Characterization of a blaNDM-1-positive Citrobacter freundii strain isolated from earthworms

OBJECTIVES

Earthworms are one of the key components of soil, and they play a crucial role in the transformation of various nutrients and pollutants in the soil. The purpose of this study is to characterize the NDM-1-producing C. freundii isolated from soil-dwelling earthworms near a hospital, exploring their potential role as carriers of carbapenem-resistant genes.

METHODS

Isolates were isolated from the intestines of earthworms and identified by MALDI-TOF MS. The presence of NDM enzyme was verified through the CARBA-5 Assay. Whole genome sequencing was conducted using the Illumina NovaSeq PE150 platform. Antimicrobial susceptibility testing and conjugation experiment were performed for phenotypic analysis.

RESULTS

This isolate exhibited a multidrug-resistant profile, including resistance to imipenem, meropenem, and ertapenem and successfully transferred blaNDM-1 gene to Escherichia coli. Whole genomic sequencing showed that blaNDM-1 gene was located on an IncFIIY-type plasmid. Phylogenetic analysis revealed a close relationship between the QY221001 strain obtained from earthworms and the human isolate F2021 in the NCBI database, both of which were collected in Hangzhou, China.

CONCLUSION

To our knowledge, this is the first report of an NDM-1-producing bacteria isolated from the intestine of an earthworm. Our finding suggested that earthworms could be a potential reservoir of carbapenem resistance genes, emphasizing the importance of enhanced environmental monitoring of antimicrobial resistance.

Detection of chromosome-mediated blaNDM-1-carrying Aeromonas spp. in the intestinal contents of fresh water river fish in Ho Chi Minh City, Vietnam

The spread of antibiotic-resistant bacteria is a global problem that should be addressed through the perspective of the "one health" concept. The purpose of this study was to determine the contamination rate of antibiotic-resistant Aeromonas spp. in fresh water river fish purchased from a fish market in Vietnam. We then defined the pattern of antibiotic resistance to assess antibiotic-resistant contamination. Antibiotic-resistant Aeromonas spp. were detected in the intestinal contents of 32 of 80 fish. blaNDM-1 was detected in seven strains. Extended-spectrum β-lactamase and AmpC β-lactamase-related genes were detected in 28 strains, including blaCTX-M-55, blaCTX-M-15, blaCTX-M-1, and blaDHA,blaFOX, and blaMOX. The blaNDM-1 detected in the seven Aeromonas spp. strains were found chromosomally. This finding suggests that the blaNDM gene is stable in the natural environment and may spread widely into animals and humans via Aeromonas spp. with a transposon. Our results suggest the importance of continuing to monitor carbapenemase genes in Aeromonas spp. to evaluate the possibility that they may spread in other Enterobacterales, and to elucidate the mechanism of spread.

Characterisation of a Novel Tigecycline Resistance Gene tet(X22) and its Coexistence with blaNDM-1 in a Pseudomonas caeni Isolate

OBJECTIVES

The emergence of pathogens that are resistant to both tigecycline and carbapenem poses a threat to public health globally. Continuous emergence of novel tet(X) variants accelerates the tigecycline resistance crisis. This study aimed to characterise the novel tigecycline resistance gene tet(X22) and its coexistence with carbapenem resistance gene blaNDM-1 in Pseudomonas caeni.

METHODS

This P. caeni isolate co-harbouring tet(X22) and blaNDM-1 was systematically investigated using antimicrobial susceptibility testing, conjugation assays, genome sequencing, bioinformatic analyses, cloning of tet(X22) and functional analysis, and protein structure prediction.

RESULTS

The carbapenem-resistant and tigecycline-resistant P. caeni isolate CE14 was obtained from chicken faeces in 2022. CE14 carried multiple antibiotic resistance genes, including the novel tet(X22) and blaNDM-1. Tet(X22) exhibited 64.72-90.48% amino acid identity with other variants [Tet(X) to Tet(X21)]. Cloning of the gene tet(X22) and protein structure prediction revealed that Tet(X22) confers resistance to tetracyclines, including tigecycline. tet(X22) and blaNDM-1 were located in two multidrug-resistant regions of the chromosome.

CONCLUSIONS

The occurrence of the novel ISCR2-flanked tet(X22) in P. caeni suggests that the tet(X) variant has adapted to new hosts and may widely spread to further expand the host range. The future global spread of such pathogens co-harbouring tet(X) and blaNDM variants needs to be continuously monitored according to the One Health approach.

