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Cui J, Zhang Y, Li X, Ding Z, Kong Y, Yu Z, Li Z, Tong J, Liu Z, Yuan J. Antimicrobial resistance profiles and genome characteristics of Klebsiella isolated from the faeces of neonates in the neonatal intensive care unit. J Med Microbiol 2024; 73. [PMID: 39150452 PMCID: PMC11329266 DOI: 10.1099/jmm.0.001862] [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] [Indexed: 08/17/2024] Open
Abstract
Introduction. Klebsiella spp. are important bacteria that colonize the human intestine, especially in preterm infants; they can induce local and systemic disease under specific circumstances, including inflammatory bowel disease, necrotizing enterocolitis and colorectal cancer.Hypothesis. Klebsiella spp. colonized in the intestine of the neonates in the neonatal intensive care unit (NICU) may be associated with disease and antibiotic resistance, which will be hazardous to the children.Aim. Our aim was to know about the prevalence, antimicrobial resistance and genome characteristics of Klebsiella spp. in neonate carriers.Methodology. Genome sequencing and analysis, and antimicrobial susceptibility testing were mainly performed in this study.Results. The isolation rates of Klebsiella spp. strains were 3.7% (16/436) in 2014 and 4.3% (18/420) in 2021. Cases with intestinal-colonized Klebsiella spp. were mainly infants with low birth weights or those with pneumonia or hyperbilirubinemia. According to the core-pan genomic analysis, 34 stains showed gene polymorphism and a sequence type (ST) of an emerging high-risk clone (ST11). Eight strains (23.5%) were found to be resistant to 2 or more antibiotics, and 46 genes/gene families along with nine plasmids were identified that conferred resistance to antibiotics. In particular, the two strains were multidrug-resistant. Strain A1256 that is related to Klebsiella quasipneumoniae subsp. similipneumoniae was uncommon, carrying two plasmids similar to IncFII and IncX3 that included five antibiotic resistance genes.Conclusion. The prevention and control of neonatal Klebsiella spp. colonization in the NICU should be strengthened by paying increased attention to preventing antimicrobial resistance in neonates.
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Affiliation(s)
- Jinghua Cui
- Capital Institute of Pediatrics, Beijing 100020, PR China
| | - Yanan Zhang
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University & Beijing Maternal and Child Health Care Hospital, Beijing 100026, PR China
| | - Xiaoran Li
- 155th Hospital of Kaifeng, Kaifeng, Henan Province, 475003, PR China
| | - Zanbo Ding
- Capital Institute of Pediatrics, Beijing 100020, PR China
| | - Yiming Kong
- Capital Institute of Pediatrics, Beijing 100020, PR China
| | - Zihui Yu
- Capital Institute of Pediatrics, Beijing 100020, PR China
| | - Zhaona Li
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University & Beijing Maternal and Child Health Care Hospital, Beijing 100026, PR China
| | - Jingjing Tong
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University & Beijing Maternal and Child Health Care Hospital, Beijing 100026, PR China
| | - Zunjie Liu
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University & Beijing Maternal and Child Health Care Hospital, Beijing 100026, PR China
| | - Jing Yuan
- Capital Institute of Pediatrics, Beijing 100020, PR China
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Jones RT, Fagbohun IK, Spencer FI, Chen-Hussey V, Paris LA, Logan JG, Hiscox A. A review of Musca sorbens (Diptera: Muscidae) and Musca domestica behavior and responses to chemical and visual cues. JOURNAL OF MEDICAL ENTOMOLOGY 2024; 61:845-860. [PMID: 38795384 DOI: 10.1093/jme/tjae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/28/2024] [Accepted: 05/08/2024] [Indexed: 05/27/2024]
Abstract
Musca flies (Diptera: Muscidae) have been found culpable in the mechanical transmission of several infectious agents, including viruses, bacteria, protozoans, and helminths, particularly in low-income settings in tropical regions. In large numbers, these flies can negatively impact the health of communities and their livestock through the transmission of pathogens. In some parts of the world, Musca sorbens is of particular importance because it has been linked with the transmission of trachoma, a leading cause of preventable and irreversible blindness or visual impairment caused by Chlamydia trachomatis, but the contribution these flies make to trachoma transmission has not been quantified and even less is known for other pathogens. Current tools for control and monitoring of house flies remain fairly rudimentary and have focused on the use of environmental management, insecticides, traps, and sticky papers. Given that the behaviors of flies are triggered by chemical cues from their environment, monitoring approaches may be improved by focusing on those activities that are associated with nuisance behaviors or with potential pathogen transmission, and there are opportunities to improve fly control by exploiting behaviors toward semiochemicals that act as attractants or repellents. We review current knowledge on the odor and visual cues that affect the behavior of M. sorbens and Musca domestica, with the aim of better understanding how these can be exploited to support disease monitoring and guide the development of more effective control strategies.
