Thirteen scientists were trained and generated data on the K. pneumoniae isolates, summarizing the AMR genes present consistently with the reported phenotypes and identifying the plasmid replicons that could transmit antibiotic resistance. Ninety per cent of the participants demonstrated an overall improvement in their post-training test scores, with an average increase of 14 %. Critical challenges were experienced in delayed delivery of equipment and supplies, power fluctuations and internet connections that were inadequate for bioinformatic analysis. Despite this, the training built the knowledge and skills to implement bacterial genomic surveillance. More advanced and immersive training experiences and building supporting infrastructure would solidify these gains to produce tangible public health outcomes.
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Affiliation(s)
- Collins Kigen
- United States Army Medical Research Directorate-Africa, P. O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Angela Muraya
- Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya
| | - Cecilia Kyanya
- United States Army Medical Research Directorate-Africa, P. O. Box 606-00621, Village Market, Nairobi, Kenya
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Leonard Kingwara
- National Public Health Laboratory Services, Kenyatta National Hospital Grounds, Hospital Road, P.O Box 20750 -00202, Nairobi, Kenya
| | - Onesmus Mmboyi
- National Public Health Laboratory Services, Kenyatta National Hospital Grounds, Hospital Road, P.O Box 20750 -00202, Nairobi, Kenya
| | - Tiffany Hamm
- Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, Maryland, USA
| | - Lillian Musila
- United States Army Medical Research Directorate-Africa, P. O. Box 606-00621, Village Market, Nairobi, Kenya
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Kariuki K, Diakhate MM, Musembi S, Tornberg-Belanger SN, Rwigi D, Mutuma T, Mutuku E, Tickell KD, Soge OO, Singa BO, Walson JL, Pavlinac PB, Kariuki S. Plasmid-mediated quinolone resistance genes detected in Ciprofloxacin non-susceptible Escherichia coli and Klebsiella isolated from children under five years at hospital discharge, Kenya. BMC Microbiol 2023; 23:129. [PMID: 37173674 PMCID: PMC10182689 DOI: 10.1186/s12866-023-02849-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 04/04/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND The increasing spread of fluoroquinolone resistant enteric bacteria is a global public health concern. Children recently discharged from the hospital are at high risk of carriage of antimicrobial resistance (AMR) due to frequent exposure to antimicrobials during inpatient stays. This study aimed to determine the prevalence, correlates of ciprofloxacin (CIP) non-susceptibility, and distribution of plasmid-mediated quinolone resistance (PMQR) genes in Escherichia coli (E. coli) and Klebsiella spp isolated from children under five years being discharged from two Kenyan Hospitals. METHODS E. coli and Klebsiella spp were isolated from fecal samples from children discharged from hospital and subjected to antimicrobial susceptibility testing (AST) by disc diffusion and E-test. CIP non-susceptible isolates were screened for seven PMQR genes using multiplex polymerase chain reaction (PCR). Poisson regression was used to determine the association between the carriage of CIP non-susceptible isolates and patient characteristics. RESULTS Of the 280 CIP non-susceptible isolates: 188 E. coli and 92 Klebsiella spp isolates identified among 266 discharged children, 195 (68%) were CIP-non-susceptible with minimum inhibitory concentrations (MICs) of ≥ 1 µg/mL. Among these 195 isolates, 130 (67%) had high-level CIP MIC = ≥ 32 µg/mL). Over 80% of the isolates had at least one PMQR gene identified: aac(6')lb-cr (60%), qnrB (24%), oqxAB (22%), qnrS (16%), and qepA (6%), however, qnrA was not identified in any isolates tested. Co-carriage of qnrB with acc(6')-lb-cr was the most predominant accounting for 20% of all the isolates. Ceftriaxone use during hospital admission and the presence of extended spectrum beta-lactamase (ESBL) production were significantly associated with the carriage of CIP non-susceptible E. coli and Klebsiella spp. CONCLUSION CIP non-susceptibility is common among E. coli and Klebsiella spp isolated from hospital discharged children in Kenya. Carriage and co-carriage of PMQR, including the newly identified qepA gene, were frequently observed. These findings suggest that children leaving the hospital may serve as an important reservoir for transmission of resistant E. coli and Klebsiella spp to the community. Enhanced surveillance for AMR determinants is critical to inform interventions to control antimicrobial-resistant bacteria.
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Affiliation(s)
- Kevin Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya.
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya.
| | | | - Susan Musembi
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | | | - Doreen Rwigi
- Centre for Microbiology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Timothy Mutuma
- Centre for Microbiology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Elizabeth Mutuku
- Centre for Microbiology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Kirkby D Tickell
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Olusegun O Soge
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Benson O Singa
- Department of Global Health, University of Washington, Seattle, WA, USA
- Centre for Clinical Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Judd L Walson
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pediatrics and Medicine (Allergy and Infectious Diseases), University of Washington, Seattle, WA, USA
| | - Patricia B Pavlinac
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Epidemiology, University of Washington, Seattle, WA, USA.
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
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Odoyo E, Matano D, Tiria F, Georges M, Kyanya C, Wahome S, Mutai W, Musila L. Environmental contamination across multiple hospital departments with multidrug-resistant bacteria pose an elevated risk of healthcare-associated infections in Kenyan hospitals. Antimicrob Resist Infect Control 2023; 12:22. [PMID: 36978195 PMCID: PMC10053033 DOI: 10.1186/s13756-023-01227-x] [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: 06/10/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Healthcare-associated infections (HAIs) are often caused by multidrug-resistant (MDR) bacteria contaminating hospital environments which can cause outbreaks as well as sporadic transmission. METHODS This study systematically sampled and utilized standard bacteriological culture methods to determine the numbers and types of MDR Enterococcus faecalis/faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species, and Escherichia coli (ESKAPEE) from high-touch environments of five Kenyan hospitals; level 6 and 5 hospitals (A, B, and C), and level 4 hospitals (D and E), in 2018. Six hundred and seventeen high-touch surfaces across six hospital departments; surgical, general, maternity, newborn, outpatient and pediatric were sampled. RESULTS 78/617 (12.6%) of the sampled high-touch surfaces were contaminated with MDR ESKAPEE; A. baumannii, 23/617 (3.7%), K. pneumoniae, 22/617 (3.6%), Enterobacter species, 19/617 (3.1%), methicillin resistant S. aureus (MRSA), 5/617 (0.8%), E. coli, 5/617 (0.8%), P. aeruginosa, 2/617 (0.3%), and E. faecalis and faecium, 2/617 (0.3%). Items found in patient areas, such as beddings, newborn incubators, baby cots, and sinks were the most frequently contaminated. Level 6 and 5 hospitals, B, 21/122 (17.2%), A, 21/122 (17.2%), and C, 18/136 (13.2%), were more frequently contaminated with MDR ESKAPEE than level 4 hospitals; D, 6/101 (5.9%), and E, 8/131 (6.1%). All the sampled hospital departments were contaminated with MDR ESKAPEE, with high levels observed in newborn, surgical and maternity. All the A. baumannii, Enterobacter species, and K. pneumoniae isolates were non-susceptible to piperacillin, ceftriaxone and cefepime. 22/23 (95.6%) of the A. baumannii isolates were non-susceptible to meropenem. In addition, 5 K. pneumoniae isolates were resistant to all the antibiotics tested except for colistin. CONCLUSION The presence of MDR ESKAPEE across all the hospitals demonstrated gaps in infection prevention practices (IPCs) that should be addressed. Non-susceptibility to last-line antibiotics such as meropenem threatens the ability to treat infections.
