New antibiotic resistance genes associated with CTX-M plasmids from uropathogenic Nigerian Klebsiella pneumoniae

ABSTRACTThere is a global emergence of multidrug-resistant (MDR) strains ofKlebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. While the epidemiology ofK. pneumoniaestrains and occurrences of specific antibiotic resistance genes, such as plasmid-borne extended-spectrum β-lactamases (ESBLs), have been extensively studied, only four complete genomes ofK. pneumoniaeare available. To better understand the multidrug resistance factors inK. pneumoniae, we determined by pyrosequencing the nearly complete genome DNA sequences of two strains with disparate antibiotic resistance profiles, broadly drug-susceptible strain JH1 and strain 1162281, which is resistant to multiple clinically used antibiotics, including extended-spectrum β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, and sulfamethoxazoles. Comparative genomic analysis of JH1, 1162281, and other publishedK. pneumoniaegenomes revealed a core set of 3,631 conserved orthologous proteins, which were used for reconstruction of whole-genome phylogenetic trees. The close evolutionary relationship between JH1 and 1162281 relative to otherK. pneumoniaestrains suggests that a large component of the genetic and phenotypic diversity of clinical isolates is due to horizontal gene transfer. Using curated lists of over 400 antibiotic resistance genes, we identified all of the elements that differentiated the antibiotic profile of MDR strain 1162281 from that of susceptible strain JH1, such as the presence of additional efflux pumps, ESBLs, and multiple mechanisms of fluoroquinolone resistance. Our study adds new and significant DNA sequence data onK. pneumoniaestrains and demonstrates the value of whole-genome sequencing in characterizing multidrug resistance in clinical isolates.

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Cohorting KPC+ Klebsiella pneumoniae (KPC-Kp)–positive patients: A genomic exposé of cross-colonization hazards in a long-term acute-care hospital (LTACH)

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2020.261 ◽

2020 ◽

Vol 41 (10) ◽

pp. 1162-1168

Author(s):

Shawn E. Hawken ◽

Mary K. Hayden ◽

Karen Lolans ◽

Rachel D. Yelin ◽

Robert A. Weinstein ◽

...

Keyword(s):

Antibiotic Resistance ◽

Klebsiella Pneumoniae ◽

Acute Care ◽

Resistance Genes ◽

Acute Care Hospital ◽

Antibiotic Resistance Genes ◽

Care Hospital ◽

Cross Transmission ◽

The Impact

AbstractObjective:Cohorting patients who are colonized or infected with multidrug-resistant organisms (MDROs) protects uncolonized patients from acquiring MDROs in healthcare settings. The potential for cross transmission within the cohort and the possibility of colonized patients acquiring secondary isolates with additional antibiotic resistance traits is often neglected. We searched for evidence of cross transmission of KPC+ Klebsiella pneumoniae (KPC-Kp) colonization among cohorted patients in a long-term acute-care hospital (LTACH), and we evaluated the impact of secondary acquisitions on resistance potential.Design:Genomic epidemiological investigation.Setting:A high-prevalence LTACH during a bundled intervention that included cohorting KPC-Kp–positive patients.Methods:Whole-genome sequencing (WGS) and location data were analyzed to identify potential cases of cross transmission between cohorted patients.Results:Secondary KPC-Kp isolates from 19 of 28 admission-positive patients were more closely related to another patient’s isolate than to their own admission isolate. Of these 19 cases, 14 showed strong genomic evidence for cross transmission (<10 single nucleotide variants or SNVs), and most of these patients occupied shared cohort floors (12 patients) or rooms (4 patients) at the same time. Of the 14 patients with strong genomic evidence of acquisition, 12 acquired antibiotic resistance genes not found in their primary isolates.Conclusions:Acquisition of secondary KPC-Kp isolates carrying distinct antibiotic resistance genes was detected in nearly half of cohorted patients. These results highlight the importance of healthcare provider adherence to infection prevention protocols within cohort locations, and they indicate the need for future studies to assess whether multiple-strain acquisition increases risk of adverse patient outcomes.