Dynamic evolution and transmission of a blaNDM-1-bearing fusion plasmid in a clinical Escherichia coli

Plasmids are the main driving forces for the rapid dissemination of blaNDM-1. In recent years, blaNDM-1-carrying fusion plasmids have been frequently reported. However, the evolutionary patterns of blaNDM-1-carrying fusion plasmids remain largely unknown. Herein, we reported a blaNDM-1-bearing fusion plasmid pZX35-269k possessing IncFII and IncA/C2 replicons from clinical ST349 E. coli 13ZX35. The backbone of pZX35-269k was structurally unstable, which was manifested in different types of structural dissociation during conjugation and passage, thereby forming various daughter plasmids. Moreover, the same events were observed in the clinical setting as well. We found that pZX35-269k exhibited highly identical to two plasmids (pZX30-70k and pZX30-192k) in 13ZX30, both of which were isolated from the same hospital. Sequence analysis highlighted that two plasmids in 13ZX30 evolved from pZX35-269k through homologous recombination of a 4856-bp fragment. Collectively, this study confirmed the transmission and structural evolution of a blaNDM-1-bearing fusion plasmid in both laboratory and clinical settings, and provided clear evidence of plasmid spread and evolution in clinical settings. Such versatile plasmids may represent a potential risk for the public health.

Identification of tmexC3-tmexD3-toprJ1b in an XDR Providencia rettgeri clinical isolate co-producing NDM-1 and OXA-10 carbapenemases

OBJECTIVES

Emergence of carbapenemase and tigecycline resistance genes in pathogens threatens the efficacy of last-resort antibiotics. High attention should be paid to the spread and convergence of such resistance genes. This study reports an extensively drug-resistant (XDR) Providencia rettgeri clinical strain co-harbouring carbapenemase genes blaNDM-1, blaOXA-10 and the tmexCD3-toprJ1b gene cluster.

METHODS

The phenotype and genotype of P. rettgeri Pre20-95 were investigated by antimicrobial susceptibility testing, conjugation assay, stability testing and whole genome sequencing. Bioinformatics tools were used to uncover the genetic structures of its multidrug-resistant (MDR) plasmid pPre20-95-1 and SXT/R391 integrative and conjugative element ICEPreChn20-95.

RESULTS

P. rettgeri strain Pre20-95 was isolated from a human clinical infection and displayed an extensively drug-resistant (XDR) phenotype. Whole genome sequencing (WGS) analysis identified a pPrY2001-like MDR plasmid, namely pPre20-95-1, co-harbouring blaNDM-1 and blaOXA-10 genes in Pre20-95. The multidrug resistance region of pPre20-95-1 was composed of a Tn6625-derived module and a ∆Tn1696 structure, and blaNDM-1 and blaOXA-10 were located in a composite Tn structure consisting of insertion sequences ISCR1 and ISAba125 and an In125-like class 1 integron, respectively. Furthermore, the novel RND efflux pump gene cluster tmexCD3-toprJ1b was identified on the SXT/R391 ICE ICEPreChn20-95 of its chromosome, and reverse PCR showed that it could form a circular intermediate for transmission.

CONCLUSION

Our findings highlight further dissemination of the tmexCD3-toprJ1b gene cluster into a clinical isolate of P. rettgeri and convergence with multiple carbapenemase genes, which increases the risk of the emergence of XDR strains and threatens the treatment of Enterobacterales bacterial infections.

Emergence of carbapenem-resistant Enterobacter hormaechei ST93 plasmids co-harbouring blaNDM-1, blaKPC-2, and mcr-9 in bloodstream infection

OBJECTIVES

We isolated a strain of Enterobacter hormaechei, ECC2783, co-harbouring blaNDM-1, blaKPC-2 and mcr-9 plasmids from a bloodstream infection and investigated its biological features.

METHODS

The presence of carbapenemase genes and mcr-9 was confirmed by polymerase chain reaction amplification. Whole genome sequencing and genomic analysis were performed on ECC2783. Experiments assessing the conjugation and stability of plasmids carrying the carbapenemase gene were performed. We also performed a colistin resistance induction experiment and studied the fitness cost of transconjugants.

RESULTS

ECC2783 has an extensive drug resistance phenotype. Multilocus sequence typing analysis results showed that ECC2783 belongs to sequence type 93. Bioinformatics analysis confirmed that ECC2783 has four plasmids, of which pECC2783_a, carrying mcr-9, is the IncHI2 type, and pECC2783_c, carrying blaNDM-1, is the IncX3 type. pECC2783_d, carrying blaKPC-2, is an unclassified type. We successfully obtained two transconjugants (J53/ECC2783_1, carrying blaNDM-1, and J53/ECC2783_2, carrying blaKPC-2 and blaNDM-1). There was no statistically significant difference in the relative growth rate between J53 and J53/ECC2783_2.

