Pathogenomic Analysis of a Novel Extensively Drug-Resistant Citrobacter freundii Isolate Carrying a blaNDM-1 Carbapenemase in South Africa

Pathogenomic analysis was performed on a novel carbapenem-resistant Citrobacter freundii isolate (H2730R) from a rectal swab of an adult male patient admitted to a tertiary hospital, Durban, South Africa. H2730R was identified using selective media and API 20e kit. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK II. H2730R was whole-genome sequenced on the Illumina MiSeq platform. H2730R was resistant to all tested antibiotics except tigecycline and was defined as ST498 by the C. freundii multilocus sequence typing (MLST) database. The estimated pathogenic potential predicted a higher probability (Pscore ≈ 0.875), supporting H2730R as a human pathogen. H2730R harbored 25 putative acquired resistance genes, 4 plasmid replicons, 4 intact prophages, a class 1 integron (IntI1), 2 predominant insertion sequences (IS3 and IS5), numerous efflux genes, and virulome. BLASTn analysis of the blaNDM-1 encoding contig (00022) and its flanking sequences revealed the blaNDM-1 was located on a plasmid similar to the multireplicon p18-43_01 plasmid reported for the spread of carbapenem resistance in South Africa. Phylogenomic analysis showed clustering of H2730R with CF003/CF004 strains in the same clade, suggesting a possible association between C. freundii strains/clones. Acquiring the p18-43_01 plasmid containing blaNDM-1, the diversity, and complex resistome, virulome, and mobilome of this pathogen makes its incidence very worrying regarding mobilized resistance. This study presents the background genomic information for future surveillance and tracking of the spread of carbapenem-resistant Enterobacteriaceae in South Africa.

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Comparative Pathogenomics of Aeromonas veronii from Pigs in South Africa: Dominance of the Novel ST657 Clone

Microorganisms ◽

10.3390/microorganisms8122008 ◽

2020 ◽

Vol 8 (12) ◽

pp. 2008

Author(s):

Yogandree Ramsamy ◽

Koleka P. Mlisana ◽

Daniel G. Amoako ◽

Akebe Luther King Abia ◽

Mushal Allam ◽

...

Keyword(s):

South Africa ◽

Orthologous Gene ◽

Gene Clusters ◽

Illumina Miseq ◽

Aeromonas Veronii ◽

Carbapenem Resistant ◽

Kwazulu Natal ◽

Miseq Platform ◽

Differential Ability ◽

Potential Pathogenicity

The pathogenomics of carbapenem-resistant Aeromonas veronii (A. veronii) isolates recovered from pigs in KwaZulu-Natal, South Africa, was explored by whole genome sequencing on the Illumina MiSeq platform. Genomic functional annotation revealed a vast array of similar central networks (metabolic, cellular, and biochemical). The pan-genome analysis showed that the isolates formed a total of 4349 orthologous gene clusters, 4296 of which were shared; no unique clusters were observed. All the isolates had similar resistance phenotypes, which corroborated their chromosomally mediated resistome (blaCPHA3 and blaOXA-12) and belonged to a novel sequence type, ST657 (a satellite clone). Isolates in the same sub-clades clustered according to their clonal lineages and host. Mobilome analysis revealed the presence of chromosome-borne insertion sequence families. The estimated pathogenicity score (Pscore ≈ 0.60) indicated their potential pathogenicity in humans. Furthermore, these isolates carried several virulence factors (adherence factors, toxins, and immune evasion), in different permutations and combinations, indicating a differential ability to establish infection. Phylogenomic and metadata analyses revealed a predilection for water environments and aquatic animals, with more recent reports in humans and food animals across geographies, making A. veronii a potential One Health indicator bacterium.

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Prevalence and mechanisms of carbapenem resistance among Klebsiella aerogenes in a tertiary hospital in China

10.21203/rs.3.rs-19281/v1 ◽

2020 ◽

Author(s):

Luxiang Liu ◽

Jingjing Quan ◽

Dongdong Zhao ◽

Weichao Liao ◽

Jiaojian Lv ◽

...