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Differences in Resolution of mwr-Containing Plasmid Dimers Mediated by the Klebsiella pneumoniae and Escherichia coli XerC Recombinases: Potential Implications in Dissemination of Antibiotic Resistance Genes

Journal of Bacteriology ◽

10.1128/jb.188.8.2812-2820.2006 ◽

2006 ◽

Vol 188 (8) ◽

pp. 2812-2820 ◽

Cited By ~ 15

Author(s):

Duyen Bui ◽

Judianne Ramiscal ◽

Sonia Trigueros ◽

Jason S. Newmark ◽

Albert Do ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Klebsiella Pneumoniae ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Recombination Site ◽

Lower Efficiency ◽

E Coli ◽

N Terminus ◽

Α Helix

ABSTRACT Xer-mediated dimer resolution at the mwr site of the multiresistance plasmid pJHCMW1 is osmoregulated in Escherichia coli containing either the Escherichia coli Xer recombination machinery or Xer recombination elements from K. pneumoniae. In the presence of K. pneumoniae XerC (XerCKp), the efficiency of recombination is lower than that in the presence of the E. coli XerC (XerCEc) and the level of dimer resolution is insufficient to stabilize the plasmid, even at low osmolarity. This lower efficiency of recombination at mwr is observed in the presence of E. coli or K. pneumoniae XerD proteins. Mutagenesis experiments identified a region near the N terminus of XerCKp responsible for the lower level of recombination catalyzed by XerCKp at mwr. This region encompasses the second half of the predicted α-helix B and the beginning of the predicted α-helix C. The efficiencies of recombination at other sites such as dif or cer in the presence of XerCKp or XerCEc are comparable. Therefore, XerCKp is an active recombinase whose action is impaired on the mwr recombination site. This characteristic may result in restriction of the host range of plasmids carrying this site, a phenomenon that may have important implications in the dissemination of antibiotic resistance genes.

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Multidrug-Resistant Klebsiella pneumoniae Isolated from Farm Environments and Retail Products in Oklahoma

Journal of Food Protection ◽

10.4315/0362-028x-68.10.2022 ◽

2005 ◽

Vol 68 (10) ◽

pp. 2022-2029 ◽

Cited By ~ 46

Author(s):

SHIN-HEE KIM ◽

CHENG-I WEI ◽

YWH-MIN TZOU ◽

HAEJUNG AN

Keyword(s):

Antibiotic Resistance ◽

Klebsiella Pneumoniae ◽

Resistance Genes ◽

Meat Products ◽

Antibiotic Resistance Genes ◽

Enteric Bacteria ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Gene Encoding ◽

Class 1

Multidrug-resistant enteric bacteria were isolated from turkey, cattle, and chicken farms and retail meat products in Oklahoma. Among the isolated species, multidrug-resistant Klebsiella pneumoniae was prevalently isolated from most of the collected samples. Therefore, a total of 132 isolates of K. pneumoniae were characterized to understand their potential roles in the dissemination of antibiotic-resistance genes in the food chains. Multidrug-resistant K. pneumoniae was most frequently recovered from a turkey farm and ground turkey products among the tested samples. All isolates were resistant to ampicillin, tetracycline, streptomycin, gentamycin, and kanamycin. Class 1 integrons located in plasmids were identified as a common carrier of the aadA1 gene, encoding resistance to streptomycin and spectinomycin. Production of β-lactamase in the K. pneumoniae isolates played a major role in the resistance to β-lactam agents. Most isolates (96%) possessed blaSHV-1. Five strains were able to express both SHV-11 (pI 6.2) and TEM-1 (pI 5.2) β-lactamase. Transfer of these antibiotic-resistance genes to Escherichia coli was demonstrated by transconjugation. The bacterial genomic DNA restriction patterns by pulsed-field gel electrophoresis showed that the same clones of multidrug-resistant K. pneumoniae remained in feathers, feed, feces, and drinking water in turkey environments, indicating the possible dissemination of antibiotic-resistance genes in the ecosystem and cross-contamination of antibiotic-resistant bacteria during processing and distribution of products.