CONCLUSION

For the first time, we isolated carbapenem-resistant E. hormaechei plasmids co-harbouring blaNDM-1, blaKPC-2, and mcr-9 from a patient with a blood stream infection. This isolate has a survival advantage in a hospital environment, and its clinical monitoring should be strengthened.

Clonal outbreak of NDM-1 producing Enterobacter hormaechei belonging to high-risk international clone ST78 with the coexistence of tmexCD2-toprJ2 and mcr-9 in China

The emergence of the carbapenem-resistant Enterobacter cloacae complex (CR-ECC) has posed significant challenges to the clinical treatment of healthcare-associated infections globally. Herein, we report the clonal outbreak of NDM-1-producing Enterobacter hormaechei with the coexistence of tmexCD2-toprJ2 and mcr-9 in China. During the outbreak (January 2018-December 2021), a total of fifteen non-repetitive multidrug-resistant E. hormaechei strains were obtained from thirteen patients in a tertiary hospital. The 15 E. hormaechei strains belonged to the high-risk international clone ST78 and co-harbored tmexCD2-toprJ2 and bla_NDM-1, of which 12 E. hormaechei strains carried the mcr-9 gene. Whole-genome sequencing analysis revealed that tmexCD2-toprJ2 and bla_NDM-1 coexisted on the IncFIB/IncFII type plasmid, which could be transferred to E. coli J53 by conjugation and had a significant effect on host fitness. The mcr-9 gene is located between two insertion sequences, IS903B and IS1R, but lacks the two-component system regulatory genes qseBC, which might be the reason for all mcr-9-positive E. hormaechei strains remained susceptible to colistin. Besides, the expression of mcr-9 is not inducible in strains confirmed by colistin induction assays. Furthermore, the phylogenetic analysis illustrated the silent spread and rapid evolution of mcr-9-carrying E. hormaechei worldwide. Collectively, this study enriched the epidemiological and genomic characterization of the coexistence of tmexCD2-toprJ2 and mcr-9 in ST78 CR-ECC isolates and demonstrated that they could prolong clonal dissemination in a tertiary hospital in China. Hence, continuous epidemiological surveillance and molecular characterization of CR-ECC should be conducted to monitor the evolution of CR-ECC around the world.

Presence and characterization of blaNDM-1-positive carbapenemase-producing Klebsiella pneumoniae from outpatients in Thailand

BACKGROUND

Presently, community-associated carbapenemase-producing Enterobacterales (CPE) remains largely unknown and require public attention. This study aimed to investigate the presence of CPE from outpatients in Thailand.

METHODS

Non-duplicate stool (n = 886) and urine (n = 289) samples were collected from outpatients with diarrhea and urinary tract infection, respectively. Demographic data and characteristics of patients were collected. Isolation of CPE was performed by plating enrichment culture on agar supplemented with meropenem. Carbapenemase genes were screened by PCR and sequencing. CPE isolates were phenotypically and genotypically characterized.

RESULTS

Fifteen samples (1.3%, 14 stool and 1 urine) yielded bla_NDM-1-positive carbapenemase-producing Klebsiella pneumoniae (CPKP). Additional resistance to colistin and tigecycline was observed in 53.3% and 46.7% of isolates, respectively. Age >60 years was identified as a risk factor for patients with CPKP (P < 0.001, adjusted odds ratio = 11.500, 95% confidence interval = 3.223-41.034). Pulsed field gel electrophoresis revealed genetic diversity of CPKP isolates; however, clonal spread has been observed. ST70 (n = 4) was common, followed by ST147 (n = 3). bla_NDM-1 from all isolates were transferable and mainly resided on IncA/C plasmid (80%). All bla_NDM-1 plasmids remained stable in bacterial host for at least 10 days in antibiotic-free environments, regardless of replicon types.

CONCLUSION

This study demonstrates that the prevalence of CPE among outpatients in Thailand remains low and the spread of bla_NDM-1-positive CPKP may be driven by IncA/C plasmid. Our results emphasize the need for a large-scale surveillance study to limit further spread of CPE in community.

Transmission and stable inheritance of carbapenemase gene (blaKPC-2 or blaNDM-1)-encoding and mcr-1-encoding plasmids in clinical Enterobacteriaceae strains

OBJECTIVES

The aim of this study was to investigate the potential for transmission and heritability of carbapenemase gene (bla_KPC-2 or bla_NDM-1)-encoding or mcr-1-encoding plasmids in clinical Enterobacteriaceae strains.