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Affiliation(s)
- Erick Odoyo
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Nairobi, Kenya
| | - Daniel Matano
- Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya
| | - Fredrick Tiria
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Nairobi, Kenya
| | - Martin Georges
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Nairobi, Kenya
| | - Cecilia Kyanya
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Nairobi, Kenya
| | | | - Winnie Mutai
- Department of Medical Microbiology, Faculty of Health Sciences, University of Nairobi, P.O. Box 30197- 00100, Nairobi, Kenya
| | - Lillian Musila
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Nairobi, Kenya.
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Akunda IK, Kariuki DW, Matulis G, Mwaura P, Maina B, Mohammed H, Paul A, Onyambu FG, Ole Kwallah A, Martins DJ, von Fricken ME, Kamau JM. Antimicrobial resistance patterns and characterisation of emerging beta-lactamase-producing Escherichia coli in camels sampled from Northern Kenya. Vet Med Sci 2023; 9:1407-1416. [PMID: 36795022 DOI: 10.1002/vms3.1090] [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: 02/17/2023] Open
Abstract
BACKGROUND Animal husbandry practices in different livestock production systems and increased livestock-wildlife interactions are thought to be primary drivers of antimicrobial resistance (AMR) in Arid and Semi-Arid Lands (ASALs). Despite a tenfold increase in the camel population within the last decade, paired with widespread use of camel products, there is a lack of comprehensive information concerning beta-lactamase-producing Escherichia coli (E. coli) within these production systems. OBJECTIVES Our study sought to establish an AMR profile and to identify and characterise emerging beta-lactamase-producing E. coli isolated from faecal samples obtained from camel herds in Northern Kenya. METHODS The antimicrobial susceptibility profiles of E. coli isolates were established using the disk diffusion method, with beta-lactamase (bla) gene PCR product sequencing performed for phylogenetic grouping and genetic diversity assessments. RESULTS Here we show, among the recovered E. coli isolates (n = 123), the highest level of resistance was observed for cefaclor at 28.5% of isolates, followed by cefotaxime at 16.3% and ampicillin at 9.7%. Moreover, extended-spectrum beta-lactamase (ESBL)-producing E. coli harbouring the blaCTX-M-15 or blaCTX-M-27 genes were detected in 3.3% of total samples, and are associated with phylogenetic groups B1, B2 and D. Multiple variants of non-ESBL blaTEM genes were detected, the majority of which were the blaTEM-1 and blaTEM-116 genes. CONCLUSIONS Findings from this study shed light on the increased occurrence of ESBL- and non-ESBL-encoding gene variants in E. coli isolates with demonstrated multidrug resistant phenotypes. This study highlights the need for an expanded One Health approach to understanding AMR transmission dynamics, drivers of AMR development, and appropriate practices for antimicrobial stewardship in camel production systems within ASALs.
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Affiliation(s)
- Irene Karegi Akunda
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya.,One Health Center, Institute of Primate Research, Nairobi, Kenya
| | - Daniel W Kariuki
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Graham Matulis
- Department of Global and Community Health, George Mason University, Fairfax County, Virginia
| | - Patrick Mwaura
- One Health Center, Institute of Primate Research, Nairobi, Kenya
| | - Brian Maina
- Centre of Microbiology, Washington State University, Nairobi, Kenya
| | - Halima Mohammed
- Centre for Molecular Biosciences and Genomics, Nairobi, Kenya
| | - Ayieko Paul
- Regional Veterinary Investigation Laboratory, Nakuru, Kenya
| | - Frank G Onyambu
- Centre for Molecular Biosciences and Genomics, Nairobi, Kenya.,School of Health Sciences, Meru University of Science and Technology, Meru, Kenya
| | - Allan Ole Kwallah
- Centre for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Dino J Martins
- Mpala Research Centre, Nanyuki, Kenya.,Turkana Basin Institute, Stony Brook University, Stony Brook, NY, USA
| | - Michael E von Fricken
- Department of Global and Community Health, George Mason University, Fairfax County, Virginia
| | - Joseph M Kamau
- One Health Center, Institute of Primate Research, Nairobi, Kenya
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11
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Pankok F, Fuchs F, Loderstädt U, Kaase M, Balczun C, Scheithauer S, Frickmann H, Hagen RM. Molecular Epidemiology of Escherichia coli with Resistance against Third-Generation Cephalosporines Isolated from Deployed German Soldiers-A Retrospective Assessment after Deployments to the African Sahel Region and Other Sites between 2007 and 2016. Microorganisms 2022; 10:microorganisms10122448. [PMID: 36557701 PMCID: PMC9788009 DOI: 10.3390/microorganisms10122448] [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: 11/12/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Colonization and infection with bacteria with acquired antibiotic resistance are among the risks for soldiers on international deployments. Enterobacterales with resistance against third-generation cephalosporines are amongst the most frequently imported microorganisms. To contribute to the scarcely available epidemiological knowledge on deployment-associated resistance migration, we assessed the molecular epidemiology of third-generation cephalosporine-resistant Escherichia coli isolated between 2007 and 2016 from German soldiers after deployments, with a particular focus on the African Sahel region. A total of 51 third-generation cephalosporine-resistant E. coli isolated from 51 military returnees from deployment collected during the assessment period between 2007 and 2016 were subjected to short-read next-generation sequencing analysis. Returnees from the Sahel region (Djibouti, Mali, South Sudan, Sudan, Sudan, and Uganda) comprised a proportion of 52.9% (27/51). Repeatedly isolated sequence types according to the Warwick University scheme from returnees from the Sahel region were ST38, ST131, and ST648, confirming previous epidemiological assessments from various sub-Saharan African regions. Locally prevalent resistance genes in isolates from returnees from the Sahel region associated with third-generation resistance were blaCTX-M-15, blaCTX-M-27, blaCTX-M-1, blaTEM-169, blaCTX-M-14, blaCTX-M-99-like, blaCTX-M-125, blaSHV-12, and blaDHA-1, while virulence genes were east1, sat, and tsh in declining order of frequency of occurrence each. In line with phenotypically observed high resistance rates for aminoglycosides and trimethoprim/sulfamethoxazole, multiple associated resistance genes were observed. A similar, slightly more diverse situation was recorded for the other deployment sites. In summary, this assessment provides first next-generation sequencing-based epidemiological data on third-generation cephalosporine-resistant E. coli imported by deployed German soldiers with a particular focus on deployments to the Sahel region, thus serving as a small sentinel. The detected sequence types are well in line with the results from previous epidemiological assessments in sub-Saharan Africa.