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Cohorting KPC+ Klebsiella pneumoniae (KPC-Kp) positive patients – a genomic exposé of cross-colonization hazards in a long-term acute care hospital (LTACH)

10.1101/2020.02.07.20020669 ◽

2020 ◽

Author(s):

Shawn E. Hawken ◽

Mary K. Hayden ◽

Karen Lolans ◽

Rachel D. Yelin ◽

Robert A. Weinstein ◽

...

Keyword(s):

Antibiotic Resistance ◽

Klebsiella Pneumoniae ◽

Acute Care ◽

Resistance Genes ◽

Acute Care Hospital ◽

Antibiotic Resistance Genes ◽

Care Hospital ◽

Cross Transmission ◽

The Impact

AbstractObjectiveCohorting patients who are colonized or infected with multidrug-resistant organisms (MDROs) has been demonstrated to protect uncolonized patients from acquiring MDROs in healthcare settings. A neglected aspect of cohorting is the potential for cross-transmission within the cohort and the possibility of colonized patients acquiring secondary isolates with additional antibiotic resistance traits. We searched for evidence of cross-transmission of KPC+ Klebsiella pneumoniae (KPC-Kp) colonization among cohorted patients in a long-term acute care hospital (LTACH), and evaluated the impact of secondary acquisitions on resistance potential.DesignGenomic epidemiological investigationSettingA high-prevalence LTACH during a bundled intervention that included cohorting KPC-Kp-positive patients.MethodsWhole-genome sequencing (WGS) and location data were analyzed to identify potential cases of cross-transmission between cohorted patients.ResultsSecondary KPC-Kp isolates from 19 of 28 admission-positive patients were more closely related to another patient’s isolate than to their own admission isolate. In 14 of these 19 cases there was strong genomic evidence for cross-transmission (<10 SNVs) and the majority of these patients occupied shared cohort floors (12 cases) or rooms (5 cases) at the same time. Of the 14 patients with strong genomic evidence of acquisition, 12 acquired antibiotic resistance genes not found in their primary isolates.ConclusionsAcquisition of secondary KPC-Kp isolates carrying distinct antibiotic resistance genes was detected in nearly half of cohorted patients. These results highlight the importance of healthcare provider adherence to infection prevention protocols within cohort locations, and motivate future studies to assess whether multiple-strain acquisition increases risk of adverse patient outcomes.

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Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dky121 ◽

2018 ◽

Vol 73 (7) ◽

pp. 1796-1803 ◽

Cited By ~ 19

Author(s):

Patricia J Simner ◽

Annukka A R Antar ◽

Stephanie Hao ◽

James Gurtowski ◽

Pranita D Tamma ◽

...

Keyword(s):

Antibiotic Resistance ◽

Klebsiella Pneumoniae ◽

Resistance Genes ◽

Antibiotic Resistance Genes

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Molecular Characterization of a Multidrug-Resistant Klebsiella pneumoniae Strain R46 Isolated from a Rabbit

International Journal of Genomics ◽

10.1155/2019/5459190 ◽

2019 ◽

Vol 2019 ◽

pp. 1-12 ◽

Cited By ~ 4

Author(s):

Fei Wu ◽

Yuanyuan Ying ◽

Min Yin ◽

Yi Jiang ◽

Chongyang Wu ◽

...

Keyword(s):

Antibiotic Resistance ◽

Klebsiella Pneumoniae ◽

Resistance Gene ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Molecular Structures ◽

