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1.
Clin Infect Dis ; 78(2): 248-258, 2024 02 17.
Article in English | MEDLINE | ID: mdl-37738153

ABSTRACT

BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAb) is 1 of the most problematic antimicrobial-resistant bacteria. We sought to elucidate the international epidemiology and clinical impact of CRAb. METHODS: In a prospective observational cohort study, 842 hospitalized patients with a clinical CRAb culture were enrolled at 46 hospitals in five global regions between 2017 and 2019. The primary outcome was all-cause mortality at 30 days from the index culture. The strains underwent whole-genome analysis. RESULTS: Of 842 cases, 536 (64%) represented infection. By 30 days, 128 (24%) of the infected patients died, ranging from 1 (6%) of 18 in Australia-Singapore to 54 (25%) of 216 in the United States and 24 (49%) of 49 in South-Central America, whereas 42 (14%) of non-infected patients died. Bacteremia was associated with a higher risk of death compared with other types of infection (40 [42%] of 96 vs 88 [20%] of 440). In a multivariable logistic regression analysis, bloodstream infection and higher age-adjusted Charlson comorbidity index were independently associated with 30-day mortality. Clonal group 2 (CG2) strains predominated except in South-Central America, ranging from 216 (59%) of 369 in the United States to 282 (97%) of 291 in China. Acquired carbapenemase genes were carried by 769 (91%) of the 842 isolates. CG2 strains were significantly associated with higher levels of meropenem resistance, yet non-CG2 cases were over-represented among the deaths compared with CG2 cases. CONCLUSIONS: CRAb infection types and clinical outcomes differed significantly across regions. Although CG2 strains remained predominant, non-CG2 strains were associated with higher mortality. Clinical Trials Registration. NCT03646227.


Subject(s)
Acinetobacter Infections , Acinetobacter baumannii , Humans , Acinetobacter baumannii/genetics , Carbapenems/pharmacology , Carbapenems/therapeutic use , Prospective Studies , Microbial Sensitivity Tests , Acinetobacter Infections/drug therapy , Acinetobacter Infections/epidemiology , Acinetobacter Infections/microbiology , beta-Lactamases/genetics , Bacterial Proteins/genetics , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use
2.
Clin Microbiol Rev ; 35(1): e0000621, 2022 01 19.
Article in English | MEDLINE | ID: mdl-34851134

ABSTRACT

Klebsiella oxytoca is actually a complex of nine species-Klebsiella grimontii, Klebsiella huaxiensis, Klebsiella michiganensis, K. oxytoca, Klebsiella pasteurii, Klebsiella spallanzanii, and three unnamed novel species. Phenotypic tests can assign isolates to the complex, but precise species identification requires genome-based analysis. The K. oxytoca complex is a human commensal but also an opportunistic pathogen causing various infections, such as antibiotic-associated hemorrhagic colitis (AAHC), urinary tract infection, and bacteremia, and has caused outbreaks. Production of the cytotoxins tilivalline and tilimycin lead to AAHC, while many virulence factors seen in Klebsiella pneumoniae, such as capsular polysaccharides and fimbriae, have been found in the complex; however, their association with pathogenicity remains unclear. Among the 5,724 K. oxytoca clinical isolates in the SENTRY surveillance system, the rates of nonsusceptibility to carbapenems, ceftriaxone, ciprofloxacin, colistin, and tigecycline were 1.8%, 12.5%, 7.1%, 0.8%, and 0.1%, respectively. Resistance to carbapenems is increasing alarmingly. In addition to the intrinsic blaOXY, many genes encoding ß-lactamases with varying spectra of hydrolysis, including extended-spectrum ß-lactamases, such as a few CTX-M variants and several TEM and SHV variants, have been found. blaKPC-2 is the most common carbapenemase gene found in the complex and is mainly seen on IncN or IncF plasmids. Due to the ability to acquire antimicrobial resistance and the carriage of multiple virulence genes, the K. oxytoca complex has the potential to become a major threat to human health.