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Affiliation(s)
- Frederik Pankok
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany
- Correspondence: (F.P.); (U.L.)
| | - Frieder Fuchs
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Medical Faculty and University Hospital of Cologne, 50931 Cologne, Germany
| | - Ulrike Loderstädt
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany
- Correspondence: (F.P.); (U.L.)
| | - Martin Kaase
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Carsten Balczun
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany
| | - Simone Scheithauer
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hospital Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Ralf Matthias Hagen
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany
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12
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Roque-Borda CA, Bento da Silva P, Rodrigues MC, Di Filippo LD, Duarte JL, Chorilli M, Vicente EF, Garrido SS, Rogério Pavan F. Pharmaceutical nanotechnology: Antimicrobial peptides as potential new drugs against WHO list of critical, high, and medium priority bacteria. Eur J Med Chem 2022; 241:114640. [PMID: 35970075 DOI: 10.1016/j.ejmech.2022.114640] [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: 03/18/2022] [Revised: 07/12/2022] [Accepted: 07/27/2022] [Indexed: 12/29/2022]
Abstract
Nanobiotechnology is a relatively unexplored area that has, nevertheless, shown relevant results in the fight against some diseases. Antimicrobial peptides (AMPs) are biomacromolecules with potential activity against multi/extensively drug-resistant bacteria, with a lower risk of generating bacterial resistance. They can be considered an excellent biotechnological alternative to conventional drugs. However, the application of several AMPs to biological systems is hampered by their poor stability and lifetime, inactivating them completely. Therefore, nanotechnology plays an important role in the development of new AMP-based drugs, protecting and carrying the bioactive to the target. This is the first review article on the different reported nanosystems using AMPs against bacteria listed on the WHO priority list. The current shortage of information implies a nanobiotechnological potential to obtain new drugs or repurpose drugs based on the AMP-drug synergistic effect.
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Affiliation(s)
- Cesar Augusto Roque-Borda
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, CEP 14800-903, Brazil; Universidad Católica de Santa María, Vicerrectorado de Investigación, Facultad de Ciencias Farmacéuticas Bioquímicas y Biotecnológicas, Brazil
| | - Patricia Bento da Silva
- Laboratory of Nanobiotechnology, Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil
| | - Mosar Corrêa Rodrigues
- Laboratory of Nanobiotechnology, Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil
| | - Leonardo Delello Di Filippo
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Department of Drugs and Medicines, Araraquara, São Paulo, CEP 14800-903, Brazil
| | - Jonatas L Duarte
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Department of Drugs and Medicines, Araraquara, São Paulo, CEP 14800-903, Brazil
| | - Marlus Chorilli
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Department of Drugs and Medicines, Araraquara, São Paulo, CEP 14800-903, Brazil
| | - Eduardo Festozo Vicente
- São Paulo State University (UNESP), School of Sciences and Engineering, Tupã, São Paulo, CEP 17602-496, Brazil
| | - Saulo Santesso Garrido
- São Paulo State University (UNESP), Institute of Chemistry, Araraquara, São Paulo, CEP 14801-902, Brazil
| | - Fernando Rogério Pavan
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, CEP 14800-903, Brazil.
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13
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Activity of ceftolozane/tazobactam against clinical isolates of Pseudomonas aeruginosa from patients in the Middle East and Africa - Study for Monitoring Antimicrobial Resistance Trends (SMART) 2017-2020. Int J Infect Dis 2022; 125:250-257. [PMID: 36244599 DOI: 10.1016/j.ijid.2022.10.014] [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: 06/28/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES We evaluated the activity of ceftolozane/tazobactam (C/T), and comparators against clinical Pseudomonas aeruginosa isolates collected for the global Study for Monitoring Antimicrobial Resistance Trends (SMART) surveillance program in ten countries in the Middle East and Africa to augment scarce standardized surveillance data in this region. METHODS Minimum inhibitory concentrations (MICs) were determined using Clinical and Laboratory Standards Institute broth microdilution and interpreted with European Committee on Antimicrobial Susceptibility Testing breakpoints. P. aeruginosa isolates testing with C/T MIC >4 mg/l or imipenem MIC >2 mg/l were screened for β-lactamase genes. RESULTS C/T was active against 91.4% and 87.0% of P. aeruginosa isolates from the Middle East and Africa, respectively (14-21 and 7-16 percentage points higher than most β-lactam comparators, respectively). Considerable variation in susceptibility was seen across countries, which largely correlated with the observed prevalence of carbapenemases and/or extended-spectrum β-lactamases. Differences across countries were smaller for C/T than for the β-lactam comparators, ranging from 81% C/T-susceptible among isolates from Jordan to 95% for Qatar. Among subsets resistant to meropenem, ceftazidime, or piperacillin/tazobactam, C/T maintained activity against 51-73% of isolates from the Middle East and against 27-54% from Africa (where metallo-β-lactamase and GES carbapenemase rates were higher). CONCLUSION Given the desirability of β-lactam use among clinicians, C/T represents an important option in the treatment of infections caused by P. aeruginosa.
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14
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Fileccia L, Wood T, Guthrie A, Ronoh C, Sleeth C, Kamath-Rayne BD, Liu C, Schaffzin JK, Rule AR. Comparison of Early-Onset Sepsis Risk-Stratification Algorithms in Neonates in a Kenyan Nursery. Hosp Pediatr 2022; 12:876-884. [PMID: 36127311 DOI: 10.1542/hpeds.2021-006228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND AND OBJECTIVES Risk stratification algorithms (RSAs) can reduce antibiotic duration (AD) and length of stay (LOS) for early-onset sepsis (EOS). Because of higher EOS and antibiotic resistance rates and limited laboratory capacity, RSA implementation may benefit low- and middle-income countries (LMIC). Our objective was to compare the impact of 4 RSAs on AD and LOS in an LMIC nursery. METHOD Neonates <5 days of age admitted for presumed sepsis to a Kenyan referral hospital in 2019 (n = 262) were evaluated by using 4 RSAs, including the current local sepsis protocol ("local RSA"), a simplified local protocol ("simple RSA"), an existing categorical RSA that uses infant clinical examination and maternal risk factors (CE-M RSA) clinical assessment, and the World Health Organization's Integrated Management of Childhood Illness guideline. For each RSA, a neonate was classified as at high, moderate, or low EOS risk. We used к coefficients to evaluate the agreement between RSAs and McNemar's test for the direction of disagreement. We used the Wilcoxon rank test for differences in observed and predicted median AD and LOS. RESULTS Local and simple RSAs overestimated EOS risk compared with CE-M RSA and the Integrated Management of Childhood Illness guideline. Compared with the observed value, CE-M RSA shortened AD by 2 days and simple RSA lengthened AD by 2 days. LOS was shortened by 4 days by using CE-M RSA and by 2 days by using the local RSA. CONCLUSIONS The local RSA overestimated EOS risk compared with CE-M RSA. If implemented fully, the local RSA may reduce LOS. Future studies will evaluate the prospective use of RSAs in LMICs with other interventions such as observation off antibiotics, biomarkers, and bundled implementation.