Comparative Genomic ◽

Animal Pathogens ◽

Resistance Plasmids

To investigate the mechanisms of multiple resistance and the horizontal transfer of resistance genes in animal pathogens, we characterized the molecular structures of the resistance gene-related sequences in a multidrug-resistant Klebsiella pneumoniae strain R46 isolated from a rabbit. Molecular cloning was performed to clone the resistance genes, and minimum inhibitory concentrations (MICs) were measured to determine the resistance characteristics of the cloned genes and related strains. A conjugation experiment was conducted to assess the transferability of the resistance plasmids. Sequencing and comparative genomic methods were used to analyze the structures of the resistance gene-related sequences. The K. pneumoniae R46 genome consisted of a chromosome and three resistance plasmids named pR46-27, pR46-42, and pR46-270, respectively. The whole genome encoded 34 antibiotic resistance genes including a newly identified chromosome-encoded florfenicol resistance gene named mdfA2. pR46-270, besides encoding 26 antibiotic resistance genes, carried four clusters of heavy metal resistance genes and several virulence-related genes or gene clusters. The plasmid-encoded resistance genes were mostly associated with mobile genetic elements. The plasmid with the most similarity to the floR gene-harboring plasmid pR46-27 was pCTXM-2271, a plasmid from Escherichia coli. The results of this work demonstrated that the plasmids with multidrug resistance genes were present in animal-derived bacteria and more florfenicol resistance genes such as mdfA2 could be present in bacterial populations. The resistance genes encoded on the plasmids may spread between the bacteria of different species or genera and cause the resistance dissemination.

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Study of the relationship between antibiotic resistance markers and virulence markers in NDM-positive Klebsiella pneumoniae strains circulating in various waters and human loci

Hygiene and Sanitation ◽

10.47470/0016-9900-2021-100-12-1366-1371 ◽

2021 ◽

Vol 100 (12) ◽

pp. 1366-1371

Author(s):

Galina V. Pay ◽

Daria V. Rakitina ◽

Mariya A. Sukhina ◽

Sergey M. Yudin ◽

Valentin V. Makarov ◽

...

Keyword(s):

Antibiotic Resistance ◽

Klebsiella Pneumoniae ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Water Sources ◽

Healthy People ◽

Virulence Markers ◽

Healthy Donors ◽

Bowel Diseases ◽

Open Question

Introduction. The propagation of multi-resistance to antibiotics among hospital isolates of Klebsiella pneumoniae (K. pneumoniae) is a subject of growing concern worldwide. At present, growing data of association between resistance and hypervirulence in clinical isolates of K. pneumoniae emerges. However, the occurrence of these pathogens in the environment remains an open question. The aim of this study was to evaluate and compare antibiotic resistance determinants occurrence in Klebsiella pneumoniae isolates from water sources (environmental and sewage), human sources (practically healthy people and patients with inflaammatory bowel disease (IBD), and extraintestinal infections (ExII)). Materials and methods. The PCR assay of carbapenemase genes IMP, NDM, VIM, KPC, OXA-48 was performed with the commercial “Amplisense” kits according to the manufacturer's instructions. The assay was used to evaluate the occurrence of antibiotic-resistance genes in 223 isolates of Klebsiella pneumoniae from various sources: 42 isolates from sewage, 19 isolates from surface water sources, 30 isolates from biological material (blood, urine, surgical wounds, bronchoalveolar lavage) of patients with extraintestinal infections (ExII), 69 isolates from patients with inflammatory bowel diseases (IBD), and 63 isolates from faeces of practically healthy people. Results. The ExII group revealed various antibiotic resistance genes. The most prevalent gene was OXA (30% had this gene only, other 26,6% had also KPC or NDM). NDM as the only resistance gene was observed in 23,3% of ExII isolates. KPC gene was observed in 3,3% of ExII group. Two isolates from IBD group contained NDM gene along with VIM gene. Only NDM gene was found in all the other groups of Klebsiella pneumoniae isolates (13-28% isolates in every group, no statistical difference). NDM was shown to be associated with virulence genes iutA and rmpA that are responsible for iron consumption and hypermucoid phenotype. Conclusion. The most abundant resistance genes in the studied Klebsiella pneumoniae isolates were NDM (13.5%) and OXA (8%). At the same time, NDM was the only gene found in all groups (11-28%). NDM metallobeta-lactamase gene was associated with rmpA and iutA genes, giving an example of the connection between virulence and resistance properties. A significant amount of resistant isolates from healthy donors and surface waters indicates the need for additional study of the role of NDM positive isolates in pathogenicity of Klebsiella pneumoniae.

