Tracking short-term changes in the genetic diversity and antimicrobial resistance of OXA-232-producing Klebsiella pneumoniae ST14 in clinical settings

Introduction. Patients with acute respiratory distress syndrome caused by coronavirus disease 2019 (COVID-19) are at risk for superadded infections, especially infections caused by multidrug resistant (MDR) pathogens. Before the COVID-19 pandemic, the prevalence of MDR infections, including infections caused by MDR Klebsiella pneumoniae (K. pneumoniae), was very high in Iran. This study is aimed at assessing the genetic diversity, antimicrobial resistance pattern, and biofilm formation in K. pneumoniae isolates obtained from patients with COVID-19 and ventilator-associated pneumonia (VAP) hospitalized in an intensive care unit (ICU) in Iran. Methods. In this cross-sectional study, seventy K. pneumoniae isolates were obtained from seventy patients with COVID-19 hospitalized in the ICU of Shahid Beheshti hospital, Kashan, Iran, from May to September, 2020. K. pneumoniae was detected through the ureD gene. Antimicrobial susceptibility testing was done using the Kirby-Bauer disc diffusion method, and biofilm was detected using the microtiter plate assay method. Genetic diversity was also analyzed through polymerase chain reaction based on enterobacterial repetitive intergenic consensus (ERIC-PCR). The BioNumerics software (v. 8.0, Applied Maths, Belgium) was used for analyzing the data and drawing dendrogram and minimum spanning tree. Findings. K. pneumoniae isolates had varying levels of resistance to antibiotics meropenem (80.4%), cefepime-aztreonam-piperacillin/tazobactam (70%), tobramycin (61.4%), ciprofloxacin (57.7%), gentamicin (55.7%), and imipenem (50%). Around 77.14% of isolates were MDR, and 42.8% of them formed biofilm. Genetic diversity analysis revealed 28 genotypes (E1–E28) and 74.28% of isolates were grouped into ten clusters (i.e., clusters A–J). Clusters were further categorized into three major clusters, i.e., clusters E, H, and J. Antimicrobial resistance to meropenem, tobramycin, gentamicin, and ciprofloxacin in cluster J was significantly higher than cluster H, denoting significant relationship between ERIC clusters and antimicrobial resistance. However, there was no significant difference among major clusters E, H, and J respecting biofilm formation. Conclusion. K. pneumoniae isolates obtained from patients with COVID-19 have high antimicrobial resistance, and 44.2% of them have genetic similarity and can be clustered in three major clusters. There is a significant difference among clusters respecting antimicrobial resistance.

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Antimicrobial resistance trends in Escherichia coli and Klebsiella pneumoniae urinary isolates from Switzerland over a 5-year period (2009-2014)

10.26226/morressier.56d6be74d462b80296c974ba ◽

2016 ◽

Author(s):

Veronica Zanichelli

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Klebsiella Pneumoniae ◽

Urinary Isolates

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Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants

Scientific Reports ◽

10.1038/s41598-021-88318-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Medelin Ocejo ◽

Beatriz Oporto ◽

José Luis Lavín ◽

Ana Hurtado

Keyword(s):

Genetic Diversity ◽

Antimicrobial Resistance ◽

Campylobacter Jejuni ◽

Resistance Genes ◽

Campylobacter Coli ◽

Whole Genome ◽

Northern Spain ◽

Sequence Alignments ◽

Phenotypic Data ◽

Wide Range

AbstractCampylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern. Considering the significant contribution of ruminants as reservoirs of resistant Campylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni and Campylobacter coli recovered from beef cattle, dairy cattle, and sheep in northern Spain. Genome analysis showed extensive genetic diversity that clearly separated both species. Resistance genotypes were identified by screening assembled sequences with BLASTn and ABRicate, and additional sequence alignments were performed to search for frameshift mutations and gene modifications. A high correlation was observed between phenotypic resistance to a given antimicrobial and the presence of the corresponding known resistance genes. Detailed sequence analysis allowed us to detect the recently described mosaic tet(O/M/O) gene in one C. coli, describe possible new alleles of blaOXA-61-like genes, and decipher the genetic context of aminoglycoside resistance genes, as well as the plasmid/chromosomal location of the different AMR genes and their implication for resistance spread. Updated resistance gene databases and detailed analysis of the matched open reading frames are needed to avoid errors when using WGS-based analysis pipelines for AMR detection in the absence of phenotypic data.