Subject(s)
Enterocolitis, Pseudomembranous , Klebsiella Infections , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Carbapenems , Drug Resistance, Bacterial/genetics , Humans , Klebsiella Infections/drug therapy , Klebsiella Infections/epidemiology , Klebsiella oxytoca/genetics , Klebsiella pneumoniae , Microbial Sensitivity Tests , Virulence , beta-Lactamases/genetics
3.
PLoS Med ; 20(6): e1004233, 2023 06.
Article in English | MEDLINE | ID: mdl-37339120

ABSTRACT

BACKGROUND: Klebsiella pneumoniae is the most common pathogen causing neonatal infections, leading to high mortality worldwide. Along with increasing antimicrobial use in neonates, carbapenem-resistant K. pneumoniae (CRKP) has emerged as a severe challenge for infection control and treatment. However, no comprehensive systematic review is available to describe the global epidemiology of neonatal CRKP infections. We therefore performed a systematic review of available data worldwide and combined a genome-based analysis to address the prevalence, clonal diversity, and carbapenem resistance genes of CRKP causing neonatal infections. METHODS AND FINDINGS: We performed a systematic review of studies reporting population-based neonatal infections caused by CRKP in combination with a genome-based analysis of all publicly available CRKP genomes with neonatal origins. We searched multiple databases (PubMed, Web of Science, Embase, Ovid MEDLINE, Cochrane, bioRxiv, and medRxiv) to identify studies that have reported data of neonatal CRKP infections up to June 30, 2022. We included studies addressing the prevalence of CRKP infections and colonization in neonates but excluded studies lacking the numbers of neonates, the geographical location, or independent data on Klebsiella or CRKP isolates. We used narrative synthesis for pooling data with JMP statistical software. We identified 8,558 articles and excluding those that did not meet inclusion criteria. We included 128 studies, none of which were preprints, comprising 127,583 neonates in 30 countries including 21 low- and middle-income countries (LMICs) for analysis. We found that bloodstream infection is the most common infection type in reported data. We estimated that the pooled global prevalence of CRKP infections in hospitalized neonates was 0.3% (95% confidence interval [CI], 0.2% to 0.3%). Based on 21 studies reporting patient outcomes, we found that the pooled mortality of neonatal CRKP infections was 22.9% (95% CI, 13.0% to 32.9%). A total of 535 neonatal CRKP genomes were identified from GenBank including Sequence Read Archive, of which 204 were not linked to any publications. We incorporated the 204 genomes with a literature review for understanding the species distribution, clonal diversity, and carbapenemase types. We identified 146 sequence types (STs) for neonatal CRKP strains and found that ST17, ST11, and ST15 were the 3 most common lineages. In particular, ST17 CRKP has been seen in neonates in 8 countries across 4 continents. The vast majority (75.3%) of the 1,592 neonatal CRKP strains available for analyzing carbapenemase have genes encoding metallo-ß-lactamases and NDM (New Delhi metallo-ß-lactamase) appeared to be the most common carbapenemase (64.3%). The main limitation of this study is the absence or scarcity of data from North America, South America, and Oceania. CONCLUSIONS: CRKP contributes to a considerable number of neonatal infections and leads to significant neonatal mortality. Neonatal CRKP strains are highly diverse, while ST17 is globally prevalent and merits early detection for treatment and prevention. The dominance of blaNDM carbapenemase genes imposes challenges on therapeutic options in neonates and supports the continued inhibitor-related drug discovery.


Subject(s)
Carbapenem-Resistant Enterobacteriaceae , Communicable Diseases , Klebsiella Infections , Infant, Newborn , Humans , Klebsiella pneumoniae/genetics , Prevalence , Klebsiella Infections/drug therapy , Klebsiella Infections/epidemiology , Carbapenem-Resistant Enterobacteriaceae/genetics , Carbapenems/pharmacology , Carbapenems/therapeutic use
4.
J Antimicrob Chemother ; 78(5): 1288-1294, 2023 05 03.
Article in English | MEDLINE | ID: mdl-36995982