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Molecular detection of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolates of chicken origin from East Java, Indonesia

Veterinary World ◽

10.14202/vetworld.2019.578-583 ◽

2019 ◽

Vol 12 (4) ◽

pp. 578-583 ◽

Cited By ~ 1

Author(s):

Meutia Hayati ◽

Agustin Indrawati ◽

Ni Luh Putu Ika Mayasari ◽

Istiyaningsih Istiyaningsih ◽

Neneng Atikah

Keyword(s):

Antibiotic Resistance ◽

Klebsiella Pneumoniae ◽

Resistance Gene ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Resistance Pattern ◽

Dilution Method ◽

Agar Dilution Method ◽

Resistance Level ◽

Extended Spectrum

Background and Aim: Klebsiella pneumoniae is one of the respiratory disease agents in human and chicken. This bacterium is treated by antibiotic, but this treatment may trigger antibiotic resistance. Resistance gene in K. pneumoniae may be transferred to other bacteria. One of the known resistance genes is extended-spectrum β-lactamase (ESBL). This research aimed to study K. pneumoniae isolated from chicken farms in East Java, Indonesia, by observing the antibiotic resistance pattern and detect the presence of ESBL coding gene within the isolates. Materials and Methods: A total of 11 K. pneumoniae isolates were collected from 141 chicken cloacal swabs from two regencies in East Java. All isolates were identified using the polymerase chain reaction method. Antimicrobial susceptibility was determined by agar dilution method on identified isolates, which then processed for molecular characterization to detect ESBL coding gene within the K. pneumoniae isolates found. Results: The result of antibiotic sensitivity test in 11 isolates showed highest antibiotic resistance level toward ampicillin, amoxicillin, and oxytetracycline (100%, 100%, and 90.9%) and still sensitive to gentamicin. Resistance against colistin, doxycycline, ciprofloxacin, and enrofloxacin is varied by 90.9%, 54.5%, 27.3%, and 18.2%, respectively. All isolates of K. pneumoniae were classified as multidrug resistance (MDR) bacteria. Resistance gene analysis revealed the isolates harbored as blaSHV (9.1%), blaTEM (100%), and blaCTX-M (90.9%). Conclusion: All the bacterial isolates were classified as MDR bacteria and harbored two of the transmissible ESBL genes. The presence of antibiotic resistance genes in bacteria has the potential to spread its resistance properties.

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Hybrid Resistance and Virulence Plasmids in “High-Risk” Clones of Klebsiella pneumoniae, Including Those Carrying blaNDM-5

Microorganisms ◽

10.3390/microorganisms7090326 ◽

2019 ◽

Vol 7 (9) ◽

pp. 326 ◽

Cited By ~ 12

Author(s):

Jane Turton ◽

Frances Davies ◽

Jack Turton ◽

Claire Perry ◽

Zoë Payne ◽

...

Keyword(s):

Antibiotic Resistance ◽

High Risk ◽

Klebsiella Pneumoniae ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Virulence Plasmid ◽

Virulence Plasmids ◽

Long Read ◽

Multiple Resistance Genes ◽

Sequence Types

Virulence plasmids are associated with hypervirulent types of Klebsiella pneumoniae, which generally do not carry antibiotic resistance genes. In contrast, nosocomial isolates are often associated with resistance, but rarely with virulence plasmids. Here, we describe virulence plasmids in nosocomial isolates of “high-risk” clones of sequence types (STs) 15, 48, 101, 147 and 383 carrying carbapenemase genes. The whole genome sequences were determined by long-read nanopore sequencing. The 12 isolates all contained hybrid plasmids containing both resistance and virulence genes. All carried rmpA/rmpA2 and the aerobactin cluster, with the virulence plasmids of two of three representatives of ST383 carrying blaNDM-5 and seventeen other resistance genes. Representatives of ST48 and ST15 had virulence plasmid-associated genes distributed between two plasmids, both containing antibiotic resistance genes. Representatives of ST101 were remarkable in all sharing virulence plasmids in which iucC and terAWXYZ were missing and iucB and iucD truncated. The combination of resistance and virulence in plasmids of high-risk clones is extremely worrying. Virulence plasmids were often notably consistent within a lineage, even in the absence of epidemiological links, suggesting they are not moving between types. However, there was a common segment containing multiple resistance genes in virulence plasmids of representatives of both STs 48 and 383.

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