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Clinical and microbiological characteristics of nosocomial, healthcare-associated, and community-acquired Klebsiella pneumoniae infections in Guangzhou, China

Antimicrobial Resistance and Infection Control ◽

10.1186/s13756-021-00910-1 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Tingting Le ◽

Ling Wang ◽

Chaoying Zeng ◽

Leiwen Fu ◽

Zhihua Liu ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Klebsiella Pneumoniae ◽

Bacterial Resistance ◽

Empirical Therapy ◽

Clonal Diversity ◽

Extended Spectrum Beta Lactamase ◽

Microbiological Characteristics ◽

Carbapenemase Gene ◽

Cross Transmission ◽

Healthcare Associated

Abstract Background Klebsiella pneumoniae (K. pneumoniae) is a common pathogen associated with hospital and community-onset infections. This study aimed to compare the clinical and microbiological characteristics of nosocomial, healthcare-associated (HCA), and community-acquired (CA) K. pneumoniae infections. Methods Clinical data were extracted from electronic medical records and analyzed retrospectively. Antimicrobial susceptibility and extended-spectrum beta-lactamase (ESBL) production were determined for all identified strains. Carbapenemase and ESBL genes were amplified by PCR. Genotyping of carbapenem-resistant K. pneumoniae (CRKP) and ESBL-producing strains was performed by pulsed-field gel electrophoresis (PFGE). Results Of 379 K. pneumoniae infections, 98 (25.9%) were nosocomial, 195 (51.5%) were healthcare-associated, and 86 (22.6%) were community-acquired. Hematological malignancy (OR = 4.467), and hypertension (OR = 2.08) and cerebral vascular disease (OR = 2.486) were associated with nosocomial and HCA infections respectively, when compared to CA infections. Overall, the incidence of antimicrobial resistance for the majority of agents tested was similar between nosocomial and HCA infections (P > 0.05) and both groups had a higher incidence than CA infections (P < 0.05). Moreover, 95.1% (78/82) of CRKP strains were isolated from the nosocomial and HCA groups. The blaKPC was the most prevalent carbapenemase gene among CRKP strains (80.5%, 66/82). ESBL-producing strains were prevalent among nosocomial (40.8%), HCA (35.9%) and CA groups (24.4%). The blaCTX-M-9-group and blaCTX-M-1-group genes were predominant in nosocomial (65.0%) and CA strains (66.7%), respectively. PFGE results showed ESBL-producing and CRKP strains were genetically diverse. Identical PFGE profiles were observed among HCA and nosocomial strains. Conclusions Nosocomial and HCA K. pneumoniae infections presented similar clinical features and antimicrobial resistance, and both two types of infections were different to CA infections. CRKP and ESBL-producing strains were disseminated mainly in HCA and nosocomial groups, and showed a clonal diversity. The cross transmission of CRKP was existed among HCA and nosocomial patients. This finding suggests that similar empirical therapy should be considered for patients with nosocomial and HCA K. pneumoniae infections and bacterial resistance surveillance of these infections is necessary.

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Geographical information system and spatial–temporal statistics for monitoring infectious agents in hospital: a model using Klebsiella pneumoniae complex

Antimicrobial Resistance and Infection Control ◽

10.1186/s13756-021-00944-5 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Priscila Pinho da Silva ◽

Fabiola A. da Silva ◽

Caio Augusto Santos Rodrigues ◽

Leonardo Passos Souza ◽

Elisangela Martins de Lima ◽

...