Keyword(s):

Intensive Care ◽

Efflux Pump ◽

Carbapenem Resistance ◽

Clonal Diversity ◽

Tertiary Hospital ◽

Molecular Characteristics ◽

Klebsiella Aerogenes ◽

Carbapenem Resistant ◽

Efflux Pump Inhibition ◽

Clonal Spread

Abstract Background: Klebsiella aerogenes has emerged as one of the most important nosocomial pathogens for patients in intensive care units (ICU) in recent years. This study aims to evaluated the prevalence and molecular characteristics of clinical carbapenem-resistant K. aerogenes (CRKA) isolates in a tertiary hospital in China.Results: Twenty CRKA were identified among all the isolates, with the rate of 5.5% (20/364). Six CRKA isolates produced KPC-2 and 1 CRKA isolate produced NDM-1. PFGE and MLST indicated that the 20 CRKA strains were clonal diversity. All the bla KPC-2 gene and bla NDM-1 gene were located on plasmids and all the plasmids with bla KPC-2 and bla NDM-1 genes could successfully transferred to EC600 or J53. Twelve of 13 CRKA strains without any carbapenemase genes were positive for efflux pump inhibition test.Conclusion: Overall, the prevalence of CRKA in the tertiary hospital in Zhejiang Province of China is 5.5%. Only 35% of CRKA produce carbapenemase and efflux pumps might play an important role in the carbapenem resistance of K. aerogenes. It is necessary to strengthen the surveillance of carbapenem resistance in the hospital to prevent the horizontal and clonal spread of CRKA.

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Predominance of Acinetobacter spp., Harboring the blaIMP Gene, Contaminating the Hospital Environment in a Tertiary Hospital in Mwanza, Tanzania: A Cross-Sectional Laboratory-Based Study

Pathogens ◽

10.3390/pathogens11010063 ◽

2022 ◽

Vol 11 (1) ◽

pp. 63

Author(s):

Vitus Silago ◽

Eveline C. Mruma ◽

Betrand Msemwa ◽

Conjester I. Mtemisika ◽

Shukurani Phillip ◽

...

Keyword(s):

Carbapenem Resistance ◽

Tertiary Hospital ◽

Hospital Environment ◽

Pcr Assay ◽

Cross Sectional ◽

Middle Income ◽

Carbapenem Resistant ◽

Multiplex Pcr Assay ◽

Genes Encoding ◽

Acinetobacter Spp

Data on colonization and hospital contamination of carbapenem-resistant Gram-negative bacteria (CR-GNB) are limited in low- and middle-income countries. We designed this study to determine the prevalence and co-existence of carbapenemase genes among CR-GNB isolated from clinical, colonization, and hospital environmental samples at a tertiary hospital in Mwanza, Tanzania. The modified Hodge test (MHT), the combined disk test (CDT), and the double-disk synergy test (DDST) were used for the phenotypic detection of carbapenemases. A multiplex PCR assay was used to detect blaIMP and blaKPC, and a singleplex PCR assay was used to detect blaOXA-48. Data were analyzed by STATA version 13.0. Overall, 68.8% (44/64) of the CR-GNB had at least one phenotype by phenotypic methods, whereby 60.9% (39/64) were both CDT and DDST positive and 31.3% (20/64) were MHT positive. A total of 23/64 (35.9%) had at least one of the genes tested with the predominance of blaIMP (91.3%; 21/23). In addition, 47.7% (21/44) of the CR-GNB phenotypes had at least one gene. Around 47.8% (11/23) of the CR-GNB carried multiple genes encoding for carbapenem resistance, with the maximum co-existence of blaIMP/blaKPC/blaOXA-48 (45.5%; 5/11). The majority of carbapenem-resistant genes were detected in Acinetobacter spp. (82.6%; 19/23) and isolated from bed swabs (69.6%; 16/23). Acinetobacter spp. carrying the blaIMP gene predominantly contaminated the hospital environment. Therefore, we recommend routine decontamination of inanimate hospital surfaces, including patient beds.

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Emergence of OXA-10 and OXA-48 like carbapenemases among Enterobacter isolates from inpatients in southern Iran

10.21203/rs.3.rs-673753/v1 ◽

2021 ◽

Author(s):

Melika Moradi ◽

Reza Khashei ◽

Yalda Malekzadegan ◽

Jamal Sarvari

Keyword(s):