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Affiliation(s)
- Robert T Jones
- Arctech Innovation, The Cube, Londoneast-uk Business and Technical Park, Yew Tree Avenue, Dagenham, UK
- Department of Disease Control, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | - Ifeoluwa K Fagbohun
- Arctech Innovation, The Cube, Londoneast-uk Business and Technical Park, Yew Tree Avenue, Dagenham, UK
| | - Freya I Spencer
- Arctech Innovation, The Cube, Londoneast-uk Business and Technical Park, Yew Tree Avenue, Dagenham, UK
| | - Vanessa Chen-Hussey
- Arctech Innovation, The Cube, Londoneast-uk Business and Technical Park, Yew Tree Avenue, Dagenham, UK
| | - Laura A Paris
- Arctech Innovation, The Cube, Londoneast-uk Business and Technical Park, Yew Tree Avenue, Dagenham, UK
| | - James G Logan
- Arctech Innovation, The Cube, Londoneast-uk Business and Technical Park, Yew Tree Avenue, Dagenham, UK
- Department of Disease Control, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | - Alexandra Hiscox
- Arctech Innovation, The Cube, Londoneast-uk Business and Technical Park, Yew Tree Avenue, Dagenham, UK
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Silva JTP, Santos FF, Valiatti TB, Valêncio A, Ribeiro ÁCDS, Oliveira LFV, Cayô R, Pignatari ACC, Gales AC. Unravelling the genomic characteristics of a Klebsiella quasipneumoniae clinical isolate carrying bla NDM-1. J Glob Antimicrob Resist 2024; 38:302-305. [PMID: 38852850 DOI: 10.1016/j.jgar.2024.05.022] [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: 10/05/2023] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/11/2024] Open
Abstract
OBJECTIVE Despite the increasing reports of blaNDM in Enterobacterales in Brazil, comprehensive whole genome sequencing (WGS) data remain scarce. To address this knowledge gap, our study focuses on the characterization of the genome of an New Delhi Metallo-β-lactamase (NDM)-1-producing Klebsiella quasipneumoniae subsp. quasipneumoniae (KQPN) clinical strain isolated in Brazil. METHODS The antimicrobial susceptibility profile of the A-73.113 strain was performed by agar dilution or broth microdilution following the Brazilian Antimicrobial Susceptibility Testing Committee/European Committee on Antimicrobial Susceptibility Testing recommendations. WGS was performed using the Illumina® NextSeq platform and the generated reads were assembled using the SPAdes software. The sequences obtained were submitted to the bioinformatics pipelines to determine the sequence type, resistome, plasmidome, and virulome. RESULTS The A-73.113 strain was identified as KQPN and was susceptible to polymyxins (MICs, ≤0.25 µg/mL), tigecycline (MIC, 0.5 µg/mL), ciprofloxacin (MIC, 0.5 µg/mL), and levofloxacin (MIC, 1 µg/mL). WGS analysis revealed the presence of genes conferring resistance to β-lactams (blaNDM-1, blaCTX-M-15, blaOXA-9, blaOKP-A-5, blaTEM-1), aminoglycosides [aph(3')-VI, aadA1, aac(6')-Ib], and fluoroquinolones (oqxAB, qnrS1, aac(6')-Ib-cr]. Additionally, the presence of the plasmid replicons Col(pHAD28), IncFIA(HI1), IncFIB(K) (pCAV1099-114), IncFIB(pQil), and IncFII(K), as well as virulence-encoding genes fimABCDEFGHIK (type 1 fimbria), pilW (type IV pili), iutA (aerobactin), entABCDEFS/fepABCDG/fes (Ent siderophores), iroE (salmochelin), and allABCDRS (allantoin utilization) was verified. Furthermore, we found that the A-73.113 strain belongs to ST1040. CONCLUSIONS Here we report the genomic characteristics of an NDM-1-producing KQPN ST1040 strain isolated from blood cultures in Brazil. These data will enhance our comprehension of how this species contributes to the acquisition and dissemination of blaNDM-1 in Brazilian nosocomial settings.