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Affiliation(s)
| | - Tristan Wood
- University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Alyssa Guthrie
- Division of Infectious Disease.,University of Cincinnati College of Medicine, Cincinnati, Ohio
| | | | | | - Beena D Kamath-Rayne
- Global Child Health and Life Support, American Academy of Pediatrics, Itasca, Illinois; and
| | | | - Joshua K Schaffzin
- Division of Infectious Disease.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Amy Rl Rule
- Perinatal Institute and Division of Hospital Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,University of Cincinnati College of Medicine, Cincinnati, Ohio
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15
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Villinger D, Schultze TG, Musyoki VM, Inwani I, Aluvaala J, Okutoyi L, Ziegler AH, Wieters I, Stephan C, Museve B, Kempf VAJ, Masika M. Genomic transmission analysis of multidrug-resistant Gram-negative bacteria within a newborn unit of a Kenyan tertiary hospital: A four-month prospective colonization study. Front Cell Infect Microbiol 2022; 12:892126. [PMID: 36093198 PMCID: PMC9452910 DOI: 10.3389/fcimb.2022.892126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/05/2022] [Indexed: 11/23/2022] Open
Abstract
Objective Multidrug-resistant organisms (MDRO), especially carbapenem-resistant organisms (CRO), represent a threat for newborns. This study investigates the colonization prevalence of these pathogens in a newborn unit at a Kenyan tertiary hospital in an integrated approach combining routine microbiology, whole genome sequencing (WGS) and hospital surveillance data. Methods The study was performed in the Kenyatta National Hospital (KNH) in 2019 over a four-month period and included 300 mother-baby pairs. A total of 1,097 swabs from newborns (weekly), mothers (once) and the hospital environment were taken. Routine clinical microbiology methods were applied for surveillance. Of the 288 detected MDRO, 160 isolates were analyzed for antimicrobial resistance genes and phylogenetic relatedness using whole genome sequencing (WGS) and bioinformatic analysis. Results In maternal vaginal swabs, MDRO detection rate was 15% (n=45/300), including 2% CRO (n=7/300). At admission, MDRO detection rate for neonates was 16% (n=48/300), including 3% CRO (n=8/300) with a threefold increase for MDRO (44%, n=97/218) and a fivefold increase for CRO (14%, n=29/218) until discharge. Among CRO, K. pneumoniae harboring blaNDM-1 (n=20) or blaNDM-5 (n=16) were most frequent. WGS analysis revealed 20 phylogenetically related transmission clusters (including five CRO clusters). In environmental samples, the MDRO detection rate was 11% (n=18/164), including 2% CRO (n=3/164). Conclusion Our study provides a snapshot of MDRO and CRO in a Kenyan NBU. Rather than a large outbreak scenario, data indicate several independent transmission events. The CRO rate among newborns attributed to the spread of NDM-type carbapenemases is worrisome.
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Affiliation(s)
- David Villinger
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Competence for Infection Control, Frankfurt, Hesse, Germany
| | - Tilman G. Schultze
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Competence for Infection Control, Frankfurt, Hesse, Germany
| | - Victor M. Musyoki
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Irene Inwani
- Pediatrics Department, Kenyatta National Hospital, Nairobi, Kenya
| | - Jalemba Aluvaala
- Pediatrics Department, Kenyatta National Hospital, Nairobi, Kenya
| | - Lydia Okutoyi
- Quality Health Department, Kenyatta National Hospital, Nairobi, Kenya
| | - Anna-Henriette Ziegler
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
| | - Imke Wieters
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- Center of Internal Medicine/Infectious Diseases Unit, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
| | - Christoph Stephan
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- Center of Internal Medicine/Infectious Diseases Unit, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
| | - Beatrice Museve
- Department of Laboratory Medicine, Kenyatta National Hospital, Nairobi, Kenya
| | - Volkhard A. J. Kempf
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Competence for Infection Control, Frankfurt, Hesse, Germany
- *Correspondence: Volkhard A. J. Kempf, ; Moses Masika,
| | - Moses Masika
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- *Correspondence: Volkhard A. J. Kempf, ; Moses Masika,
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16
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Thapa A, Upreti MK, Bimali NK, Shrestha B, Sah AK, Nepal K, Dhungel B, Adhikari S, Adhikari N, Lekhak B, Rijal KR. Detection of NDM Variants ( bla NDM-1, bla NDM-2, bla NDM-3) from Carbapenem-Resistant Escherichia coli and Klebsiella pneumoniae: First Report from Nepal. Infect Drug Resist 2022; 15:4419-4434. [PMID: 35983298 PMCID: PMC9379106 DOI: 10.2147/idr.s369934] [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: 04/09/2022] [Accepted: 07/13/2022] [Indexed: 11/25/2022] Open
Abstract
Background Increasing burden of carbapenem resistance among Enterobacterales is attributable to their ability to produce carbapenemase enzymes like metallo-beta-lactamase (MBL), Klebsiella pneumoniae carbapenemase (KPC), and OXA-type. This study aimed to determine the prevalence of carbapenemases and MBL genes ((blaNDM-1,blaNDM-1 and blaNDM-3) among E. coli and K. pneumoniae isolates. Methods A total of 2474 urine samples collected during the study period (July–December 2017) were processed at the microbiology laboratory of Kathmandu Model Hospital, Kathmandu. Isolates of E. coli and K. pneumoniae were processed for antimicrobial susceptibility testing (AST) by disc diffusion method. Carbapenem-resistant isolates were subjected to Modified Hodge Test (MHT) for phenotypic confirmation, and inhibitor-based combined disc tests for the differentiation of carbapenemase (MBL and KPC). MBL-producing isolates were screened for NDM genes by polymerase chain reaction (PCR). Results Of the total urine samples processed, 19.5% (483/2474) showed the bacterial growth. E. coli (72.6%; 351/483) was the predominant isolate followed by K. pneumoniae (12.6%; 61/483). In AST, 4.4% (18/412) isolates of E. coli (15/351) and K. pneumonia (3/61) showed resistance towards carbapenems, while 1.7% (7/412) of the isolates was confirmed as carbapenem-resistant in MHT. In this study, all (3/3) the isolates of K. pneumoniae were KPC-producers, whereas 66.7% (10/15), 20% (3/15) and 13.3% (2/15) of the E. coli isolates were MBL, KPC and MBL/KPC (both)-producers, respectively. In PCR assay, 80% (8/10), 90% (9/10) and 100% (10/10) of the isolates were positive for blaNDM-1, blaNDM-2 and blaNDM-3, respectively. Conclusion Presence of NDM genes among carbapenemase-producing isolates is indicative of potential spread of drug-resistant variants. This study recommends the implementation of molecular diagnostic facilities in clinical settings for proper infection control, which can optimize the treatment therapies, and curb the emergence and spread of drug-resistant pathogens.