Carbapenem Resistance ◽

Common Species ◽

Resistance Rate ◽

Health Concern ◽

Multi Drug Resistance ◽

Class 1 Integron ◽

Carbapenem Resistant ◽

Microbiological Methods ◽

Global Spread ◽

Class 1

Abstract Background The global spread of carbapenemase-producing Enterobacteriaceae represents a public health concern. The aim of this study was to investigate prevalence of carbapenem resistance, oxacillinase types and the presence of class 1–3 integrons among Enterobacter clinical isolates from an Iranian inpatients’ population. Methods Ninety Enterobacter isolates recovered from hospitalized patients were diagnosed by the standard microbiological methods. Antibiogram pattern was also determined. The presence of class 1–3 integrons and four types of oxacillinase genes were assessed using PCR. Results Of the 90 Enterobacter isolates, the most common species was identified as E. aerogenes, (45.6%), followed by E. cloacae (30%). The highest resistance rate was against to ampicillin (96.7%). Multi-drug resistance (MDR) was substantial (93%). Carbapenemase producers were detected in 96% of carbapenem resistant isolates by mCIM test. The frequency of evaluated genes was as follows: intI1 = 50 (55.6%), intI2 = 12 (13.3%), blaoxa−1 =6 (6.7%), blaoxa−2 =5 (5.6%), blaoxa−10 =18 (20%), and blaoxa−48 =18 (20%). Conclusion The determinants of class 1 integron with OXA-10 and OXA-48 like carbapememases have been responsible of relatively considerable of carbapenem resistance among isolates. This is the first OXA-10 and OXA-48-producing Enterobacter spp. in Iran, indicating that the prevalence of oxacillinases might be on the rise in country.

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The Predominance of Strain Replacement Among Enterobacteriaceae Pairs With Emerging Carbapenem Resistance During Hospitalization

The Journal of Infectious Diseases ◽

10.1093/infdis/jiz586 ◽

2020 ◽

Vol 221 (Supplement_2) ◽

pp. S215-S219

Author(s):

Baixing Ding ◽

Zhen Shen ◽

Xiaohua Qin ◽

Yang Yang ◽

Xiaogang Xu ◽

...

Keyword(s):

Antimicrobial Therapy ◽

Gel Electrophoresis ◽

Carbapenem Resistance ◽

Tertiary Hospital ◽

Pulsed Field Gel Electrophoresis ◽

Pulsed Field ◽

Carbapenem Resistant ◽

Sequence Types ◽

Carbapenem Resistant Enterobacteriaceae

Abstract Isolates of Enterobacteriaceae collected from the same patient can lose carbapenem susceptibility during antimicrobial therapy, but little attention has been given to how this conversion takes place. In the current study, we retrospectively analyzed microbiological and clinical data from patients with enterobacterial infections at a tertiary hospital in Shanghai, China. After screening 4795 patients and 7120 Enterobacteriaceae isolates over the 3-year study period, we found the change from carbapenem susceptible to carbapenem resistant in 41 pairs of isolates, of which 35 pairs (85.4%) were K. pneumoniae and 25 (61.0%) were from the same anatomic sites. Thirty-six isolate pairs showed different pulsed-field gel electrophoresis patterns between the carbapenem-susceptible and the corresponding resistant strain, and 5 pairs displayed identical pulsed-field gel electrophoresis patterns. Thirty-three (91.7%) of the 36 pairs of Enterobacteriaceae isolates were carbapenem-resistant K. pneumoniae with blaKPC-2, and 28 pairs (90.3%) of K. pneumoniae isolates had different sequence types (STs), with ST11 the most common ST found in carbapenem-resistant K. pneumoniae isolates. Forty of the 41 patients had received antimicrobial therapy such as carbapenems, cephalosporins, and fluoroquinolones, before the isolation of carbapenem-resistant Enterobacteriaceae. These results demonstrated that strain replacement is the main cause of emerging carbapenem resistance in Enterobacteriaceae during hospitalization. The loss of carbapenem susceptibility was not mainly due to in vivo development of carbapenem resistance.

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First Report ofblaIMP-14on a Plasmid Harboring Multiple Drug Resistance Genes in Escherichia coli Sequence Type 131

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00840-16 ◽

2016 ◽

Vol 60 (8) ◽

pp. 5068-5071 ◽

Cited By ~ 10

Author(s):

Nicole Stoesser ◽

Anna E. Sheppard ◽

Gisele Peirano ◽

Robert P. Sebra ◽

Tarah Lynch ◽

...

Keyword(s):

Escherichia Coli ◽

Pseudomonas Aeruginosa ◽

Multiple Drug Resistance ◽

Carbapenem Resistance ◽

Sequence Type ◽

Multiple Drug ◽

Class 1 Integron ◽

Content Type ◽

Carbapenem Resistant ◽

Class 1

ABSTRACTTheblaIMP-14carbapenem resistance gene has largely previously been observed inPseudomonas aeruginosaandAcinetobacterspp. As part of global surveillance and sequencing of carbapenem-resistantEscherichia coli, we identified a sequence type 131 strain harboringblaIMP-14within a class 1 integron, itself nested within an ∼54-kb multidrug resistance region on an epidemic IncA/C2plasmid. The emergence ofblaIMP-14in this context in the ST131 lineage is of potential clinical concern.