METHODS

Potential for transmission of carbapenemase gene (bla_KPC-2 or bla_NDM-1)-encoding or mcr-1-encoding plasmids in clinical Enterobacteriaceae strains was tested in three conjugation models, namely filter-mating conjugation in laboratory conditions, a meat product model and the gastrointestinal (GI) tract of rats. Plasmid stability in Enterobacteriaceae strains was also determined.

RESULTS

We demonstrated that plasmids carrying a carbapenemase gene (bla_KPC-2 or bla_NDM-1) could be efficiently conjugated to strains carrying the mcr-1 gene and vice versa, and that these plasmids could stably co-exist in clinical Enterobacteriaceae strains. These findings suggest that Enterobacteriaceae can readily acquire phenotypic resistance to both carbapenems and colistin in natural environments such as food products and the GI tract of human and animals.

CONCLUSION

Gene transfer events are common among members of the Enterobacteriaceae and serve as a key mechanism facilitating adaptation to new environments. Development of innovative strategies and surveillance measures to curtail the dissemination of multidrug resistance plasmids is necessary. Transmission and stable inheritance of these two types of plasmids would lead to the emergence of multidrug-resistant pathogens that are resistant to all currently available last-line antibiotics for Gram-negative bacterial infections.

Draft genome sequence of a blaNDM-1- and blaOXA-244-carrying multidrug-resistant Escherichia coli D-ST69 clinical isolate from Egypt

OBJECTIVES

This study describes the first draft genome sequence of a multidrug-resistant (MDR) Escherichia coli D-ST69 clinical isolate from Egypt carrying bla_NDM-1 and bla_OXA-244.

METHODS

The strain was isolated in December 2014 from a wound pus swab of a male patient in the city of Kafr El-Sheikh using MacConkey agar containing 2 μg/mL meropenem. The strain was subjected to antimicrobial susceptibility testing, conjugation experiments, and whole-genome sequencing using an Illumina MiSeq platform.

RESULTS

The draft genome of the strain (HR14_AS) was 5.08 Mbp in size containing a total of 90 contigs encoding 4677 predicted genes with an average G+C content of 50.7%. Strain HR14_AS belongs to sequence type 69 (ST69), phylogroup D and exhibits an MDR phenotype, with minimum inhibitory concentrations (MICs) of 64 μg/mL and 32 μg/mL for meropenem and doripenem, respectively. Multiple acquired antimicrobial resistance genes conferring resistance to macrolides [mdf(A)], fluoroquinolones [aac(6')-Ib-cr], quinolones (qnrS1), trimethoprim (dfrA14), β-lactams (bla_NDM-1, bla_OXA-244, bla_CTX-M-15, bla_OXA-9 and bla_TEM-1B) and aminoglycosides [aac(3)-IId, aac(6')-Ib, aadA1 and aph(3')-VI] were detected. The bla_OXA-244 and bla_NDM-1 genes were located on the chromosome (Tn6237) and on an IncI1-type self-conjugative plasmid of >93 kb in size, respectively.

CONCLUSIONS

Here we report the first draft genome sequence of a MDR E. coli D-ST69 isolate carrying bla_NDM-1 and bla_OXA-244. Besides clonal expansion of the E. coli ST38 pandemic clone, this study further identified that the spread of OXA-244-producing E. coli could be related to mobilisation of the IS1R-made composite transposon (Tn6237) carrying bla_OXA-244.

Genetic characterization and virulence of a carbapenem-resistant Raoultella ornithinolytica isolated from well water carrying a novel megaplasmid containing blaNDM-1

Infections caused by carbapenem-resistant Enterobacteriaceae are a growing concern worldwide. Raoultella ornithinolytica is a species in the Enterobacteriaceae family which can cause hospital-acquired infections and is sporadically reported as carbapenem-resistant from human and environmental sources. In this study, we firstly report on an NDM-1-producing R. ornithinolytica, Rao166, isolated from drinking water in an animal cultivation area in China. In addition to carbapenem-resistance, Rao166 was resistant to several other antibiotics including gentamicin, sulfamethoxazole-trimethoprim, tetracycline and fosfomycin. Rao166 carried a novel IncFIC-type megaplasmid, 382,325 bp in length (pRAO166a). A multidrug resistance region, 60,600 bp in length, was identified in the plasmid containing an aac(3)-IId-like gene, aac(6')-Ib-cr, bla_DHA-1, bla_TEM-1B, bla_CTX-M-3, bla_OXA-1, bla_NDM-1, qnrB4, catB3, arr-3, sul1, and tet(D). Results from virulence assays implied that Rao166 has considerable pathogenic potential. Although pRAO166a was found to be non-transmissible, dissemination of the NDM-1 producing strain may occur from well water to humans or animals through cross-contamination during food preparation or directly via drinking water, and potentially lead to difficult-to-treat infections. Thus, contamination of well water by this carbapenem-resistant and presumptively virulent strain of R. ornithinolytica should be considered a potential public health risk.