ABSTRACT

BACKGROUND: We found a carbapenem-resistant Escherichia coli without known carbapenemase-encoding genes and performed a study to identify the possible new carbapenemase. METHODS: The production of carbapenemase was examined using the modified carbapenem inactivation method. The strain was subjected to short- and long-read genome sequencing and the complete genome was obtained by hybrid assembly. The gene encoding a potential new OXA-type carbapenemase was cloned. The enzyme was purified and was then subjected to kinetic assays. Molecular docking analysis of the enzyme was performed using the MOE software suite. Mating experiments were attempted to obtain the plasmid carrying the corresponding gene. RESULTS: We identified and characterized a novel class D carbapenem-hydrolysing ß-lactamase, OXA-1041, in a carbapenem-resistant E. coli clinical strain. OXA-1041 had 89.77% (237/264) amino acid identity with OXA-427, a known carbapenemase. By cloning in an E. coli laboratory strain, blaOXA-1041 was found to reduce susceptibility to ertapenem by 16 times (MIC 0.25 versus 0.016 mg/L) and meropenem by four times (MIC 0.06 versus 0.016 mg/L) but did not significantly reduce susceptibility to imipenem and doripenem. Enzyme kinetic measurement of purified OXA-1041 showed that OXA-1041 could hydrolyse ertapenem and meropenem with a turnover number (kcat)/Michaelis constant (KM) of 8.57 and 3.63 mM-1s-1, respectively. The complete genome contained a single plasmid (223 341 bp, IncF, containing five replicons), which was self-transmissible. blaOXA-1041 was downstream of insertion sequence ISCR1 and there were three tandem copies of ISCR1-blaOXA-1041-creDΔ (encoding an envelope protein) on this plasmid. CONCLUSIONS: The above findings suggest OXA-1041 is a new plasmid-encoded carbapenemase with preferential activity against ertapenem.


Subject(s)
Carbapenems , Escherichia coli , Carbapenems/pharmacology , Carbapenems/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/metabolism , Meropenem , Ertapenem/pharmacology , Molecular Docking Simulation , beta-Lactamases/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Microbial Sensitivity Tests
5.
Int J Syst Evol Microbiol ; 73(10)2023 Oct.
Article in English | MEDLINE | ID: mdl-37889259

ABSTRACT

In 1989, Bouvet and Jeanjean delineated five proteolytic genomic species (GS) of Acinetobacter, each with two to four human isolates. Three were later validly named, whereas the remaining two (GS15 and GS16) have been awaiting nomenclatural clarification. Here we present the results of the genus-wide taxonomic study of 13 human strains classified as GS16 (n=10) or GS15 (n=3). Based on core genome phylogenetic analysis, the strains formed two respective but closely related phylogroups within the Acinetobacter haemolytic clade. The intraspecies genomic average nucleotide identity based on blast (ANIb) values for GS16 and GS15 reached ≥94.9 % and ≥98.7, respectively, whereas ANIb values between them were 92.5-93.5% and those between them and the known species were ≤91.5 %. GS16 and GS15 could be differentiated from the other Acinetobacter species by their ability to lyse gelatin and sheep blood and to assimilate d,l-lactate, along with their inability to acidify d-glucose and assimilate glutarate. In contrast, GS16 and GS15 were indistinguishable from one another by metabolic/physiological features or whole-cell MALDI-TOF mass spectra. All the GS15/GS16 genomes contained genes encoding a class D ß-lactamase, Acinetobacter-derived cephalosporinase and aminoglycoside 6'-N-acetyltransferase. Searching NCBI databases revealed genome sequences of three additional isolates of GS16, but none of GS15. We conclude that our data support GS16 as representing a novel species, but leave the question of the taxonomic status of GS15 open, given its close relatedness to GS16 and the small number of available strains. We propose the name Acinetobacter higginsii sp. nov. for GS16, with the type strain NIPH 1872T (CCM 9243T=CIP 70.18T=ATCC 17988T).


Subject(s)
Acinetobacter , Humans , Animals , Sheep , Sequence Analysis, DNA , Phylogeny , Fatty Acids/chemistry , Bacterial Typing Techniques , DNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Base Composition , Genomics , Nucleic Acid Hybridization
6.
Eur J Clin Microbiol Infect Dis ; 42(4): 513-517, 2023 Apr.
Article in English | MEDLINE | ID: mdl-36773190

ABSTRACT

We found a carbapenem-resistant Enterobacter clinical strain which was susceptible to cefotaxime and ceftazidime. This unusual susceptibility profile promoted the investigation. This strain had blaFRI-11, a rare carbapenemase-encoding gene, on a 93,864-bp plasmid containing two replicons of IncFII(pECLA) and IncFIA(HI1). FRI-11, FRI-2, FRI-3, FRI-4, FRI-6, FRI-7, and FRI-9 belong to the same group of FRI ß-lactamases based on the amino acid sequence similarity and their encoding genes are carried by plasmids containing an IncFII(pECLA) replicon. Awareness should be raised towards FRI carbapenemases that are plasmid-encoded and confer an unusual carbapenem-resistant but 3rd-generation-cephalosporin-susceptible resistance profile.