Keyword(s):

Information System ◽

Antimicrobial Resistance ◽

Klebsiella Pneumoniae ◽

Tertiary Hospital ◽

Physical Structure ◽

Space Time ◽

Geographical Information ◽

Infectious Agents ◽

Healthcare Associated Infection ◽

Temporal Statistics

Abstract Background The emergence and spread of antimicrobial resistance and infectious agents have challenged hospitals in recent decades. Our aim was to investigate the circulation of target infectious agents using Geographic Information System (GIS) and spatial–temporal statistics to improve surveillance and control of healthcare-associated infection and of antimicrobial resistance (AMR), using Klebsiella pneumoniae complex as a model. Methods A retrospective study carried out in a 450-bed federal, tertiary hospital, located in Rio de Janeiro. All isolates of K. pneumoniae complex from clinical and surveillance cultures of hospitalized patients between 2014 and 2016, identified by the use of Vitek-2 system (BioMérieux), were extracted from the hospital's microbiology laboratory database. A basic scaled map of the hospital’s physical structure was created in AutoCAD and converted to QGis software (version 2.18). Thereafter, bacteria according to resistance profiles and patients with carbapenem-resistant K. pneumoniae (CRKp) complex were georeferenced by intensive and nonintensive care wards. Space–time permutation probability scan tests were used for cluster signals detection. Results Of the total 759 studied isolates, a significant increase in the resistance profile of K. pneumoniae complex was detected during the studied years. We also identified two space–time clusters affecting adult and paediatric patients harbouring CRKp complex on different floors, unnoticed by regular antimicrobial resistance surveillance. Conclusions In-hospital GIS with space–time statistical analysis can be applied in hospitals. This spatial methodology has the potential to expand and facilitate early detection of hospital outbreaks and may become a new tool in combating AMR or hospital-acquired infection.

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A case of neck abscess caused by rare hypervirulent Klebsiella pneumoniae, capsular type K20 and sequence type 420

Annals of Clinical Microbiology and Antimicrobials ◽

10.1186/s12941-021-00453-8 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

John Alexander McHardy ◽

Vathshalan Selvaganeshapillai ◽

Priya Khanna ◽

Ashley Michael Whittington ◽

Jane Turton ◽

...

Keyword(s):

Public Health ◽

Case Report ◽

Antimicrobial Resistance ◽

Klebsiella Pneumoniae ◽

East Asia ◽

South East Asia ◽

Neck Abscess ◽

Global Challenge ◽

Life Threatening ◽

The Uk

Abstract Background This case report describes a neck abscess caused by a strain of Hypervirulent Klebsiella pneumoniae in a middle aged man with diabetes without a history of travel to East and South East Asia. This case report is of notable significance as Hypervirulent Klebsiella pneumoniae neck abscesses are rarely seen in the UK and are very infrequently documented in individuals who have not first travelled to the high prevalence areas of East and South East Asia. Case presentation This case report describes a 53 year old diabetic man who contracted a Hypervirulent Klebsiella pneumoniae neck abscess which led to the development of sepsis. Klebsiella pneumoniae was cultured from blood cultures and fluid aspirated from the abscess grew the pathogen with same antimicrobial susceptibility. Hypervirulence was demonstrated after the samples were analysed, at the Antimicrobial Resistance and Healthcare Associated Infections Reference Unit Public Health England Colindale, and found to contain the K20 (rmp)A and rmpA2 virulence genes. Discussion Hypervirulent Klebsiella pneumoniae is a Gram-negative, encapsulated, non-motile bacillus notable for its ability to metastatically spread and cause potentially life threatening infections in otherwise healthy adults, but especially in those with diabetes. Genes responsible for the production of hyperviscous mucoid polysaccharide capsules and siderophores, such as those isolated in this case, enable the bacteria to more efficiently evade the hosts immune system and disseminate and invade surrounding and distant tissues. Data from Public Health England shows Hypervirulent Klebsiella pneumoniae are rare in the UK. A review of current literature also showed Hypervirulent Klebsiella pneumoniae almost exclusively occur in those who have traveled to East and South East Asia. Conclusions This case reported a rare Hypervirulent Klebsiella pneumoniae neck abscess outside of, and without travel to, East and South East Asia. This raises concerns about future, potentially life threatening, Hypervirulent Klebsiella pneumoniae infections becoming more widespread without the need for endemic travel. This concern is further exacerbated by the growing global challenge of antimicrobial resistance.