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Affiliation(s)
- Anisha Thapa
- Department of Microbiology, Golden Gate International College, Kathmandu, Nepal
| | - Milan Kumar Upreti
- Department of Microbiology, Golden Gate International College, Kathmandu, Nepal
| | - Nabin Kishor Bimali
- Department of Microbiology, Golden Gate International College, Kathmandu, Nepal
| | | | - Anil Kumar Sah
- Annapurna Neurological Institute and Allied Sciences, Kathmandu, Nepal
| | - Krishus Nepal
- Department of Microbiology, Golden Gate International College, Kathmandu, Nepal
| | - Binod Dhungel
- Central Department of Microbiology, Tribhuvan University, Kathmandu, Nepal
| | - Sanjib Adhikari
- Central Department of Microbiology, Tribhuvan University, Kathmandu, Nepal
| | - Nabaraj Adhikari
- Central Department of Microbiology, Tribhuvan University, Kathmandu, Nepal
| | - Binod Lekhak
- Department of Microbiology, Golden Gate International College, Kathmandu, Nepal.,Central Department of Microbiology, Tribhuvan University, Kathmandu, Nepal
| | - Komal Raj Rijal
- Central Department of Microbiology, Tribhuvan University, Kathmandu, Nepal
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Hamed SM, Hussein AFA, Al-Agamy MH, Radwan HH, Zafer MM. Genetic Configuration of Genomic Resistance Islands in Acinetobacter baumannii Clinical Isolates From Egypt. Front Microbiol 2022; 13:878912. [PMID: 35935207 PMCID: PMC9353178 DOI: 10.3389/fmicb.2022.878912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
In Acinetobacter baumannii (A. baumannii), a wide repertoire of resistance genes is often carried within genomic resistance islands (RIs), particularly in high-risk global clones (GCs). As the first in Egypt, the current study aimed at exploring the diversity and genetic configuration of RIs in the clinical isolates of A. baumannii. For this purpose, draft genomes of 18 isolates were generated by Illumina sequencing. Disk diffusion susceptibility profiling revealed multidrug resistance (MDR) and extensive drug resistance (XDR) phenotypes in 27.7 and 72.2%, respectively. The highest susceptibility was noted for tigecycline (100.0%) followed by colistin (94.4%), for which an MIC50 of 0.25 μg/ml was recorded by the broth microdilution assay. Sequence typing (ST) showed that the majority of the isolates belonged to high-risk global clones (GC1, GC2, and GC9). A novel Oxford sequence type (ST2329) that also formed a novel clonal complex was submitted to the PubMLST database. A novel blaADC variant (blaADC−258) was also identified in strain M18 (ST85Pas/1089Oxf). In addition to a wide array of resistance determinants, whole-genome sequencing (WGS) disclosed at least nine configurations of genomic RIs distributed over 16/18 isolates. GC2 isolates accumulated the largest number of RIs (three RIs/isolate) followed by those that belong to GC1 (two RIs/isolate). In addition to Tn6022 (44.4%), the comM gene was interrupted by AbaR4 (5.5%) and three variants of A. baumanniigenomic resistance island 1(AbGRI)-type RIs (44.4%), including AbaR4b (16.6%) and two novel configurations of AbGRI1-like RIs (22.2%). Three of which (AbaR4, AbaR4b, and AbGRI1-like-2) carried blaOXA−23 within Tn2006. With less abundance (38.8%), IS26-bound RIs were detected exclusively in GC2 isolates. These included a short version of AbGRI2 (AbGRI2-15) carrying the genes blaTEM−1 and aphA1 and two variants of AbGRI3 RIs carrying up to seven resistance genes [mphE-msrE-armA-sul1-aadA1-catB8-aacA4]. Confined to GC1 (22.2%), sulfonamide resistance was acquired by an ISAba1 bracketed GIsul2 RI. An additional RI (RI-PER-7) was also identified on a plasmid carried by strain M03. Among others, RI-PER-7 carried the resistance genes armA and blaPER−7. Here, we provided a closer view of the diversity and genetic organization of RIs carried by a previously unexplored population of A. baumannii.
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Affiliation(s)
- Samira M. Hamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Amira F. A. Hussein
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed H. Al-Agamy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Hesham H. Radwan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mai M. Zafer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ahram Canadian University, Cairo, Egypt
- *Correspondence: Mai M. Zafer
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Kariuki S, Kering K, Wairimu C, Onsare R, Mbae C. Antimicrobial Resistance Rates and Surveillance in Sub-Saharan Africa: Where Are We Now? Infect Drug Resist 2022; 15:3589-3609. [PMID: 35837538 PMCID: PMC9273632 DOI: 10.2147/idr.s342753] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/16/2022] [Indexed: 01/03/2023] Open
Abstract
Introduction Although antimicrobials have traditionally been used to treat infections and improve health outcomes, resistance to commonly used antimicrobials has posed a major challenge. An estimated 700,000 deaths occur globally every year as a result of infections caused by antimicrobial-resistant pathogens. Antimicrobial resistance (AMR) also contributes directly to the decline in the global economy. In 2019, sub-Saharan Africa (SSA) had the highest mortality rate (23.5 deaths per 100,000) attributable to AMR compared to other regions. Methods We searched PubMed for articles relevant to AMR in pathogens in the WHO-GLASS list and in other infections of local importance in SSA. In this review, we focused on AMR rates and surveillance of AMR for these priority pathogens and some of the most encountered pathogens of public health significance. In addition, we reviewed the implementation of national action plans to mitigate against AMR in countries in SSA. Results and Discussion The SSA region is disproportionately affected by AMR, in part owing to the prevailing high levels of poverty, which result in a high burden of infectious diseases, poor regulation of antimicrobial use, and a lack of alternatives to ineffective antimicrobials. The global action plan as a strategy for prevention and combating AMR has been adopted by most countries, but fewer countries are able to fully implement country-specific action plans, and several challenges exist in many settings. Conclusion A concerted One Health approach will be required to ramp up implementation of action plans in the region. In addition to AMR surveillance, effective implementation of infection prevention and control, water, sanitation, and hygiene, and antimicrobial stewardship programs will be key cost-effective strategies in helping to tackle AMR.
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Affiliation(s)
- Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya,Correspondence: Samuel Kariuki, Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya, Email
| | - Kelvin Kering
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Celestine Wairimu
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Robert Onsare
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Cecilia Mbae
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
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Research Updates of Plasmid-Mediated Aminoglycoside Resistance 16S rRNA Methyltransferase. Antibiotics (Basel) 2022; 11:antibiotics11070906. [PMID: 35884160 PMCID: PMC9311965 DOI: 10.3390/antibiotics11070906] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 01/27/2023] Open
Abstract
With the wide spread of multidrug-resistant bacteria, a variety of aminoglycosides have been used in clinical practice as one of the effective options for antimicrobial combinations. However, in recent years, the emergence of high-level resistance against pan-aminoglycosides has worsened the status of antimicrobial resistance, so the production of 16S rRNA methyltransferase (16S-RMTase) should not be ignored as one of the most important resistance mechanisms. What is more, on account of transferable plasmids, the horizontal transfer of resistance genes between pathogens becomes easier and more widespread, which brings challenges to the treatment of infectious diseases and infection control of drug-resistant bacteria. In this review, we will make a presentation on the prevalence and genetic environment of 16S-RMTase encoding genes that lead to high-level resistance to aminoglycosides.