Subject(s)
Anti-Bacterial Agents , Enterobacter , Humans , Enterobacter/genetics , Anti-Bacterial Agents/pharmacology , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , beta-Lactamases/genetics , beta-Lactamases/metabolism , Carbapenems/pharmacology , Plasmids/genetics , Microbial Sensitivity Tests
7.
Eur J Clin Microbiol Infect Dis ; 42(5): 529-541, 2023 May.
Article in English | MEDLINE | ID: mdl-36856898

ABSTRACT

Carbapenem-resistant Klebsiella pneumoniae (CRKP) infection is a major public health threat in the world. To inform the prevention and control of CRKP infection in hospitals, this study analyzed the factors associated with CRKP infection and resistance to carbapenems in K. pneumoniae. This case-case-control study was carried out in a large general hospital in China from January 2016 to December 2018, comprising 494 hospitalized patients infected with CRKP (case group 1) and 2429 hospitalized patients infected with carbapenem-susceptible K. pneumoniae (CSKP, case group 2). We selected control groups from hospitalized patients without K. pneumoniae infections for the two case groups separately, with a 1:3 case-control ratio, to analyze the risk factors of the two case groups using the conditional logistic regression. Multivariate analysis showed that the risk factors of CRKP infection were intensive care unit (ICU) admission (odds ratio [OR], 6.85; 95% confidence interval [CI], 4.90-9.58; P < 0.001), respiratory failure (OR, 1.93; 95% CI, 1.34-2.77; P < 0.001), age-adjusted Charlson comorbidity index (aCCI; OR, 1.08; 95% CI, 1.02-1.15; P = 0.007), admission from the Emergency (OR, 1.37; 95% CI, 1.02-1.85; P = 0.036), and imipenem use (OR, 1.80; 95% CI, 1.30-2.49; P < 0.001). Among the aforementioned five risk factors, aCCI (OR, 1.09; 95% CI, 1.06-1.13; P < 0.001) was also identified as a risk factor of CSKP infections in multivariate analysis. The risk factors for resistance to carbapenems in K. pneumoniae were ICU admission, respiratory failure, admission from the Emergency, and imipenem use.


Subject(s)
Carbapenem-Resistant Enterobacteriaceae , Cross Infection , Klebsiella Infections , Humans , Case-Control Studies , Anti-Bacterial Agents/adverse effects , Klebsiella pneumoniae , Hospitals, General , Klebsiella Infections/drug therapy , Klebsiella Infections/epidemiology , Drug Resistance, Bacterial , Carbapenems/pharmacology , Carbapenems/therapeutic use , Imipenem/pharmacology , Risk Factors , Cross Infection/epidemiology , Cross Infection/drug therapy , Delivery of Health Care
8.
Ann Clin Microbiol Antimicrob ; 22(1): 49, 2023 Jun 26.
Article in English | MEDLINE | ID: mdl-37365592

ABSTRACT

Aztreonam-avibactam is an important option against Enterobacterales producing metallo-ß-lactamases (MBLs). We obtained an aztreonam-avibactam-resistant mutant of an MBL-producing Enterobacter mori strain by induced mutagenesis. Genome sequencing revealed an Arg244Gly (Ambler position) substitution of SHV-12 ß-lactamase in the mutant. Cloning and susceptibility testing verified that the SHV-12 Arg244Gly substitution led to significantly reduced susceptibility to aztreonam-avibactam (MIC, from 0.5/4 to 4/4 mg/L) but with the loss of resistance to cephalosporins as tradeoff. Arg244 of SHV involves in the binding of avibactam by forming an arginine-mediated salt bridge and is a critical residue to interact with ß-lactams. Molecular modeling analysis demonstrated that the Arg244Gly substitution hindered the binding of avibactam to SHV with higher binding energy (from - 5.24 to -4.32 kcal/mol) and elevated inhibition constant Ki (from 143.96 to 677.37 µM) to indicate lower affinity. This substitution, however, resulted in loss of resistance to cephalosporins as tradeoff by impairing substrate binding. This represents a new aztreonam-avibactam resistance mechanism.