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Genetic diversity analyses of antimicrobial resistance genes in clinical Chryseobacterium meningosepticum isolated from Hefei, China

International Journal of Antimicrobial Agents ◽

10.1016/j.ijantimicag.2012.03.020 ◽

2012 ◽

Vol 40 (2) ◽

pp. 186-188 ◽

Cited By ~ 10

Author(s):

Xiang-Hong Lin ◽

Yuan-Hong Xu ◽

Xiao-Hong Sun ◽

Ying Huang ◽

Jia-Bing Li

Keyword(s):

Genetic Diversity ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Antimicrobial Resistance Genes

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Diversity and Prevailing Antimicrobial Resistance in Blood Stream Pathogens at NICU of a Tertiary Care Institute in Kolkata

Journal of Evidence Based Medicine and Healthcare ◽

10.18410/jebmh/2021/167 ◽

2021 ◽

Vol 8 (14) ◽

pp. 854-860

Author(s):

Nandita Pal ◽

Sanat Kumar Dolui ◽

Bhuban Majhi ◽

Manisha Das

Keyword(s):

Antimicrobial Resistance ◽

Blood Culture ◽

Klebsiella Pneumoniae ◽

Late Onset ◽

Tertiary Care ◽

Burkholderia Cepacia Complex ◽

Multi Drug Resistance ◽

Coagulase Negative Staphylococcus ◽

Neonatal Septicaemia ◽

Early Onset Sepsis

BACKGROUND Septicaemia is a leading cause of morbidity and mortality in neonates. Antimicrobial prescription for neonatal septicaemia (NS) should be wisely used depending on the regional spectra of infecting microbes and their antimicrobial resistance (AMR) patterns which vary over time, place and host factors. METHODS This was a descriptive cross-sectional study conducted from January 2017 to June 2017 among 102 cases of NS admitted in neonatal intensive care units (NICU). Demographic data of the concerned neonates was collected through a predesigned checklist. Blood collected from neonates was processed for culture and sepsis screen. Antimicrobial susceptibility testing was performed for the cultured isolates and phenotypic AMR patterns were observed. RESULTS Most of the studied neonates had subnormal birth weight (86). Blood culture showed predominance of gram-negative bacilli (GNB) among which Klebsiella pneumoniae was the most common followed by Burkholderia cepacia complex. Coagulase negative staphylococcus species (CoNS) was most numerous among the cultured gram-positive cocci (GPC). Candidemia of late onset was confirmed in 25 neonates. Early onset sepsis was predominantly caused by GNB (29 / 31) predominated by Klebsiella pneumoniae. Multi drug resistant (MDR) pathogens viz., extended spectrum beta-lactamase (ESBL) producing GNB, carbapenem resistant-GNB (CR-GNB) and methicillin resistant staphylococcus (MRS) phenotypes were notably prevalent. CONCLUSIONS Multidrug resistant microorganisms are notably prevalent in neonatal septicaemia. In clinically suspected very sick septicaemic neonates not showing much improvement with guideline-led empirical antimicrobial therapy, an early antibiogram guided change over to meropenem and amikacin or even to colistin in case of reported carbapenem resistance, is highly recommended. KEYWORDS Antimicrobial Resistance, Blood Culture, Multi Drug Resistance, Neonatal Septicaemia

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