Characterization of an NDM-1-Producing Citrobacter koseri Isolate from China

Purpose

The continuous rise in carbapenemase-producing Enterobacteriaceae infections is a major public health concern. However, there is limited information available on New Delhi metallo-β-lactamase-1 (NDM-1) producing Citrobacter koseri. In this study, we isolated a blaNDM-1-carrying C. koseri from a stool sample of an inpatient. Our aim was to investigate the phenotypic and genomic features of this clinically derived carbapenem-resistant C. koseri isolate and to characterize the transmission pattern of the IncFII/IncN plasmid that carries the blaNDM-1 gene.

Methods and Results

S1-PFGE, Southern blot and conjugation assay confirmed the presence of blaNDM-1 gene in a conjugative plasmid. C. koseri L2395 and transconjugant L2395-EC600 strains showed similar resistance spectrum. Whole-genome analysis revealed that pL2395_NDM is an IncFII/IncN plasmid with a length of 67,839 bp. Moreover, blaNDM-1 gene was found encoded in the ISKpn19-blaNDM-1-ble-tnpF-dsbD-cutA-ISKpn19 cassette array. Phylogenetic analysis revealed that strain L2395 was close to an IMP-4-bearing C. koseri from Australia.

Conclusion

Ongoing surveillance will be essential to control and prevent the spread of carbapenem-resistant Citrobacter spp. in the future.

Complete genome sequencing and comparative analysis of Citrobacter koseri CKNJ, a strain isolated from patient with endogenous endophthalmitis

Citrobacter koseri is an opportnistic pathogen can cause a variety of diseases. Though the mortality rate of C. koseri infections is high but there is a paucity of clinical information on them. Furthermore, the genomic features of this species are poorly studied. Herein, we presented a patient with endogenous endophthalmitis secondary to septicaemia, and collected a C. koseri isolate, CKNJ, from the blood of the patient. Whole genome sequencing revealed that the CKNJ harbors no plasmid and codes for 67 putative virulence factors. Whole genome SNP-based phylogenetic analysis revealed that strain CKNJ was close to the strains with same isolation sites. Compared to the other sequenced C. koseri chromosomes, CKNJ contains several strain-variable regions, including one prophage and two large genomic islands. The sequencing of the first complete genome of a clinical strain from China should reinforce our understanding of the genomic features and pathogenicity of this invasive infection-causing C. koseri with clinical significance.

Microbial Etiology and Prognostic Factors of Ventilator-associated Pneumonia: A Multicenter Retrospective Study in Shanghai

Background

The microbial etiology and mortality risk factors of ventilator-associated pneumonia (VAP) have not been investigated extensively in Shanghai.

Methods

VAP cases were identified from the patients hospitalized during the period from 1 January 2013 to 30 December 2017 in Shanghai. The relevant data were reviewed and analyzed retrospectively.

Results

One hundred ninety-four VAP cases were included in this analysis. The overall mortality rate was 32.47%. The respiratory pathogens isolated from these patients included 212 bacterial strains and 54 fungal strains. The leading pathogens were Acinetobacter baumannii (33.96%), Klebsiella pneumoniae (23.58%), Pseudomonas aeruginosa (19.81%), and Staphylococcus aureus (7.08%). Candida colonization was associated with higher mortality of VAP patients compared to those without Candida colonization (45.45% vs 28.67%, P < .05). The VAP patients with Candida colonization also showed higher prevalence of P. aeruginosa, carbapenem-resistant P. aeruginosa (CRPA), K. pneumoniae, carbapenem-resistant K. pneumoniae (CRKP), A. baumannii, and carbapenem-resistant A. baumannii (CRAB) (P < .05). VAP nonsurvivors had higher prevalence of CRPA, K. pneumoniae, CRAB, and Candida than VAP survivors (P < .05). Multivariate analysis showed that prior antibiotic use was a significant risk factor for Candida colonization, while hypertension and length of hospital stay were significant risk factors of VAP mortality (P < .05).

Conclusions

The top pathogens of VAP patients in Shanghai tertiary teaching hospitals are A. baumannii, K. pneumoniae, and P. aeruginosa, with high prevalence of carbapenem resistance. Carbapenem-resistant bacterial pathogens and Candida may predict poor outcome.

Genome sequence of carbapenem-resistant Citrobacter koseri carrying blaOXA-181 isolated from sewage sludge

OBJECTIVES

This study reported the resistome content of sewage sludge-isolated carbapenem-resistant Citrobacter koseri (C. koseri) carrying bla_OXA-181. It also provided a general phylogenomic analysis highlighting antibiotic resistance genes (ARGs), plasmids and pathogenicity of C. koseri genomes.

METHODS

The carbapenem-resistantC. koseri AS1 strain was isolated from sewage sludge on CHROMagar™ mSuperCARBA™ media. Whole genome sequencing of C. koseri AS1 was performed using an HiSeq X™ Ten instrument. Additional C. koseri genomes were downloaded from National Center for Biotechnology Information (NCBI). Phylogenomic analysis was established through CSI Phylogeny. ARGs, plasmids and pathogenicity were identified using ResFinder 3.1, PlasmidFinder 2.0 and PathogenFinder 1.1, respectively.