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Affiliation(s)
- Juliana Thalita P Silva
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Fernanda F Santos
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil.
| | - Tiago B Valiatti
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - André Valêncio
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Ághata Cardoso da Silva Ribeiro
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | | | - Rodrigo Cayô
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil; Universidade Federal de São Paulo (UNIFESP), Laboratório de Bacteriologia e Imunologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia, Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema SP, Brazil
| | - Antônio Carlos C Pignatari
- Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Ana Cristina Gales
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil; Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
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Zagui GS, Almeida OGGD, Moreira NC, Abichabki N, Machado GP, De Martinis ECP, Darini ALC, Andrade LN, Segura-Muñoz SI. A set of antibiotic-resistance mechanisms and virulence factors in GES-16-producing Klebsiella quasipneumoniae subsp. similipneumoniae from hospital wastewater revealed by whole-genome sequencing. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120645. [PMID: 36375580 DOI: 10.1016/j.envpol.2022.120645] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/20/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Klebsiella quasipneumoniae subsp. similipneumoniae has emerged as a human pathogen and sporadic isolates from non-clinical sources were reported. Here, we described the phenotypic- and genomic-characteristics of a multidrug-resistant (MDR) and potentially hypervirulent (MDR-hv) Klebsiella quasipneumoniae subsp. similipneumoniae (KqA1) isolated from hospital wastewater. The antibiotic susceptibility profile of KqA1 was investigated using disk-diffusion method, broth microdilution method, and agar dilution method, and the genetic characteristics of antimicrobial resistance, mobile genetics elements, and virulence were evaluated by genomic DNA sequencing on the Illumina® NovaSeq6000 platform as well as by bioinformatic analysis. Resistome analyses revealed the presence of genes related to resistance to β-lactams, aminoglycosides, quinolones, tetracyclines, sulfonamides, trimethoprim, chloramphenicol, macrolides, and fosfomycin. New genetic contexts to blaGES-16 (carbapenemase gene) and to fosA (fosfomycin resistance gene) were described. A set of mechanisms that can contribute to antibiotic resistance, commonly detected in Klebsiella spp., was also found including chromosomal mutations, efflux systems, proteins, and regulators. Moreover, KqA1 presented genes related to tolerance to metals (arsenic, copper, nickel, cobalt, magnesium, cadmium, zinc, tellurium, selenium) and to biocides (quaternary-ammonium compounds). The isolate was classified as potentially hypervirulent due to a wide range of virulence factors found associated to regulation, motility, biofilm, effector delivery systems, immune modulation, nutritional/metabolic factors, adherence, invasion, and competitive advantage. The occurrence of MDR-hv KqA1 in hospital wastewater points out how this environment matrix plays a crucial role in the maintenance and selection of critical bacterial pathogens. Regarding One Health perspective, it is evident the need for multidisciplinary implementation of control measures for antibiotic-resistant bacteria, not only in hospital settings but also in a general environmental context to mitigate the dissemination of MDR and hv bacteria.
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Affiliation(s)
| | | | | | - Nathália Abichabki
- School of Pharmaceuticals Sciences of Ribeirao Preto, University of Sao Paulo, Brazil
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Morgado S, Fonseca E, Vicente AC. Genomics of Klebsiella pneumoniae Species Complex Reveals the Circulation of High-Risk Multidrug-Resistant Pandemic Clones in Human, Animal, and Environmental Sources. Microorganisms 2022; 10:2281. [PMID: 36422351 PMCID: PMC9697336 DOI: 10.3390/microorganisms10112281] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/03/2023] Open
Abstract
The Klebsiella species present a remarkable genetic and ecological diversity, being ubiquitous in nature. In particular, the Klebsiella pneumoniae species complex (KpSC) has emerged as a major public health threat in the world, being an interesting model to assess the risk posed by strains recovered from animals and the environment to humans. We therefore performed a genomic surveillance analysis of the KpSC using every public genome in Brazil, aiming to show their local and global relationships, and the connectivity of antibiotic resistance and virulence considering human, animal, and environmental sources. The 390 genomes from distinct sources encompassed the K. pneumoniae, Klebsiella quasipneumoniae subsp. quasipneumoniae, Klebsiella quasipneumoniae subsp. similipneumoniae, Klebsiella variicola subsp. variicola, Klebsiella variicola subsp. tropica, and Klebsiella grimontii species and subspecies. K. pneumoniae harbored dozens of antibiotic resistance genes, while most of the genomes belong to the high-risk pandemic CC258 occurring in humans, animals, and the environment. In K. pneumoniae ST11, a high prevalence of the virulence determinants yersiniabactin, colibactin, and T6SS was revealed in association with multi-drug resistance (MDR), including carbapenem resistance. A diversity of resistance genes is carried by plasmids, some shared between strains from different STs, regions, and sources. Therefore, here were revealed some factors driving the success of KpSC as a pathogen.
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Affiliation(s)
| | | | - Ana Carolina Vicente
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute, Av. Brasil, 4365—Manguinhos, Rio de Janeiro 21040-900, Brazil
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