Subject(s)
Anti-Bacterial Agents , Aztreonam , Humans , Aztreonam/pharmacology , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , beta-Lactamases/genetics , beta-Lactamases/metabolism , Cephalosporins/pharmacology , Enterobacter/genetics , Mutation , Microbial Sensitivity Tests , Drug Combinations , Ceftazidime/pharmacology
9.
Antonie Van Leeuwenhoek ; 116(7): 643-651, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37101063

ABSTRACT

Two Enterobacter strains 155092T and 170,225 were isolated from clinical samples, pus and sputum, from two hospitalised patients separately, in China. Preliminary identification using Vitek II microbiology system assigned the strains to the Enterobacter cloacae complex. The two strains were subjected to genome sequencing and genome-based taxonomy analysis with type strains of all Enterobacter species and those within closely related genera Huaxiibacter, Leclercia, Lelliottia, and Pseudoenterobacter. The average nucleotide identity (ANI) and in silico DNA-DNA hybridisation (isDDH) values between the two strains were 98.35% and 89.4%, respectively, suggesting that they belong to one species. The two strains had the highest ANI (95.02% and 95.04%) with the type strain of Enterobacter quasiroggenkampii. Their highest isDDH values, also seen with the type strain of E. quasiroggenkampii, were 59.5% and 59.8%, well below the 70% cutoff to define species. The two strains were also characterised for morphological and biochemical features by a set of experiments and observations. The abilities of metabolising gelatin and L-rhamnose could differentiate the two strains from all currently known Enterobacter species. Collectively, the two strains represent a novel Enterobacter species, for which we propose Enterobacter pseudoroggenkampii sp. nov. as the species name. The type strain of this novel species is155092T (= GDMCC 1.3415T = JCM 35646T). The two strains also carried multiple virulence factors comprising aerobactin-encoding iucABCD-iutA and salmochelin-encoding iroN. The two strains also had chromosomally located qnrE, a gene associated with reduced susceptibility to quinolones, suggesting that this species is a potential reservoir of qnrE genes.


Subject(s)
Enterobacter , Quinolones , Humans , Sequence Analysis, DNA , Fatty Acids , Phylogeny , Bacterial Typing Techniques , DNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Enterobacteriaceae/genetics , China
10.
Antimicrob Agents Chemother ; 66(3): e0218321, 2022 03 15.
Article in English | MEDLINE | ID: mdl-35007133

ABSTRACT

Klebsiella oxytoca complex comprises nine closely related species causing human infections. We curated genomes labeled Klebsiella (n = 14,256) in GenBank and identified 588 belonging to the complex, which were examined for precise species, sequence types, K- and O-antigen types, and virulence and antimicrobial resistance genes. The complex and Klebsiella pneumoniae share many K- and O-antigen types. Of the complex, K. oxytoca and Klebsiella michiganensis appear to carry more virulence genes and be more commonly associated with human infections.


Subject(s)
Klebsiella Infections , Klebsiella oxytoca , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Drug Resistance, Bacterial/genetics , Humans , Klebsiella Infections/drug therapy , Klebsiella oxytoca/genetics , Klebsiella pneumoniae/genetics , Virulence/genetics
11.
Antimicrob Agents Chemother ; 66(3): e0222721, 2022 03 15.
Article in English | MEDLINE | ID: mdl-35041510

ABSTRACT

In-silico analysis and cloning experiments identified a fosC2-like fosfomycin resistance gene in the chromosome of Aliidiomarina shirensis, with our data suggesting that this bacterium might be added to the list of species identified as reservoirs of fos-like genes that were subsequently acquired by other Gram-negative species. Indeed, the fosC2 gene was identified as acquired in Providencia huaxinensis and Aeromonas hydrophila isolates, with this gene being located in class 1 integron structures in the latter cases. Biochemical characterization and site-directed mutagenesis showed a higher catalytic efficiency for the intrinsic FosC2AS (from A. shirensis) than for the acquired FosC2 (from P. huaxinensis) enzyme due to a single substitution in the amino acid sequence (Gly43Glu). Notably, this study constitutes the first identification of the likely natural reservoir of a complete gene cassette (including its attC site).


Subject(s)
Fosfomycin , Anti-Bacterial Agents/pharmacology , Fosfomycin/pharmacology , Gammaproteobacteria , Integrons/genetics , Microbial Sensitivity Tests , Plasmids/genetics , Polymerase Chain Reaction
12.
Crit Care Med ; 50(2): 307-316, 2022 02 01.
Article in English | MEDLINE | ID: mdl-34473657