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Physiological and molecular characteristics of carbapenem resistance in Klebsiella pneumoniae and Enterobacter aerogenes

The Journal of Infection in Developing Countries ◽

10.3855/jidc.6821 ◽

2016 ◽

Vol 10 (06) ◽

pp. 592-599 ◽

Cited By ~ 3

Author(s):

Rito Santo Pereira ◽

Vanessa Cordeiro Dias ◽

Alessandra Barbosa Ferreira-Machado ◽

Juliana Alves Resende ◽

André Netto Bastos ◽

...

Keyword(s):

Oxidative Stress ◽

Klebsiella Pneumoniae ◽

Genetic Markers ◽

Bacterial Resistance ◽

Enterobacter Aerogenes ◽

Carbapenem Resistance ◽

Tertiary Hospital ◽

Resistant Bacteria ◽

Molecular Characteristics ◽

Carbapenem Resistant

Introduction: Bacterial resistance is a growing concern in the nosocomial environment in which Klebsiella pneumoniae and Enterobacter aerogenes play an important role due to their opportunism and carbapenemase-production. This work aimed to evaluate physiological and molecular characteristics of carbapenem-resistant K. pneumoniae and E. aerogenes isolated in a Brazilian tertiary hospital. Methodology: In total, 42 carbapenem-resistant bacteria isolated from clinical specimens were included (21 K. pneumoniae and 21 E. aerogenes). Drug-sensitive K. pneumoniae (n = 27) were also included. Antimicrobial susceptibility and biocide tolerance patterns, hemolytic activity, tolerance to oxidative stress, and aggregative ability were assessed. Genetic markers related to carbapenem resistance, or ESBL-production were screened by PCR. Results: Compared to drug-sensitive strains, carbapenem-resistant K. pneumoniae were more tolerant to biocides and to oxidative stress, and they displayed an increase in biofilm formation. The genetic markers blaKPC (95.2%) and blaTEM (90.5%) were the most frequent. Among the carbapenem-resistant E. aerogenes strains, blaKPC, and blaTEM were detected in all bacteria. Drug-sensitive E. aerogenes were not isolated in the same period. blaSHV, blaVIM, and blaCTX markers were also observed among carbapenem-resistant bacteria. Conclusions: Results suggest that carbapenemase-producing enterobacteria might show peculiar characteristics regarding their physiology associated with their environmental persistency, virulence, and multidrug resistance. The observed phenomenon may have implications not only for antimicrobial chemotherapy, but also for the prognosis of infectious diseases and infection control.

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Next-Generation-Sequencing-Based Hospital Outbreak Investigation Yields Insight intoKlebsiella aerogenesPopulation Structure and Determinants of Carbapenem Resistance and Pathogenicity

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02577-18 ◽

2019 ◽

Vol 63 (6) ◽

Cited By ~ 9

Author(s):

Adel Malek ◽

Kelly McGlynn ◽

Samantha Taffner ◽

Lynn Fine ◽

Brenda Tesini ◽

...

Keyword(s):

Intensive Care ◽

Carbapenem Resistance ◽

Phylogenomic Analysis ◽

Nucleotide Polymorphisms ◽

Content Type ◽

Hospital Outbreak ◽

Carbapenem Resistant ◽

Emerging Trends ◽

Scaling Analyses ◽

Human Infections

ABSTRACTKlebsiella aerogenesis a nosocomial pathogen associated with drug resistance and outbreaks in intensive care units. In a 5-month period in 2017, we experienced an increased incidence of cultures for carbapenem-resistantK. aerogenes(CR-KA) from an adult cardiothoracic intensive care unit (CICU) involving 15 patients. Phylogenomic analysis following whole-genome sequencing (WGS) identified the outbreak CR-KA isolates to group together as a tight monoclonal cluster (with no more than six single nucleotide polymorphisms [SNPs]), suggestive of a protracted intraward transmission event. No clonal relationships were identified between the CICU CR-KA strains and additional hospital CR-KA patient isolates from different wards and/or previous years. Carbapenemase-encoding genes and drug-resistant plasmids were absent in the outbreak strains, and carbapenem resistance was attributed to mutations impacting AmpD activity and membrane permeability. The CICU outbreak strains harbored an integrative conjugative element (ICE) which has been associated with pathogenicKlebsiella pneumoniaelineages (ICEKp10). Comparative genomics with globalK. aerogenesgenomes showed our outbreak strains to group closely with global sequence type 4 (ST4) strains, which, along with ST93, likely represent dominantK. aerogeneslineages associated with human infections. For poorly characterized pathogens, scaling analyses to include sequenced genomes from public databases offer the opportunity to identify emerging trends and dominant clones associated with specific attributes, syndromes, and geographical locations.