RESULTS

The phylogenomic tree indicated a polyclonal pattern ofC. koseri genomes. Resistome analysis of C. koseri AS1 revealed β-lactam resistance genes (bla_MAL-1 and bla_OXA-181) as well as a fosfomycin resistance gene (fosA7). Three plasmids (ColKP3, ColRNAI and IncX30) were identified in the C. koseri AS1 genome. In addition, 25 ARGs were found in downloaded genomes. Of these, clinically significant ARGs such as bla_KPC-2 and bla_OXA-48 were found in two and four genomes, respectively. Assessment of the genomes using PathogenFinder revealed all genomes as putative human pathogens.

CONCLUSIONS

It is believed that noC. koseri genome has been reported to carry bla_OXA-181; therefore, C. koseri AS1 is the first of its kind. This study also highlighted the resistome contents of C. koseri genomes.

IncC blaKPC-2-positive plasmid characterised from ST648 Escherichia coli

OBJECTIVES

This study describes the characterisation of type 2 IncC plasmids pC-Ec20-KPC and pC-Ec2-KPC, carrying thebla_KPC-2 gene, from two multiresistant Escherichia coli recovered in University Hospital of Larissa (Greece) in 2018.

METHODS

E. coli strains Ec-2Lar and Ec-20Lar were recovered from rectal swabs of two patients during monthly surveillance cultures. Transfer experiments by conjugation were carried out using rifampicin-resistant E. coli A15 laboratory strain as recipient. bla_KPC-carrying plasmids were characterised by S1 profiling. Isolates were typed by MLST. Whole-genome sequencing was performed using the Sequel platform.

RESULTS

Both E. coli isolates, belonging to ST648, transferred bla_KPC-2 to E. coli A15 by conjugation. Plasmid analysis revealed that the transconjugants harboured bla_KPC-positive plasmids of different sizes. Analysis of plasmid sequences showed that in both isolates the bla_KPC-2 gene was carried on a type 2 IncC plasmid (pC-Ec20-KPC and pC-Ec2-KPC, respectively). Both plasmids carried the ARI-B resistance island consisting of several resistance genes, intact and truncated copies of several mobile elements, and a 25 571-bp segment harbouring coding sequences for an iron transporter. The bla_KPC-2 gene was part of transposon Tn4401a, which was bounded by 5-bp direct repeats (TCCTT) suggesting its transposition into the IncC plasmids.

CONCLUSION

To our knowledge, this is the first report on complete nucleotide sequences of type 2 IncC plasmids. These findings, which hypothesise the acquisition of KPC-2-encoding transposon Tn4401a by an IncC replicon, indicate the ongoing need for molecular surveillance studies of multidrug-resistant pathogens. In addition, they underline the increasing clinical importance of the IncC plasmid family.

First genome sequence of a blaKPC-2-carrying Citrobacter koseri isolate collected from a patient with diarrhoea

OBJECTIVES

The bla_KPC gene is rarely reported in Citrobacter koseri. Here we report the first draft genome sequence of a bla_KPC-2-carrying C. koseri isolate from a patient with diarrhoea.

METHODS

Transferability of the bla_KPC-2-bearing plasmid was determined by the filter mating method. The whole genome sequence of C. koseri L168 was determined using an Illumina HiSeq platform. The genome was de novo assembled using Velvet 1.2.10. Acquired antimicrobial resistance genes and plasmid replicons were identified using ResFinder 2.1 and PlasmidFinder 1.3, respectively.

RESULTS

Antimicrobial susceptibility testing (AST) showed that C. koseri L168 was resistant to multiple antibiotics but was susceptible to ciprofloxacin, gentamicin, tobramycin, amikacin, tigecycline and colistin. A KPC-2-harbouring plasmid was conjugative and the transconjugants conferred increased resistance to carbapenems confirmed by conjugation experiments and AST. In silico analysis revealed the presence of the β-lactam resistance genes bla_KPC-2 and bla_MAL-1. Additionally, plasmids of incompatibility groups IncFII and IncX4 were identified in the genome by PlasmidFinder. BLAST analysis revealed that bla_KPC-2 was located on a Tn3 transposon element in C. koseri L168 with the conserved linear structure ISKpn27-bla_KPC-2-ΔISKpn6-korC-klcA.

CONCLUSIONS

To our knowledge, this is only the second report of C. koseri producing KPC-2, and we report the first draft genome sequence of a bla_KPC-2-carrying C. koseri isolate from a patient with diarrhoea in China. This work may facilitate our understanding of the pathogenesis, multidrug resistance mechanisms and genomic features of this species. Further monitoring of bacteria carrying carbapenemase genes in patients' gut microbiota is warranted.