ABSTRACT

OBJECTIVES: Fluid therapy is an important component of intensive care management, however, optimal fluid management is unknown. The relationship between fluid balance and ventilator-associated events has not been well established. This study investigated the dose-response relationship between fluid balance and ventilator-associated events. DESIGN: Nested case-control study. SETTING: The study was based on a well-established, research-oriented registry of healthcare-associated infections at ICUs of West China Hospital system (Chengdu, China). PATIENTS: A total of 1,528 ventilator-associated event cases with 3,038 matched controls, who consistently underwent mechanical ventilation for at least 4 days from April 1, 2015, to December 31, 2018, were included. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: We calculated cumulative fluid balance within 4 days prior to ventilator-associated event occurrence. A weighted Cox proportional hazards model with restricted cubic splines was used to evaluate the dose-response relationship. A nonlinear relationship between fluid balance and all three tiers of ventilator-associated events, patients with fluid balance between -1 and 0 L had the lowest risk (p < 0.05 for nonlinear test). The risk of ventilator-associated event was significantly higher in patients with positive fluid balance (4 d cumulative fluid balance: 1 L: 1.19; 3 L: 1.92; 5 L: 2.58; 7 L: 3.24), but not in those with negative fluid balance (-5 L: 1.34; -3 L: 1.14; -1 L: 0.98). CONCLUSIONS: There was nonlinear relationship between fluid balance and all three tiers of ventilator-associated event, with an fluid balance between -1 and 0 L corresponding to the lowest risk. Positive but not negative fluid balance increased the risk of ventilator-associated events, with higher positive fluid balance more likely to lead to ventilator-associated events.


Subject(s)
Respiration, Artificial/adverse effects , Ventilators, Mechanical/adverse effects , Water-Electrolyte Balance/physiology , Aged , Case-Control Studies , China/epidemiology , Female , Fluid Therapy/adverse effects , Fluid Therapy/methods , Fluid Therapy/statistics & numerical data , Humans , Intensive Care Units/organization & administration , Intensive Care Units/statistics & numerical data , Male , Middle Aged , Respiration, Artificial/instrumentation , Ventilators, Mechanical/statistics & numerical data , Water-Electrolyte Balance/drug effects
13.
Article in English | MEDLINE | ID: mdl-35976100

ABSTRACT

Strain 155047T was recovered from human sputum in China in 2021. Preliminary species identification based on limited phenotypic tests assigned the strain to the genus Enterobacter of the family Enterobacteriaceae. The genome sequence of the strain was obtained and had ≤84.43 % average nucleotide identity (ANI) and ≤26.3 % in silico DNA-DNA hybridization (isDDH) values with the genomes of type strains of known Enterobacteriaceae species. The highest ANI and isDDH matches were with Lelliottia nimipressuralis and Enterobacter asburiae, respectively. The ANI and isDDH values support that the strain belongs to a novel species of the family Enterobacteriaceae. Phylogenomic analysis based on core genes revealed that strain 155047T was located in the Enterobacter-Leclercia-Lelliottia-Pseudenterobacter lineage. The highest ANI and average amino acid identity values between 155047T and any species of the Enterobacter-Leclercia-Lelliottia-Pseudenterobacter lineage were 84.43 % and 90.21 %, respectively, lower than the maximum inter-genus pairwise values. This indicates that 155047T belongs to a novel species of a novel genus in the lineage. Strain 155047T could be differentiated from Enterobacter, Lelliottia, Leclercia and Pseudenterobacter species by a negative reaction for ß-galactosidase and the ability to produce acid from l-fucose but not from sucrose. The names Huaxiibacter gen. nov. and Huaxiibacter chinensis sp. nov. are proposed for the novel genus and species, respectively. The type strain is 155047T (= GDMCC 1.2980T=JCM 35262T).


Subject(s)
Fatty Acids , Sputum , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Humans , Nucleic Acid Hybridization , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
14.
BMC Infect Dis ; 22(1): 557, 2022 Jun 18.
Article in English | MEDLINE | ID: mdl-35717143

ABSTRACT

BACKGROUND: Splenic cyst complicated by non-typhoid Salmonella infection is rare in healthy individuals in the era of antibiotics. Salmonella enterica subsp. enterica serovar Livingstone causing infection of giant splenic cyst has not been previously reported. CASE PRESENTATION: We report a case of giant splenic cyst (maximum diameter, 21 cm) complicated with Salmonella Livingstone infection, which resulted in splenic abscess, in a 16-year-old previously healthy adolescent male. The splenic abscess was successfully treated with ultrasonography-guided percutaneous drainage and antimicrobial therapy. CONCLUSION: Infection of splenic cyst may be caused by S. Livingstone in immunocompetent individuals. This case may help clinicians to raise awareness towards splenic abscess and highlights the importance of drainage and antimicrobial agents to avoid splenectomy.