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Genomic characterization of Citrobacter freundii strains coproducing OXA-48 and VIM-1 carbapenemase enzymes isolated in leukemic patient in Spain

Antimicrobial Resistance and Infection Control ◽

10.1186/s13756-019-0630-3 ◽

2019 ◽

Vol 8 (1) ◽

Author(s):

Rym Lalaoui ◽

Ana Djukovic ◽

Sofiane Bakour ◽

Linda Hadjadj ◽

Jaime Sanz ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Resistance Mechanism ◽

Carbapenem Resistance ◽

Bioinformatic Analysis ◽

Whole Genome ◽

Citrobacter Freundii ◽

Fecal Samples ◽

Carbapenem Resistant ◽

High Risk Populations

Abstract Background The emergence of carbapenemase-producing (CP) Citrobacter freundii poses a significant threat to public health, especially in high-risk populations. In this study, whole genome sequencing was used to characterize the carbapenem resistance mechanism of three C. freundii clinical isolates recovered from fecal samples of patients with acute leukemia (AL) from Spain. Materials and methods Twelve fecal samples, collected between 2013 and 2015 from 9 patients with AL, were screened for the presence of CP strains by selecting them on MacConkey agar supplemented with ertapenem (0.5 mg/L). Bacteria were identified by MALDI-TOF mass spectrometry and were phenotypically characterized. Whole genome sequencing of C. freundii isolates was performed using the MinION and MiSeq Illumina sequencers. Bioinformatic analysis was performed in order to identify the molecular support of carbapenem resistance and to study the genetic environment of carbapenem resistance encoding genes. Results Three carbapenem-resistant C. freundii strains (imipenem MIC≥32 mg/L) corresponding to three different AL patients were isolated. Positive modified Carba NP test results suggested carbapenemase production. The genomes of each C. freundii tested were assembled into a single chromosomal contig and plasmids contig. In all the strains, the carbapenem resistance was due to the coproduction of OXA-48 and VIM-1 enzymes encoded by genes located on chromosome and on an IncHI2 plasmid, respectively. According to the MLST and the SNPs analysis, all strains belonged to the same clone ST169. Conclusion We report in our study, the intestinal carrying of C. freundii clone ST169 coproducing OXA-48 and VIM-1 identified in leukemic patients.

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OXA-198, an Acquired Carbapenem-Hydrolyzing Class D β-Lactamase from Pseudomonas aeruginosa

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00522-11 ◽

2011 ◽

Vol 55 (10) ◽

pp. 4828-4833 ◽

Cited By ~ 29

Author(s):

Farid El Garch ◽

Pierre Bogaerts ◽

Carine Bebrone ◽

Moreno Galleni ◽

Youri Glupczynski

Keyword(s):

Pseudomonas Aeruginosa ◽

Carbapenem Resistance ◽

Amino Acid Identity ◽

Ventilator Associated Pneumonia ◽

Class 1 Integron ◽

Content Type ◽

New Class ◽

Carbapenem Resistant ◽

Class D ◽

Class 1

ABSTRACTA carbapenem-resistantPseudomonas aeruginosastrain (PA41437) susceptible to expanded-spectrum cephalosporins was recovered from several consecutive lower-respiratory-tract specimens of a patient who developed a ventilator-associated pneumonia while hospitalized in an intensive care unit. Cloning experiments identified OXA-198, a new class D β-lactamase which was weakly related (less than 45% amino acid identity) to other class D β-lactamases. Expression inEscherichia coliTOP10 and inP. aeruginosaPAO1 led to transformants that were resistant to ticarcillin and showed reduced susceptibility to carbapenems and cefepime. TheblaOXA-198gene was harbored by a class 1 integron carried by a ca. 46-kb nontypeable plasmid. This study describes a novel class D β-lactamase involved in carbapenem resistance inP. aeruginosa.

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