Behavior of last resort antibiotic resistance genes (mcr-1 and blaNDM-1) in a drinking water supply system and their possible acquisition by the mouse gut flora

Mcr-1 and bla_NDM-1 antibiotic resistance genes (ARGs) confer resistance to colistins and carbapenems, which are often antibiotics used as a last resort in tertiary care hospitals. Dissemination of these two ARGs in drinking water supply systems and their effect on healthy gut bacteria are poorly studied. In this study, the dissemination of mcr-1 and bla_NDM-1 in a drinking water supply system, and their effect on the antibiotic resistance of mouse gut bacteria are explored. Metagenome analysis revealed that source water (Taipu river and Jinze reservoir) was polluted with ARGs. Mcr-1 and bla_NDM-1 can be disseminated through the water distribution system. Even advanced water treatments (ozone and biological activated carbon (BAC)) could not effectively remove mcr-1 and bla_NDM-1. Low concentrations of chloramine disinfectants in the water distribution system were not effective at limiting ARG abundance. Mobile genetic elements were also found to play a major role in the dissemination of ARGs via horizontal gene transfer (HGT) throughout the water supply system. Statistical analysis revealed that there was no effect of temperature on the abundance of mcr-1 and bla_NDM-1 throughout the water supply system. A last resort ARG, mcr-1 can disseminate from drinking water to the healthy mouse gut. The presence of mcr-1 in a strain belonging to Enterococcus hirae, which is different from the strain belonging to the Bacillus cereus group isolated from drinking water, strongly supports the phenomena of HGT inside the gut. This research provides novel insights into the role of drinking water in disseminating ARGs to the gut and strongly suggests that drinking water may also play a major role apart from other factors known to be involved in the prevalence of last resort ARGs in the gut.

Detection of Acinetobacter pittii ST220 co-producing NDM-1 and OXA-820 carbapenemases from a hospital sink in a non-endemic country of NDM

OBJECTIVES

NDM-1 is by far one of the most commonly prevalent carbapenemases in Enterobacteriaceae and Acinetobacter baumannii. This study presented an Acinetobacter pittii (A. pittii) isolate co-harboring bla_NDM-1 and bla_OXA-820 from a university hospital sink, where New Delhi metallo-β-lactamase (NDM) producers have not been found in either patients or their environments.

METHODS

Whole-genome sequencing was performed on the HiSeq 4000 platform, and the reads were de novo assembled using the A5-miSeq Assembly pipeline. Annotation of the resulting scaffolds were performed by using the DDBJ Fast Annotation and Submission Tool (DFAST). The bla_NDM-1-carrying plasmid was determined.

RESULTS

The A. pittii ST220 strain SU1805 detected from a sink strainer in the treatment room was resistant to imipenem and meropenem. Antimicrobial resistance genes bla_NDM-1, bla_OXA-820, bla_ADC-43, and aphA6 were found in this strain. The bla_NDM-1 was found to be located downstream of an ISAba125 element on a plasmid pSU1805NDM with a size of 41,022 bp, and GC content of 38.3% harbouring 48 protein-coding genes. The aphA6 gene was also located upstream of the ISAba125 on the same plasmid. The A. pittii intrinsic bla_OXA-213-like gene bla_OXA-820 was located between fxsA and yncA genes in the chromosome. The strain also harboured biofilm-associated genes such as ompA, the csu operon and their regulating genes bfmRS.

CONCLUSION

This study described the first isolation of NDM-1-producing A. pittii in Japan, and highlighted the importance of proper implementation of measures against AMR for sink drainage systems, since NDM producers may have already been hidden in such environments in a non-endemic country of NDM.

