Characterization of Plasmid Co-Harboring NDM-1 and SHV-12 from a Multidrug-Resistant Citrobacter freundii Strain ZT01-0079 in China

Coexistence of a novel NDM-1-encoding MDR plasmid and an IMP-4-encoding IncN-IncU hybrid plasmid in a clinical isolate of Citrobacter freundii BC73

Objectives

To investigate the genetic characteristics and transmission mechanism of the NDM-1-, IMP-4-, and SHV-12-producing multidrug-resistant (MDR) clinical isolate, Citrobacter freundii BC73.

Methods

C. freundii BC73 was isolated from a urine specimen of a urological patient diagnosed with bladder cancer at a Chinese teaching hospital. Antimicrobial susceptibility testing was carried out using DL-120E susceptibility cards and DL-96A system. Whole genome sequencing (WGS) of the isolate was performed using the Illumina and Oxford Nanopore platforms to analyze the genetic context of drug resistance genes and plasmid characteristics. The phylogenetic tree was constructed and visualized by KSNP3.0 software and iTOL5.0 online database.

Results

C. freundii isolate BC73 co-carrying bla NDM-1, bla IMP-4 and bla SHV-12 were multidrug-resistant. bla NDM-1 and bla IMP-4 were located on a novel IncFIB-like plasmid, pCFBC1, and an IncN-IncU hybrid plasmid, pCFBC2, respectively. The transferability of bla NDM-1 and bla IMP-4 from C. freundii BC73 to E. coli J53 was successfully demonstrated. The genetic context of the bla NDM-1 and bla IMP-4 genes were ISCR27-groEL-∆groES-cutA-dsbD-trpF-ble MBL-bla NDM-1-∆ISAba125-IS3000 and intI1-bla IMP-4-Kl.pn.13-mobC-IS6100, respectively. Additionally, two extensive transposition units (MGE1 in pCFBC1, MGE2 in pCFBC2) were identified and numerous antimicrobial resistance genes were discovered on it.

Conclusion

To our knowledge, our study represents the first characterization of a ST22 C. freundii isolate co-harboring bla NDM-1, bla IMP-4, and bla SHV-12, obtained from a urine sample. The dissemination of this MDR isolate should be of close concern in future clinical surveillance.

Global phylogeography and genomic characterization of blaKPC and blaNDM-positive clinical Klebsiella aerogenes isolates from China, 2016-2022

Carbapenem-resistant Klebsiella aerogenes (CRKA), being one of the members of carbapenem-resistant Enterobacteriaceae (CRE), has caused great public health concern, but with fewer studies compared to other CRE members. Furthermore, studies on phylogenetic analysis based on whole genome Single-Nucleotide Polymorphism (SNP) of CRKA were limited. Here, 20 CRKA isolates (11 blaKPC-2-bearing and 9 blaNDM-1/5-harboring) were characterized by antimicrobial susceptibility testing, conjugation assay, whole genome sequencing (WGS) and bioinformatics analysis. Additionally, the phylogeographic relationships of K. aerogenes were further investigated from public databases. All isolates were multidrug-resistant (MDR) bacteria, and they demonstrated susceptibility to colistin. Most blaKPC-2 or blaNDM-1/5-carrying plasmids were found to be conjugative. Phylogenetic analysis revealed the clonal dissemination of K. aerogenes primarily occurred within clinical settings. Notably, some strains in this study showed the potential for clonal transmission, sharing few SNPs between K. aerogenes and KPC- and/or NDM-positive K. aerogenes isolated from various countries. The STs of K. aerogenes strains had significant diversity. WGS analysis showed that the IncFIIK plasmid was the most prevalent carrier of blaKPC-2, and, blaNDM-1/5 were detected on the IncX3 plasmids. The Tn6296 and Tn3000 transposons were most common vehicles for facilitating the transmission of blaKPC-2 and blaNDM-1/5, respectively. This study highlights the importance of continuous screening and surveillance by WGS for analysis of drug-resistant strains in hospital settings, and provide clinical information that supports epidemiological and public health research on human pathogens.

Requiring Reconsideration of Differences of Aeromonas Infections Between Extra-Intestinal and Intestinal in Hospitalized Patients

Purpose

The purpose of this study is to examine the variations between extra-intestinal and intestinal infections of Aeromonas in terms of strain types, risk factors, drug susceptibility results, and the distribution of drug resistance and virulence genes.

Patients and Methods

A total of 188 Aeromonas strains were identified to the species level using housekeeping genes (rpoD, gyrB, and gyrA). The risk factors for Aeromonas extra-intestinal and intestinal infection, as well as mortality, were retrospectively examined in this study. The broth microdilution method was used to investigate the antimicrobial susceptibility profiles. Touchdown polymerase chain reaction (PCR) assays and DNA sequencing were employed to confirm virulence and the presence of drug resistance genes.

Results

The housekeeping genes identified 188 strains into 7 species. Extra-intestinal isolates generally contained A. caviae and A. hydrophila, while intestinal were A. veronii (p=0.0001). Extra-intestinal infections (158/188) were the main type and accounted for 24/27 of all fatalities. Malignant tumors, hepatobiliary diseases, anemia, and hypoproteinemia were linked to infections. Poor results were associated with septic shock. Using the broth microdilution method, over 80% isolates were susceptible to most antimicrobials, except for ceftazidime (79.8%) and ceftriaxone (69.7%). Except for imipenem, intestinal strains were more susceptible to other medications than extra-intestinal. Using touch-down polymerase chain reaction testing and DNA sequencing, 6 strains, 31 strains, and a strain only had bla _TEM, bla _CphA, and bla _VIM, respectively. Two Aeromonas hydrophila each possessed bla _CphA+ bla _CTXM-M-9, and bla _CphA + bla _CTX-M-1 + bla _{CTX-M-15-like} + bla _TEM; two Aeromonas caviae each possessed bla _NDM + bla _CTX-M-1 +bla _{CTX-M-15-like} + bla _TEM, and bla _NDM + bla _TEM. Thirty-four of the 42 strains mentioned above were isolated from extra-intestinal. Act, aexT, and ascF-G, were in intestinal more frequently, but alt, hlyA, ela, and lip were in extra-intestinal more frequently.