Draft Genome Sequences of blaKPC-Containing Enterobacter aerogenes, Citrobacter freundii, and Citrobacter koseri Strains

We report here the draft genome sequences of four bla_KPC-containing bacteria identified as Klebsiella aerogenes, Citrobacter freundii, and Citrobacter koseri. Additionally, we report the draft genome sequence of a K. aerogenes strain that did not contain a bla_KPC gene but was isolated from the patient who had the bla_KPC-2-containing K. aerogenes strain.

In vitro susceptibility and resistance phenotypes in contemporary Citrobacter isolates in a University Hospital in Crete, Greece

BACKGROUND

Data on Citrobacter spp. susceptibility are scarce. We sought to study the evolution in the susceptibility of 385 Citrobacter spp. at the University Hospital of Heraklion, Crete, Greece during a six-year period (2010-2015).

METHODS

Non-duplicate strains isolated from inpatients (intensive care unit, oncology, surgery, internal medicine, paediatrics) and outpatients were studied using Vitek 2. Phenotypic confirmatory tests were applied for detection of β-lactamases and aminoglycoside modifying enzymes.

RESULTS

C. freundii (172, 44.7%) and C. koseri (166, 43.1%) were the most commonly isolated species. C. braakii (34), C. amalonaticus (6), C. youngae (6) and C. sedlakii (1) were the remaining isolates. Colistin and fosfomycin were the most active antibiotics (both 99.2%) followed by carbapenems (99%) aminoglycosides (96.6-98.4%), tigecycline (96.1%), cefepime (94.8%), ciprofloxacin (94.3%), tetracycline (92.7%), trimethoprim/sulphamethoxazole (91.4%), chloramphenicol (88.1%), piperacillin/tazobactam (86.5%) and 3rd generation cephalosporins (85.7%). C. freundii were more resistant than C. koseri. Antibiotic resistance did not increase during the study period for most antibiotics. Lower susceptibility to all antibiotics was observed among multi-drug resistant (MDR) strains. AmpC was the most common resistant mechanism (10.9%); carbapenemases (1.3%) and aminoglycoside modifying enzymes (2.9%) were also detected. All AmpC producers were resistant to cephalosporins but not to carbapenems. In all but one isolates aminoglycoside resistance was accompanied by acquired β-lactamases.

CONCLUSIONS

Although Citrobacter species in general were susceptible, antibiotic susceptibility testing is required for the detection of resistant isolates.

Double- and multi-carbapenemase-producers: the excessively armored bacilli of the current decade

Multidrug-resistant (MDR) and extensively drug-resistant (XDR) Gram-negative nosocomial pathogens commonly carry one carbapenemase gene conferring resistance to carbapenems and other beta-lactam antibiotics. However, increasing reports show that double-carbapenemase-producing (DCP) and even multi-carbapenemase-producing (MCP) bacteria are emerging in some parts of the world, diminishing further, in some cases, the already limited treatment options. In the present review, the up-to-date reports of DCP and MCP isolates are summarized and concerns regarding their emergence are discussed.

Risk factors for carbapenem-resistant Klebsiella pneumoniae infection/colonization and predictors of mortality: a retrospective study

OBJECTIVE

To identify risk factors associated with carbapenem-resistant Klebsiella pneumoniae (CRKP) infection/colonization and death and to investigate the resistance and homology of CRKP.

METHODS

A retrospective 1:1 case-control study was conducted at Changhai Hospital, China, from January 2010 to December 2011.The study population included 30 patients with CRKP infection/colonization and 30 matched patients with carbapenem-susceptible K. pneumoniae (CSKP) infection/colonization at the same site. Homology analysis was conducted by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Potential resistance genes were detected by PCR.

RESULTS

Independent risk factors for CRKP infection/colonization were admission to exposure to glycopeptides [Odds ratio (OR): 43.84, 95% confidence interval (CI): 1.73-1111.91, P = 0.020], cefoperazone plus sulbactam (OR: 49.56, 95% CI: 1.42-1726.72, P = 0.030) and tracheostomy (OR: 677.82, 95% CI: 2.76-1667, P = 0.020). Age (OR: 1.07, 95% CI: 1.00-1.14, P = 0.04), renal dysfunction (OR: 17.63, 95% CI: 2.34-132.87, P = 0.005) and exposure to cefoperazone plus sulbactam (OR: 8.87, 95% CI: 1.29-61.07, P = 0.026) were independent risk factors for the death of patients with K. pneumoniae infection/colonization. Older age (OR: 1.16, 95% CI: 1.01-1.39, P = 0.011) was an independent risk factor for the death of patients with CRKP infection/colonization. Thirty CRKP strains were all KPC-2-producing resistant strains with genotype of ST-11.

CONCLUSION

Exposure to glycopeptides, cefoperazone plus sulbactam and tracheostomy were independent risk factors for CRKP infection/colonization, and older age was an independent risk factor for CRKP infection/colonization caused death.