Characterisation of a cointegrate plasmid harbouring blaNDM-1 in a clinical Salmonella Lomita strain

This study aimed to characterise the molecular events underlying formation and evolution of a cointegrate plasmid harbouring bla_NDM-1 and bla_CMY-2 in a clinical Salmonella Lomita (S. Lomita) strain. The Salmonella strain SL131 was found to harbour two multidrug resistant (MDR) plasmids. One plasmid, pSL131_IncHI2, is a typical IncHI2 plasmid containing bla_OXA-1, catB3, arr-3, sul1, qnrB4 and bla_DHA-1 in a complex class 1 integron. The other plasmid, pSL131_IncA/C-IncX3, is a bla_NDM-1-bearing cointegrate plasmid consisting of IncX3 and IncA/C backbones, the formation of which is mediated by IS26. Stability assay showed that the cointegrate plasmid was highly stable in its natural host - S. Lomita - but would readily resolve into single plasmids upon conjugation, during which the IncX3 bla_NDM-1-bearing plasmid could be transferred to Escherichia coli strain EC600. Plasmid evolution through integration of two or more MDR plasmids would not only expand the resistance profile of the resultant plasmid, but also broaden the host spectrum of such resistance-encoding mobile elements. Better understanding of the underlying and triggering mechanisms of cointegration may facilitate development of intervention measures to curb formation and dissemination of such elements.

Effect of concentration gradient carbapenem exposure on expression of blaNDM-1 and acrA in carbapenem resistant Escherichia coli

Escherichia coli, one of the major pathogens, frequently exhibits carbapenem resistance. It would be of interest to investigate which of the mechanisms responds when a strain that carries both bla_NDM-1 and over expressed AcrAB-TolC efflux pump system is exposed against carbapenem under differential concentration gradient stress. Four different sets of strains were used in the study; (i) Strain that have bla_NDM-1 and over expressed AcrAB-TolC system (ii) Strain that harbour bla_NDM-1 and express AcrAB-TolC at basal level (iii) the strain that is devoid of bla_NDM-1 but having over expressed AcrAB-TolC systems and (iv) E. coli AG100A (ΔAcrAB) and E. coli HUE 1 (ΔAcrAB-TolC) where bla_NDM-1was cloned. The Quantitative Real time PCR showed bla_NDM-1 was over expressed under meropenem and imipenem stress irrespective of concentration gradient. In case of ertapenem, at lower concentration AcrA were over expressed whereas, at higher concentration bla_NDM-1 showed elevated expression. A consistent elevated expression of AcrA and AcrB was observed against all carbapenems in the strains devoid of bla_NDM-1 where as in case of the strain with basal level expression of AcrA, no significant over expression could be observed for bla_NDM-1. In case of clones in group IV, expression of bla_NDM-1 was elevated in the presence of carbapenem stress.

Whole-genome analysis of New Delhi Metallo-Beta-Lactamase-1-producing Acinetobacter haemolyticus from China

OBJECTIVE

Infections caused by multidrug-resistant Acinetobacter spp. have generated worldwide attention. With the increasing isolation of non-baumannii Acinetobacter, the nature of associated infection and resistance needs to be explored. This study aimed to analyse the characteristics of New Delhi Metallo-Beta-Lactamase-1 (NDM-1)-producing Acinetobacter haemolyticus (named sz1652) isolated from Shenzhen city, China.

METHODS

The antibiotic spectrum was analysed after antimicrobial susceptibility testing. Combined disk test (CDT) was used to detect the metallo-beta-lactamases (MBLs). Transferability of carbapenem resistance was tested by filter mating experiments and plasmid transformation assays. Whole-genome sequencing (WGS) was performed using HiSeq 2000 and PacBio RS system.

RESULTS

The Acinetobacter haemolyticus strain sz1652 was resistant to carbapenems and other tested agents except for amikacin, tigecycline and colistin. Production of MBLs was confirmed by CDT. Transfer of carbapenem resistance was unsuccessful. WGS analysis showed that the genome of sz1652 comprised a chromosome and two plasmids; 16 genomic islands (GIs) were predicted. Genes associated with resistance were found in this strain, including the beta-lactamase genes bla_NDM-1, bla_OXA-214 and bla_LRA-18, the fluoroquinolone resistant-related mutations [GyrA subunits (Ser81Ile) and ParC subunits (Ser84Tyr)], and efflux pump genes related to tetracycline and macrolide resistance. Analysis of the genetic environment showed that bla_NDM-1 was embedded in Tn125 transposon. The Tn125 structure was chromosomally located and shared > 99% sequence identity with the previously reported bla_NDM-1 carrying region.

CONCLUSION

The NDM-1-producing Acinetobacter haemolyticus coexisted with multiple drug-resistant determinants. The acquisition of the bla_NDM-1 gene was probably facilitated by Tn125 in this strain. Non-Acinetobacter baumannii species also contained GIs.

Genomic mapping of ST85 blaNDM-1 and blaOXA-94 producing Acinetobacter baumannii isolates from Syrian Civil War Victims

OBJECTIVES

The rapid emergence of carbapenem-resistant Acinetobacter baumannii is a global health concern. A comparative genomic analysis was performed on two ST85 A. baumannii strains harboring bla_NDM-1 and bla_OXA-94 collected in Lebanon from Syrian Civil War victims.