Conclusion

Aeromonas inside and outside intestinal differed in their clinical characteristics, drug susceptibility, drug resistance and virulence genes.

Genetic Characterization of bla NDM-1-Carrying Citrobacter portucalensis Sequence Type 328 and Citrobacter freundii Sequence Type 98

Purpose

NDM-1-producing Citrobacter portucalensis and Citrobacter freundii simultaneously occurred in a hospital. This study aims to characterize the bla_NDM-1-carrying plasmids in these Citrobacter strains.

Methods

Cf7303, Cf7308, and Cf7313 were recovered from three patients in a teaching hospital from September 24 to October 1, 2021. Bacteria were identified by MALDI-TOF mass spectrometry, and antibiotics susceptibility tests were determined by VITEK^® 2 compact system. Whole-genome sequencing (WGS) was performed using the HiSeq Illumina and QNome platform to characterize the genomes.

Results

Cf7303 was identified as C. portucalensis Sequence Type 328 by WGS, and harbored two plasmids, namely pCf7303 and a novel IncFIB pNDM-Cf7303 on which antibiotic-resistant genes (bla_TEM-1, bla_CTX-M-14, bla_NDM-1, aac (3)-IId, aadA2, fosA3, sul1, sul2, catA2, tetD, dfrA12, qacEdelta1, mph(A), and ble_MBL) are located. C. freundii strain Cf7308 and Cf7313 belonged to the same Sequence Type 98. Cf7308 contained two plasmids, pCf7308, and an IncN1 pNDM-Cf7308 with homology to pNDM-BTR in E. coli and pNDM-CWH001 in C. freundii.

Conclusion

We characterized a putatively novel IncFIB plasmid carrying bla_NDM-1 in C. portucalensis. In addition, the closely related bla_NDM-1-carrying IncN1 plasmids in E. coli and C. freundii suggest that interspecies or intraspecies horizontal transfer occurs in China.

Co-Production of NDM-1 and OXA-10 β-Lactamase in Citrobacter braakii Strain Causing Urinary Tract Infection

In this study, we describe, for the first time, the co-existence of bla_NDM-1and bla_OXA-10 in a carbapenem-resistant Citrobacter braakii strain DY2019 isolated from a patient with urinary tract infection in China. We aimed to investigate the genomic context of two β-lactamase-producing plasmids and characterize the transmission mechanism of the carbapenemase-encoding gene. Whole-genome sequencing of strain DY2019 was performed with Nanopore and Illumina platforms, which revealed a chromosome sequence with the length of 4,830,928 bp, an IncC group plasmid pDY2019-OXA (size of 178,134 bp), and a novel IncHI2 group plasmid pDY2019-NDM (length 348,495 bp). A total of 16 antimicrobial resistance genes (ARGs) that confer resistance to nine different antibiotic groups were identified in strain DY2019, and 11 of them were carried by plasmid pDY2019-OXA. These data and analyses suggest that the carbapenem-resistant C. braakii strains may serve as potential reservoir of carbapenemase and highlight the need for further close surveillance of this species in clinical settings.

Occurrence of NDM-1, VIM-1, and OXA-10 Co-Producing Providencia rettgeri Clinical Isolate in China

Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections related to hospital-acquired Infections. In recent years, P. rettgeri clinical strains producing New Delhi Metallo-β-lactamase (NDM) and other β-lactamase which reduce the efficiency of antimicrobial therapy have been reported. However, there are few reports of P. rettgeri co-producing two metallo-β-lactamases in one isolate. Here, we first reported a P. rettgeri strain (P138) co-harboring bla_NDM-1, bla_VIM-1, and bla_OXA-10. The specie were identified using MALDI-TOF MS. The results of antimicrobial susceptibility testing by broth microdilution method indicated that P. rettgeri P138 was resistant to meropenem (MIC = 64μg/ml), imipenem (MIC = 64μg/ml), and aztreonam (MIC = 32μg/ml). Conjugation experiments revealed that the bla_NDM-1-carrying plasmid was transferrable. The carbapenemase genes were detected using PCR and confirmed by PCR-based sequencing. The complete genomic sequence of the P. rettgeri was identified using Illumina (Illumina, San Diego, CA, USA) short-read sequencing (150bp paired-end reads), and many common resistance genes had been identified, including bla_NDM-1, bla_VIM-1, bla_OXA-10, aac(6’)-Il, aadA5, ant(2’’)-Ia, aadA1, aac(6’)-Ib3, aadA1, aph(3’)-Ia, aac(6’)-Ib-cr, qnrD1, qnrA1, and catA2. The bla_NDM-1 gene was characterized by the following structure: IS110–TnpA–IntI1–aadB–IS91–GroEL–GroES–DsbD–PAI–ble–bla_NDM-1–IS91–QnrS1–IS110. Blast comparison revealed that the bla_NDM-1 gene structure shared >99% similarity with plasmid p5_SCLZS62 (99% nucleotide identity and query coverage). In summary, we isolated a P. rettgeri strain coproducing bla_NDM-1, bla_VIM-1, and blaOXA-10. To the best of our acknowledge, this was first reported in the world. The occurrence of the strain needs to be closely monitored.