Subject(s)
Abdominal Abscess , Cysts , Intraabdominal Infections , Salmonella Infections , Salmonella enterica , Splenic Diseases , Abdominal Abscess/drug therapy , Abscess/drug therapy , Adolescent , Anti-Bacterial Agents/therapeutic use , Drainage/methods , Humans , Intraabdominal Infections/drug therapy , Male , Salmonella , Salmonella Infections/complications , Salmonella Infections/diagnosis , Salmonella Infections/drug therapy , Serogroup , Splenic Diseases/complications , Splenic Diseases/diagnosis , Splenic Diseases/surgery
15.
Emerg Infect Dis ; 27(1): 161-169, 2021 01.
Article in English | MEDLINE | ID: mdl-33350909

ABSTRACT

The clinical importance of Enterobacter spp. remains unclear because phenotype-based Enterobacter species identification is unreliable. We performed a genomic study on 48 cases of Enterobacter-caused bloodstream infection by using in silico DNA-DNA hybridization to identify precise species. Strains belonged to 12 species; Enterobacter xiangfangensis (n = 21) and an unnamed species (taxon 1, n = 8) were dominant. Most (63.5%) Enterobacter strains (n = 349) with genomes in GenBank from human blood are E. xiangfangensis; taxon 1 (19.8%) was next most common. E. xiangfangensis and taxon 1 were associated with increased deaths (20.7% vs. 15.8%), lengthier hospitalizations (median 31 d vs. 19.5 d), and higher resistance to aztreonam, cefepime, ceftriaxone, piperacillin-tazobactam, and tobramycin. Strains belonged to 37 sequence types (STs); ST171 (E. xiangfangensis) was most common (n = 6). Four ST171 strains belonged to a defined clone. Precise species identification has greater implications for epidemiology and infection control than treatment.


Subject(s)
Bacteremia , Enterobacteriaceae Infections , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Bacteremia/drug therapy , Bacteremia/epidemiology , China/epidemiology , Enterobacter/genetics , Enterobacteriaceae Infections/drug therapy , Enterobacteriaceae Infections/epidemiology , Humans , Microbial Sensitivity Tests
16.
Emerg Infect Dis ; 27(10): 2740-2742, 2021 10.
Article in English | MEDLINE | ID: mdl-34546163

ABSTRACT

Emergomyces is a newly described dimorphic fungus genus; it may cause fatal infections in immunocompromised patients, but diagnosis is often delayed. We report a case of disseminated emergomycosis caused by the novel species Emergomyces orientalis in a kidney transplant recipient from Tibet. Infection was diagnosed early by metagenomic next-generation sequencing.


Subject(s)
Mycoses , High-Throughput Nucleotide Sequencing , Humans , Metagenomics , Mycoses/diagnosis , Onygenales
17.
Antimicrob Agents Chemother ; 65(12): e0159621, 2021 11 17.
Article in English | MEDLINE | ID: mdl-34516244

ABSTRACT

We performed whole-genome sequencing for 17 Enterobacter clinical strains and analyzed all available Enterobacter genomes and those of its closely related genera (n = 3,389) from NCBI. The exact origins of plasmid-borne blaCMH and blaMIR genes are Enterobacter cloacae and Enterobacter roggenkampii, respectively, while plasmid-borne blaACT genes originated from multiple other Enterobacter species, including Enterobacter xiangfangensis, Enterobacter hoffmannii, Enterobacter asburiae, Enterobacter ludwigii, and Enterobacter kobei. The genus Enterobacter represents a large reservoir of plasmid-borne AmpC ß-lactamase.


Subject(s)
Enterobacter , beta-Lactamases , Bacterial Proteins/genetics , Enterobacter/genetics , Enterobacter cloacae/genetics , Microbial Sensitivity Tests , Plasmids/genetics , beta-Lactamases/genetics
18.
Article in English | MEDLINE | ID: mdl-33199393

ABSTRACT

mcr-10 is a newly identified plasmid-borne colistin resistance gene, but its mobilization mechanism remains unclear. In this study, mcr-10 was found on an IncFIB plasmid carrying virulence genes mrkABCDFJ, iucABCD/iutA, and eitCBAD in a Cronobacter sakazakii isolate. By comparison with closely related plasmids, two recombination sites were identified flanking the genetic element containing mcr-10 and an integrase-encoding gene, suggesting that site-specific recombination mediated by an integrase of an integrative mobile element is a potential mechanism for mobilizing mcr-10.