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Muraya A, Kyany’a C, Kiyaga S, Smith HJ, Kibet C, Martin MJ, Kimani J, Musila L. Antimicrobial Resistance and Virulence Characteristics of Klebsiella pneumoniae Isolates in Kenya by Whole-Genome Sequencing. Pathogens 2022; 11:545. [PMID: 35631066 PMCID: PMC9144577 DOI: 10.3390/pathogens11050545] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Klebsiella pneumoniae is a globally significant opportunistic pathogen causing healthcare-associated and community-acquired infections. This study examined the epidemiology and the distribution of resistance and virulence genes in clinical K. pneumoniae strains in Kenya. A total of 89 K. pneumoniae isolates were collected over six years from five counties in Kenya and were analyzed using whole-genome sequencing and bioinformatics. These isolates were obtained from community-acquired (62/89) and healthcare-associated infections (21/89), and from the hospital environment (6/89). Genetic analysis revealed the presence of blaNDM-1 and blaOXA-181 carbapenemase genes and the armA and rmtF genes known to confer pan-aminoglycoside resistance. The most abundant extended-spectrum beta-lactamase genes identified were blaCTX-M-15 (36/89), blaTEM (35/89), and blaOXA (18/89). In addition, one isolate had a mobile colistin resistance gene (mcr-8). Fluoroquinolone resistance-conferring mutations in gyrA and parC genes were also observed. The most notable virulence factors were those associated with hyper-virulence (rmpA/A2 and magA), yersiniabactin (ybt), salmochelin (iro), and aerobactin (iuc and iutA). A total of 38 distinct sequence types were identified, including known global lineages ST14, ST15, ST147, and ST307, and a regional clone ST17 implicated in regional outbreaks. In addition, this study genetically characterized two potential hypervirulent isolates and two community-acquired ST147 high-risk clones that contained carbapenemase genes, yersiniabactin, and other multidrug resistance genes. These results demonstrate that the resistome and virulome of Kenyan clinical and hospital environmental K. pneumoniae isolates are diverse. The reservoir of high-risk clones capable of spreading resistance, and virulence factors have the potential to cause unmanageable infection outbreaks with high morbidity and mortality.
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Affiliation(s)
- Angela Muraya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya; (A.M.); (C.K.); (J.K.)
| | - Cecilia Kyany’a
- United States Army Medical Research Directorate-Africa, Village Market, Nairobi P.O. Box 606-00621, Kenya; (C.K.); (H.J.S.)
- Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya
| | - Shahiid Kiyaga
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala P.O. Box 7072, Uganda;
| | - Hunter J. Smith
- United States Army Medical Research Directorate-Africa, Village Market, Nairobi P.O. Box 606-00621, Kenya; (C.K.); (H.J.S.)
| | - Caleb Kibet
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya; (A.M.); (C.K.); (J.K.)
- International Center for Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Melissa J. Martin
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA;
| | - Josephine Kimani
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya; (A.M.); (C.K.); (J.K.)
| | - Lillian Musila
- United States Army Medical Research Directorate-Africa, Village Market, Nairobi P.O. Box 606-00621, Kenya; (C.K.); (H.J.S.)
- Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya
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Yang WT, Chiu IJ, Huang YT, Liu PY. Comparative Genomics Revealed Fluoroquinolone Resistance Determinants and OmpF Deletion in Carbapenem-Resistant Escherichia coli. Front Microbiol 2022; 13:886428. [PMID: 35516434 PMCID: PMC9062692 DOI: 10.3389/fmicb.2022.886428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/22/2022] [Indexed: 12/13/2022] Open
Abstract
Escherichia coli (E. coli) is a major causative organism of complicated urinary tract infections, bloodstream infections, and pneumonia. With the widespread use of antimicrobial agents, the prevalence of carbapenem resistance in E. coli has been increasing with limited therapeutic options. Fluoroquinolone remains a choice in carbapenem-resistant E. coli (CREc) that were once susceptible to the drug. Despite robust studies on the fluoroquinolone-resistant mechanisms of E. coli, few studies focused specifically on the group of CREc. In this study, we used comparative genomics to identify the fluoroquinolone-resistant mechanisms of CREc and detected gyrA D87N mutation in all the fluoroquinolone-resistant and CREc. Moreover, to investigate the mechanism underlying non-carbapenemase-producing carbapenem-resistant E. coli, we targeted the complete genome sequences for in-depth analysis and found a deletion in OmpF (DEL264-269) that might contribute to carbapenem resistance, which has not been reported before. Further studies focusing on the impact of these mutations on the expression levels are warranted. We further investigate the MLST, serotype, fimH type, phylogroup, and clinical characteristics of the CREc. Combination analysis of clinical and genomic characteristics suggests the polyclonal and highly diverse nature of the CREc in Taiwan. This study provides an insight into the molecular epidemiology of CREc in Taiwan.
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Affiliation(s)
- Wan-Ting Yang
- Division of Infection, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - I-Ju Chiu
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan,Yao-Ting Huang
| | - Po-Yu Liu
- Division of Infection, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan,*Correspondence: Po-Yu Liu
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22
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Loucif L, Chelaghma W, Cherak Z, Bendjama E, Beroual F, Rolain JM. Detection of NDM-5 and MCR-1 antibiotic resistance encoding genes in Enterobacterales in long-distance migratory bird species Ciconia ciconia, Algeria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152861. [PMID: 34998768 DOI: 10.1016/j.scitotenv.2021.152861] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
β-lactams and colistin resistance in Enterobacterales is a global public health issue. In this study we aimed to investigate the occurrence and genetic determinants of Extended-Spectrum β-lactamases, carbapenemases and mcr-encoding-genes in Enterobacterales isolates recovered from the migratory bird species Ciconia ciconia in an Algerian city. A total of 62 faecal samples from white storks were collected. Samples were then subjected to selective isolation of β-lactams and colistin-resistant-Enterobacterales. The representative colonies were identified using Matrix-Assisted Laser Desorption-Ionisation Time-of-Flight Mass Spectrometry. Susceptibility testing was performed using the disk-diffusion method. ESBL, carbapenemases, and colistin resistance determinants were searched for by PCR and sequencing. The clonality relationships of the obtained isolates were investigated by multilocus sequence typing assays. Mating experiments were carried out to evaluate the transferability of the carbapenemase and mcr-genes. Forty-two isolates were identified as follows: Escherichia coli (n = 33), Klebsiella pneumoniae (n = 4), Proteus mirabilis (n = 4) and Citrobacter freundii (n = 1). Molecular analysis showed that twelve isolates carried the blaESBL genes alone, fifteen E. coli isolates were positive for the blaOXA-48 gene, six isolates were NDM-5-carriers (two P. mirabilis, two K. pneumoniae and two E. coli) and eight E. coli strains were positive for the mcr-1 gene. MLST results showed a high clonal diversity, where NDM-5-producing strains were assigned to two sequence types (ST167 for E. coli and ST198 for K. pneumoniae), whereas the mcr-1 positive E. coli isolates belonged to ST58, ST224, ST453, ST1286, ST2973, ST5542, ST9815 and the international high-risk resistant lineage ST101. To the best of our knowledge, this is the first report of blaNDM-5 gene in white storks and also the first describing the mcr-1 gene in white storks in Algeria. This study underlines the important role of migratory white storks as carriers of high-level drug-resistant bacteria, allowing their possible implication as indicators and sentinels for antimicrobial resistance surveillance.