METHODS

Genome sequencing data of ACMH-6200 and ACMH-6201 were used for in silico extraction of multilocus sequence types (MLST), resistance genes, and virulence factors. Plasmids were genetically mapped in silico and using PCR-based replicon typing (PBRT). The genetic environment of bla_NDM-1 and bla_OXA-94 was determined, and whole-genome single nucleotide polymorphism (wgSNP) analysis in comparison with 41 publicly available A. baumannii genomes was performed.

RESULTS

Tn125 carrying bla_NDM-1 was truncated by the insertion of ISAba14 downstream of dct, generating ΔTn125. bla_OXA-94 was upstream of ISAba13 and ISAba17. Resistance to ceftazidime could be attributed to AmpC cephalosporinase encoded by bla_ADC-25, and to bla_NDM-1 on plasmids_. GyrA (S83L) and ParC (S80L) substitutions conferred resistance to fluoroquinolones. wgSNP analysis separated the isolates based on their sequence types.

CONCLUSIONS

The role of refugees in the transmission of antimicrobial resistance in developing countries is understudied. As such, this study sheds light on the correlation between population mobility and the importation of drug-resistant pathogens. It also highlights the manifold mechanisms underlying antibiotic resistance in A. baumannii.

Draft genome sequence of an NDM-1-, OXA-421- and AmpC-producing Acinetobacter pittii ST220 in Anhui Province, China

OBJECTIVES

Acinetobacter pittii carrying the bla_NDM-1 gene is frequently reported in the world recently, however most of the bla_NDM-1 genes are located on plasmids. Here we report a multidrug-resistant (MDR) A. pittii isolated in China co-harbouring bla_NDM-1, bla_OXA-421 and bla_AmpC in the genome.

METHODS

Bacterial genomic DNA was extracted using the cetyl trimethylammonium bromide (CTAB) method. Whole-genome sequencing of A. pittii was performed using an Illumina MiSeq system (2×251bp) in combination with PacBio single-molecule real-time (SMRT) sequencing. De novo genome assembly was performed using SPAdes v.3.9.0, A5-miseq v.20150522 and Canu v.1.4, respectively. The genome sequence was analysed by bioinformatics methods.

RESULTS

The 4211131-bp genome with 38.99% G+C content displayed several resistance genes, including bla_NDM-1, bla_OXA-421 and bla_AmpC. Meanwhile, 4426 protein-coding sequences were predicted within the genome.

CONCLUSION

The genome sequence reported here can be compared with the already published genomes of NDM-1-producing isolates. These data might facilitate further understanding of the specific genomic feature of MDR A. pittii in China.

Emerge of blaNDM-1 and blaOXA-48-like harboring carbapenem-resistant Klebsiella pneumoniae isolates from hospitalized patients in southwestern Iran

BACKGROUND

One of the most important emerging carbapenem-resistant bacteria is Klebsiella pneumoniae (K. pneumoniae). The present study aimed to investigate the antibiotic susceptibility pattern of K. pneumoniae isolates and detection of carbapenemase producing K. pneumoniae obtained from Iranian hospitalized patients.

METHODS

This cross-sectional study was performed on 211 K. pneumoniae isolates which were recovered from different clinical specimens from 2014 to 2015. Modified Hodge test (MHT) and double disk synergy test (DDST) were done for detection of carbapenemase and metallo-beta-lactamase (MBL) producing K. pneumoniae. The presence of antibiotic resistance determinants was investigated by polymerase chain reaction (PCR) method.

RESULTS

The results of antibiotic susceptibility showed that all isolates were resistant to ampicillin, and then mostly resistant to piperacillin and ceftazidime with 76.3% and 66.8%, respectively. On the other hand, the highest sensitivity was toward polymyxin B, followed by carbapenems. Of 29 carbapenem-resistant isolates, all were high-level imipenem-resistant isolates (Minimum inhibitory concentration ≥4), except 4 isolates. The results of MHT and DDST showed that 93.1% (27/29) of carbapenem-resistant isolates were carbapenemase and MBL producing isolates, respectively. The presence of bla_NDM-1 and bla_OXA-48-like genes was detected in 27 (10.9%) and 2 (0.9%) isolates, respectively.

CONCLUSION

This is the first identification of bla_NDM-1 and bla_OXA-48-like in K. pneumoniae in Southwestern Iran and the highest reported prevalence of bla_NDM in this bacterium from Iran. Since carbapenem-resistant isolates containing New Delhi metallo-beta-lactamase 1 (NDM-1) were almost resistant to all the tested antibiotics, the resistance due to this gene may be increased in the near future as a potential health threat.