Subject(s)
Cronobacter sakazakii , Escherichia coli Proteins , Anti-Bacterial Agents/pharmacology , Colistin , Cronobacter sakazakii/genetics , Drug Resistance, Bacterial/genetics , Escherichia coli Proteins/genetics , Plasmids/genetics , Recombination, Genetic
19.
Eur J Clin Microbiol Infect Dis ; 40(8): 1761-1766, 2021 Aug.
Article in English | MEDLINE | ID: mdl-33595757

ABSTRACT

KPC-12 is a variant of KPC-2 with a L169M substitution in the Ω loop, but its resistance spectrum was not reported. blaKPC-12 was cloned, and KPC-12 exhibited significantly decreased activities against imipenem, meropenem, aztreonam, and piperacillin-tazobactam with ≥4-fold lower MICs than KPC-2. However, unlike the L169P substitution in KPC-35, activities against ceftazidime and ceftazidime-avibactam of KPC-12 were unaltered. This highlights that different substitutions at the same position of carbapenemases may have varied impact on the activity.


Subject(s)
Bacterial Proteins/metabolism , Drug Resistance, Multiple, Bacterial , Klebsiella pneumoniae/enzymology , beta-Lactamases/chemistry , beta-Lactamases/metabolism , Amino Acid Substitution , Gene Expression Regulation, Enzymologic , Humans , Klebsiella pneumoniae/drug effects , Microbial Sensitivity Tests , Models, Molecular , Mutation , Protein Conformation , beta-Lactamases/genetics
20.
Crit Care ; 25(1): 44, 2021 02 02.
Article in English | MEDLINE | ID: mdl-33531078

ABSTRACT

BACKGROUND: Ventilator-associated pneumonia (VAP) is the most common hospital-acquired infection (HAI) in intensive care units (ICUs). Ventilator-associated event (VAE), a more objective definition, has replaced traditional VAP surveillance and is now widely used in the USA. However, the adoption outside the USA is limited. This study aims to describe the epidemiology and clinical outcomes of VAEs in China, based on a prospectively maintained registry. METHODS: An observational study was conducted using an ICU-HAI registry in west China. Patients that were admitted to ICUs and underwent mechanical ventilation (MV) between April 1, 2015, and December 31, 2018, were included. The characteristics and outcomes were compared between patients with and without VAEs. The rates of all VAEs dependent on different ICUs were calculated, and the pathogen distribution of patients with possible VAP (PVAP) was described. RESULTS: A total of 20,769 ICU patients received MV, accounting for 21,723 episodes of mechanical ventilators and 112,697 ventilator-days. In all, we identified 1882 episodes of ventilator-associated condition (VAC) events (16.7 per 1000 ventilator-days), 721 episodes of infection-related ventilator-associated complications (IVAC) events (6.4 per 1000 ventilator-days), and 185 episodes of PVAP events (1.64 per 1000 ventilator-days). The rates of VAC varied across ICUs with the highest incidence in surgical ICUs (23.72 per 1000 ventilator-days). The median time from the start of ventilation to the onset of the first VAC, IVAC, and PVAP was 5 (3-8), 5 (3-9), and 6 (4-13) days, respectively. The median length of hospital stays was 28.00 (17.00-43.00), 30.00 (19.00-44.00), and 30.00 (21.00-46.00) days for the three VAE tiers, which were all longer than that of patients without VAEs (16.00 [12.00-23.00]). The hospital mortality among patients with VAEs was more than three times of those with non-VAEs. CONCLUSIONS: VAE was common in ICU patients with ≥ 4 ventilator days. All tiers of VAEs were highly correlated with poor clinical outcomes, including longer ICU and hospital stays and increased risk of mortality. These findings highlight the importance of VAE surveillance and the development of new strategies to prevent VAEs.


Subject(s)
Intensive Care Units/statistics & numerical data , Outcome Assessment, Health Care/statistics & numerical data , Respiration, Artificial/adverse effects , Adolescent , Adult , Aged , Aged, 80 and over , China/epidemiology , Female , Hospital Mortality/trends , Humans , Intensive Care Units/organization & administration , Male , Middle Aged , Pneumonia, Ventilator-Associated/epidemiology , Pneumonia, Ventilator-Associated/mortality , Registries/statistics & numerical data , Respiration, Artificial/methods , Respiration, Artificial/trends , Ventilator-Induced Lung Injury/epidemiology , Ventilator-Induced Lung Injury/mortality
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