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Affiliation(s)
- Lotfi Loucif
- Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Faculté des Sciences de la Nature et de la Vie, Université Batna 2, Batna 05000, Algeria.
| | - Widad Chelaghma
- Département de Biologie, Université Abou Bekr Belkaid-, Tlemcen 13000, Algeria
| | - Zineb Cherak
- Faculté des Sciences Exactes et des Sciences de la Nature et de la Vie, Université Mohamed Khider, Biskra 07000, Algeria
| | - Esma Bendjama
- Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Faculté des Sciences de la Nature et de la Vie, Université Batna 2, Batna 05000, Algeria
| | - Ferhat Beroual
- Département de Microbiologie et de Biochimie, Faculté des Sciences de la Nature et de la Vie, Université Batna 2, Batna 05000, Algeria
| | - Jean-Marc Rolain
- Aix Marseille Université, IRD, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France; IHU Méditerranée Infection, Marseille, France; Assistance Publique des Hôpitaux de Marseille, Marseille 13000, France
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23
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Pulusu CP, Manivannan B, Raman SS, Singh S, Khamari B, Lama M, Peketi ASK, Datta C, Prasad KN, Nagaraja V, Pradeep BE. Localized outbreaks of Pseudomonas aeruginosa belonging to international high-risk clones in a south Indian hospital. J Med Microbiol 2022; 71. [PMID: 35286253 DOI: 10.1099/jmm.0.001500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Pseudomonas aeruginosa is now considered as a major bacterial pathogen associated with hospital infections. Frequently, multidrug-resistant (MDR) and extensively drug-resistant (XDR) P. aeruginosa are being encountered. Unusual increase in the P. aeruginosa infections led to the suspicion of outbreaks in the urology ward and cardiothoracic and vascular surgery intensive care unit (CTVS-ICU).Hypothesis. We hypothesize that the localized outbreaks may have originated from environmental sources within the hospital premises. An alternative possibility is the transmission from a previously infected patient or hospital attendant. Understanding the drug-resistance profile and genome characteristics of these clinical samples would determine the likely source of infection and spread.Aim. To perform epidemiological and molecular investigations on the suspected outbreaks of P. aeruginosa in the study centre and identify potential sources of infection.Methodology. Fourteen drug-resistant P. aeruginosa isolated from patients of the urology ward, CTVS-ICU and tap waters collected during the suspected outbreaks were subjected to microbiological and genomic analysis. Comparative genome (CG) analysis of these 14 study genomes with 284 complete P. aeruginosa genomes was performed.Results. Multilocus sequence typing analysis revealed that the isolates belonged to five different sequence types (ST235, ST357, ST639, ST654 and ST1203) and clustered into three distinct groups while two CTVS-ICU isolates remained as singletons. Genome analysis distinguished that the outbreaks in the urology ward and CTVS-ICU are independent, epidemiologically unrelated to each other and with the tap-water isolates.Conclusion. This study highlights the presence of distinct, clonally unrelated, drug-resistant P. aeruginosa within a hospital setting. The genome analysis of the two localized outbreaks revealed their distinct genetic background and phylogenetically unrelated origin. Vigilant screening and effective implementation of infection control measures led to the successful containment of potential environmental reservoirs of P. aeruginosa within the premises.
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Affiliation(s)
- Chanakya Pachi Pulusu
- AMR Laboratory, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, India
| | - Bhavani Manivannan
- AMR Laboratory, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, India
| | - Sai Suguna Raman
- Infection Control, Sri Sathya Sai Institute of Higher Medical Sciences, Prasanthigram, India
| | - Sanjay Singh
- Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Balaram Khamari
- AMR Laboratory, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, India
| | - Manmath Lama
- AMR Laboratory, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, India
| | - Arun Sai Kumar Peketi
- AMR Laboratory, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, India
| | - Chandreyee Datta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Kashi Nath Prasad
- Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India.,Department of Microbiology, Apollo Medics Super Speciality Hospital, Lucknow, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, India
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24
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Kiyaga S, Kyany'a C, Muraya AW, Smith HJ, Mills EG, Kibet C, Mboowa G, Musila L. Genetic Diversity, Distribution, and Genomic Characterization of Antibiotic Resistance and Virulence of Clinical Pseudomonas aeruginosa Strains in Kenya. Front Microbiol 2022; 13:835403. [PMID: 35369511 PMCID: PMC8964364 DOI: 10.3389/fmicb.2022.835403] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/15/2022] [Indexed: 11/17/2022] Open
Abstract
Pseudomonas aeruginosa is a leading cause of nosocomial infections worldwide. It can produce a range of debilitating infections, have a propensity for developing antimicrobial resistance, and present with a variety of potent virulence factors. This study investigated the sequence types (ST), phenotypic antimicrobial susceptibility profiles, and resistance and virulence genes among clinical isolates from urinary tract and skin and soft tissue infections. Fifty-six P. aeruginosa clinical isolates were obtained from six medical centers across five counties in Kenya between 2015 and 2020. Whole-genome sequencing (WGS) was performed to conduct genomic characterization, sequence typing, and phylogenetic analysis of the isolates. Results showed the presence of globally distributed high-risk clones (ST244 and ST357), local high-risk clones (ST2025, ST455, and ST233), and a novel multidrug-resistant (MDR) clone carrying virulence genes (ST3674). Furthermore, 31% of the study isolates were found to be MDR with phenotypic resistance to a variety of antibiotics, including piperacillin (79%), ticarcillin-clavulanic acid (57%), meropenem (34%), levofloxacin (70%), and cefepime (32%). Several resistance genes were identified, including carbapenemases VIM-6 (ST1203) and NDM-1 (ST357), fluoroquinolone genes, crpP, and qnrVCi, while 14 and 22 different chromosomal mutations were detected in the gyrA and parC genes, respectively. All isolates contained at least three virulence genes. Among the virulence genes identified, phzB1 was the most abundant (50/56, 89%). About 21% (12/56) of the isolates had the exoU+/exoS- genotype, while 73% (41/56) of the isolates had the exoS+/exoU- genotype. This study also discovered 12 novel lineages of P. aeruginosa, of which one (ST3674) demonstrated both extensive antimicrobial resistance and the highest number of virulence genes (236/242, 98%). Although most high-risk clones were detected in Nairobi County, high-risk and clones of interest were found throughout the country, indicating the local spread of global epidemic clones and the emergence of new strains. Thus, this study illustrates the urgent need for coordinated local, regional, and international antimicrobial resistance surveillance efforts.