Effect of single-dose carbapenem exposure on transcriptional expression of blaNDM-1 and mexA in Pseudomonas aeruginosa

The therapeutic option of a carbapenem antibiotic is compromised in Pseudomonas aeruginosa owing both to acquired and intrinsic resistance mechanisms. In recent years, New Delhi metallo-β-lactamase has been the focus as a predominant carbapenem resistance determinant. However, it is unclear which of the mechanisms might be adopted by a P. aeruginosa strain possessing both bla_NDM-1 and an overexpressed MexAB-OprM system during carbapenem therapy. This study investigated the interplay of both mechanisms in clinical isolates of P. aeruginosa when exposed to meropenem. Five strains were used: (i) strain overexpressing MexAB-OprM but with no bla_NDM-1; (ii) strain harbouring bla_NDM-1 but expressing MexAB-OprM at basal level; (iii) strain possessing bla_NDM-1 and overexpressing MexAB-OprM; (iv) P. aeruginosa PAO1; and (v) P. aeruginosa K2733-PAO1 (ΔMexAB-OprMΔMexCD-OprJΔMexEF-OprNΔMexXY-OprM) into which bla_NDM-1 was cloned. Strains were incubated in Luria-Bertani broth with and without 1μg/mL meropenem. Total RNA was isolated at 45-min intervals and was immediately reverse transcribed to cDNA. This was repeated for 6h. Quantitative real-time PCR was performed for both resistance mechanisms. Meropenem exposure did not significantly elevate transcription of either the bla_NDM-1 or mexA gene. However, an interesting finding was that upon single-dose exposure to carbapenem, the efflux pump system played a major role in bacterial survival compared with NDM-1. This study gives an insight into the bacterial response to carbapenem antibiotic when two different resistance mechanisms coexist. This type of study would be helpful in designing future antimicrobials.

Co-occurrence of blaNDM-1 with blaOXA-23 or blaOXA-58 in clinical multidrug-resistant Acinetobacter baumannii isolates in Algeria

The aim of this study was to characterise the mechanisms of carbapenem resistance in Acinetobacter baumannii strains isolated in an Algerian hospital. A total of 43 imipenem-resistant A. baumannii clinical isolates collected between 2010 and 2013 were identified using API 20NE and were confirmed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Antibiotic susceptibility testing was performed by the disk diffusion and Etest methods. Carbapenemase activity was detected using microbiological tests and PCR. Genetic transfer of the blaNDM-1 gene was performed by conjugation using sodium azide-resistant Escherichia coli J53 as recipient strain. Clonal relationships were studied by multilocus sequence typing (MLST) using partial sequences of the csuE and blaOXA-51 genes. All 43 A. baumannii isolates were resistant to imipenem with high minimum inhibitory concentrations (MICs) (>32μg/mL). The strains harboured blaOXA-23, blaNDM-1, blaOXA-58 and/or blaOXA-24 genes. Co-existence of blaNDM-1 and blaOXA-23 or blaOXA-58 was detected in two isolates and one isolate, respectively. NDM-1 plasmid transfer to E. coli J53 was successful only for one of the three strains harbouring both blaNDM-1 and blaOXA-23 or blaOXA-58. The phylogenetic tree obtained from concatenation of the partial sequences of csuE and blaOXA-51 showed that there was no genetic relationship between the isolates and the blaNDM-1 resistance gene. Here we report for the first time the co-occurrence of blaNDM-1 along with blaOXA-23 or blaOXA-58 in recent clinical isolates of A. baumannii from Northeast Algeria. These findings re-emphasise the dissemination and rapid spread of blaNDM-1 carbapenemase genes in multidrug-resistant clinical A. baumannii isolates in Algeria.

Draft genome sequence of a multidrug-resistant New Delhi metallo-β-lactamase NDM-1-producing Acinetobacter pittii sequence type 207 isolate from China

The increasing emergence of carbapenem-resistant Acinetobacter spp. worldwide has resulted in the limited availability of effective antimicrobial agents and has become a major public health concern. In this study, the draft genome sequence of Acinetobacter pittii TCM292 belonging to sequence type 207 (ST207), a multidrug-resistant (MDR) isolate harbouring the New Delhi metallo-β-lactamase blaNDM-1 gene, was determined using an Illumina HiSeq™ 2000 platform. The genome sequence was analysed by bioinformatics methods. The A. pittii TCM292 genome size was estimated to be 3791758bp with 3486 predicted coding regions. These data might facilitate further understanding of the specific genomic features of MDR A. pittii in China.