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Affiliation(s)
- Shahiid Kiyaga
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Cecilia Kyany'a
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
- Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Angela W. Muraya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Hunter J. Smith
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Emma G. Mills
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Caleb Kibet
- Molecular Biology and Bioinformatics Unit, International Center for Insect Physiology and Ecology, Nairobi, Kenya
| | - Gerald Mboowa
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Lillian Musila
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
- Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
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Clonal Dissemination of Plasmid-Mediated Carbapenem and Colistin Resistance in Refugees Living in Overcrowded Camps in North Lebanon. Antibiotics (Basel) 2021; 10:antibiotics10121478. [PMID: 34943690 PMCID: PMC8698793 DOI: 10.3390/antibiotics10121478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 11/26/2022] Open
Abstract
Carbapenem and colistin-resistant bacteria represent a global public health problem. Refugees carrying these bacteria and living in inadequate shelters can spread these microorganisms. The aim of this study was to investigate the intestinal carriage of these bacteria in Syrian refugees in Lebanon. Between June and July 2019, 250 rectal swabs were collected from two refugee camps in North Lebanon. Swabs were cultured on different selective media. Antibiotic susceptibility testing was performed using the disk diffusion method. Carbapenemase-encoding genes and mcr genes were investigated using real-time polymerase chain reaction (RT-PCR) and standard polymerase chain reaction (PCR). Epidemiological relatedness was studied using multilocus sequence typing (MLST). From 250 rectal swabs, 16 carbapenem-resistant, 5 colistin-resistant, and 4 colistin and carbapenem-resistant Enterobacteriaceae were isolated. The isolates exhibited multidrug-resistant phenotypes. Seven Klebsiella pneumoniae isolates harboured the blaOXA-48 gene, and in addition four K. pneumoniae had mutations in the two component systems pmrA/pmrB, phoP/phoQ and co-harboured the blaNDM-1 gene. Moreover, the blaNDM-1 gene was detected in six Escherichia coli and three Enterobacter cloacae isolates. The remaining five E. coli isolates harboured the mcr-1 gene. MLST results showed several sequence types, with a remarkable clonal dissemination. An urgent strategy needs to be adopted in order to avoid the spread of such resistance in highly crowded underserved communities.
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Lengliz S, Benlabidi S, Raddaoui A, Cheriet S, Ben Chehida N, Najar T, Abbassi MS. High occurrence of carbapenem-resistant Escherichia coli isolates from healthy rabbits (Oryctolagus cuniculus): first report of bla IMI and bla VIM type genes from livestock in Tunisia. Lett Appl Microbiol 2021; 73:708-717. [PMID: 34487562 DOI: 10.1111/lam.13558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/06/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022]
Abstract
We aimed to study the antibiotic susceptibility and possible occurrence of extended-spectrum beta-lactamases (ESBL)/carbapenemase-producing Escherichia coli isolates collected from rabbits in Tunisia. In all, 35 faecal samples from healthy rabbits were collected from one farm and E. coli were isolated from three media: antibiotic-free TBX agar, TBX+2 mg l-1 cefotaxime and TBX+1 mg l-1 imipenem. In total, 39 E. coli isolates were recovered; the majority showed resistance to at least one antibiotic and none was ESBL producer. Carbapenem resistance was detected in 16 isolates from either selective or un-selective media. Phenotypic methods used to detect carbapenemase production showed two positive isolates by Modified Hodge Test, six metallo-carbapenemase producers (Imipenem disc+EDTA) and all were temocillin resistant (possible OXA-48 carbapenemase). blaVIM and blaIMP type genes were detected in two and one isolates, respectively; one of them harboured both genes. Isolates contained common genes encoding resistance to sulphonamides (sul1, sul2), tetracycline (tetA, tetB, tetC) and fluoroquinolones (qnrS, aac(6')-Ib-cr). Class 1 and 2 integrons were detected in five and four isolates, respectively. These findings highlight the importance of rabbit production as reservoir of carbapenem-resistant E. coli and argument the first report of blaVIM and blaIMP genes in livestock in Tunisia.
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Affiliation(s)
- S Lengliz
- Institute of Veterinary Research of Tunisia, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Materials, Molecules and Application, Preparatory Institute for Scientific and Technical Studies LR11ES22, University of Carthage, Tunis, Tunisia
| | - S Benlabidi
- Institute of Veterinary Research of Tunisia, University of Tunis El Manar, Tunis, Tunisia
| | - A Raddaoui
- Laboratory Ward, National Bone Marrow Transplant Center, Tunis, Tunisia.,LR18ES39, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - S Cheriet
- Institute of Veterinary Research of Tunisia, University of Tunis El Manar, Tunis, Tunisia
| | - N Ben Chehida
- Institute of Veterinary Research of Tunisia, University of Tunis El Manar, Tunis, Tunisia
| | - T Najar
- Laboratory of Materials, Molecules and Application, Preparatory Institute for Scientific and Technical Studies LR11ES22, University of Carthage, Tunis, Tunisia.,Department of Animal Sciences, National Institute of Agronomy of Tunisia, University of Carthage, Tunis, Tunisia
| | - M S Abbassi
- Institute of Veterinary Research of Tunisia, University of Tunis El Manar, Tunis, Tunisia.,Faculty of Medicine of Tunis, Research Laboratory «Antimicrobial Resistance» LR99ES09, University of Tunis El Manar, Tunis, Tunisia
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27
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Zacharias N, Löckener I, Essert SM, Sib E, Bierbaum G, Kistemann T, Schreiber C. Antibiotic-Resistant Bacteria in Clams-A Study on Mussels in the River Rhine. Antibiotics (Basel) 2021; 10:antibiotics10050571. [PMID: 34066054 PMCID: PMC8150577 DOI: 10.3390/antibiotics10050571] [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: 03/30/2021] [Revised: 04/29/2021] [Accepted: 05/08/2021] [Indexed: 11/30/2022] Open
Abstract
Bacterial infections have been treated effectively by antibiotics since the discovery of penicillin in 1928. A worldwide increase in the use of antibiotics led to the emergence of antibiotic resistant strains in almost all bacterial pathogens, which complicates the treatment of infectious diseases. Antibiotic-resistant bacteria play an important role in increasing the risk associated with the usage of surface waters (e.g., irrigation, recreation) and the spread of the resistance genes. Many studies show that important pathogenic antibiotic-resistant bacteria can enter the environment by the discharge of sewage treatment plants and combined sewage overflow events. Mussels have successfully been used as bio-indicators of heavy metals, chemicals and parasites; they may also be efficient bio-indicators for viruses and bacteria. In this study an influence of the discharge of a sewage treatment plant could be shown in regard to the presence of E. coli in higher concentrations in the mussels downstream the treatment plant. Antibiotic-resistant bacteria, resistant against one or two classes of antibiotics and relevance for human health could be detected in the mussels at different sampling sites of the river Rhine. No multidrug-resistant bacteria could be isolated from the mussels, although they were found in samples of the surrounding water body.
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Affiliation(s)
- Nicole Zacharias
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany; (S.M.E.); (E.S.); (T.K.); (C.S.)
- Correspondence: ; Tel.: +49-(0)228-287-19874
| | - Iris Löckener
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany;
| | - Sarah M. Essert
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany; (S.M.E.); (E.S.); (T.K.); (C.S.)
| | - Esther Sib
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany; (S.M.E.); (E.S.); (T.K.); (C.S.)
| | - Gabriele Bierbaum
- Institute of Immunology, Medical Microbiology and Parasitology, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany;
| | - Thomas Kistemann
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany; (S.M.E.); (E.S.); (T.K.); (C.S.)
- Department of Geography, University of Bonn, Meckenheimer Allee 166, 53115 Bonn, Germany
| | - Christiane Schreiber
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany; (S.M.E.); (E.S.); (T.K.); (C.S.)
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