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Genes Jun 2023is a Gram-negative opportunistic pathogen inherently resistant to colistin. This species causes various clinical and community-acquired infections. This study...
is a Gram-negative opportunistic pathogen inherently resistant to colistin. This species causes various clinical and community-acquired infections. This study investigated the virulence factors, resistance mechanisms, functional pathways, and comparative genomic analysis of strain UM869 with 79 publicly available genomes. The multidrug resistance strain UM869 harbored 65 genes associated with 30 virulence factors, including efflux pump, hemolysin, urease, adherence, toxin, and endotoxin. Additionally, this strain contained 11 genes related to target alteration, antibiotic inactivation, and efflux resistance mechanisms. Further, the comparative genomic study revealed a high genetic relatedness (98.37%) among the genomes, possibly due to the dissemination of genes between adjoining countries. The core proteome of 79 genomes contains the 2692 core, including 2447 single-copy orthologues. Among them, six were associated with resistance to major antibiotic classes manifested through antibiotic target alteration (, ) and antibiotic efflux (, , ; ; ). Similarly, 47 core orthologues were annotated to 27 virulence factors. Moreover, mostly core orthologues were mapped to transporters ( = 576), two-component systems ( = 148), transcription factors ( = 117), ribosomes ( = 114), and quorum sensing ( = 77). The presence of diversity in serotypes (type 2, 3, 6, 8, and 11) and variation in gene content adds to the pathogenicity, making them more difficult to treat. This study highlights the genetic similarity among the genomes of and their restricted emergence, mostly in Asian countries, in addition to their growing pathogenicity and resistance. However, steps must be taken to undertake large-scale molecular surveillance and to direct suitable therapeutic interventions.
Topics: Virulence; Genome, Bacterial; Anti-Bacterial Agents; Virulence Factors; Drug Resistance, Multiple, Bacterial; Genomics
PubMed: 37372459
DOI: 10.3390/genes14061279 -
Infectious Diseases and Therapy Jul 2023Gram-negative resistance is a well-acknowledged public health threat. Surveillance data can be used to monitor resistance trends and identify strategies to mitigate...
INTRODUCTION
Gram-negative resistance is a well-acknowledged public health threat. Surveillance data can be used to monitor resistance trends and identify strategies to mitigate their threat. The objective of this study was to assess antibiotic resistance trends in Gram-negative bacteria.
METHODS
The first cultures of Pseudomonas aeruginosa, Citrobacter, Escherichia coli, Enterobacter, Klebsiella, Morganella morganii, Proteus mirabilis, and Serratia marcescens per hospitalized patient per month collected from 125 Veterans Affairs Medical Centers (VAMCs) between 2011 to 2020 were included. Time trends of resistance phenotypes (carbapenem, fluoroquinolone, extended-spectrum cephalosporin, multi-drug, and difficult-to-treat) were analyzed with Joinpoint regression to estimate average annual percent changes (AAPC) with 95% confidence intervals and p values. A 2020 antibiogram of reported antibiotic percent susceptibilities was also created to evaluate resistance rates at the beginning of the COVID-19 pandemic.
RESULTS
Among 40 antimicrobial resistance phenotype trends assessed in 494,593 Gram-negative isolates, there were no noted increases; significant decreases were observed in 87.5% (n = 35), including in all P. aeruginosa, Citrobacter, Klebsiella, M. morganii, and S. marcescens phenotypes (p < 0.05). The largest decreases were seen in carbapenem-resistant phenotypes of P. mirabilis, Klebsiella, and M. morganii (AAPCs: - 22.9%, - 20.7%, and - 20.6%, respectively). In 2020, percent susceptibility was over 80% for all organisms tested against aminoglycosides, cefepime, ertapenem, meropenem, ceftazidime-avibactam, ceftolozane-tazobactam, and meropenem-vaborbactam.
CONCLUSION
We observed significant decreases in antibiotic resistance for P. aeruginosa and Enterobacterales over the past decade. According to the 2020 antibiogram, in vitro antimicrobial activity was observed for most treatment options. These results may be related to the robust infection control and antimicrobial stewardship programs instituted nationally among VAMCs.
PubMed: 37326931
DOI: 10.1007/s40121-023-00827-9 -
Microbiology Spectrum Aug 2023Scombrotoxin (histamine) fish poisoning is a common seafood-borne illness attributed to toxin production by histamine-producing bacteria (HPB) in fish tissues during...
Scombrotoxin (histamine) fish poisoning is a common seafood-borne illness attributed to toxin production by histamine-producing bacteria (HPB) in fish tissues during decomposition. In laboratory studies, growth of HPB and other bacterial species is affected by physical and chemical attributes, but natural communities of HPB are not well understood. To determine how environmental and water quality variables may affect density of HPB in the natural aquatic environment, we compared presence and abundance of HPB to ambient temperature, salinity, dissolved oxygen, fecal coliforms, male-specific coliphage, nutrient concentrations, carbon and nitrogen stable isotope ratios, and C:N in water samples collected from July 2017 to February 2018 along a natural salinity gradient in a tidal river on the coast of northern Gulf of Mexico. HPB in water samples were quantified using a real-time PCR, most probable number method. HPB species were identified via 16S rRNA gene sequences. Temperature and salinity were determined to be the main factors driving HPB presence and concentration. Canonical correspondence analysis revealed that different HPB were associated with different environmental conditions. Photobacterium damselae was found under warmer, higher-salinity conditions; Raoultella planticola was found at colder, lower-salinity conditions; Enterobacter aerogenes was found at warmer, lower-salinity conditions; and Morganella morganii was found at most sites, independent of environmental conditions. These results showed that naturally occurring HPB abundance and species composition can be affected by environmental conditions, which could manifest in various potentials for histamine formation and scombrotoxin fish poisoning risk based on environmental factors. This study determined the effects of environmental conditions on presence and abundance of naturally occurring histamine-producing bacteria in the northern Gulf of Mexico. Here, we show that HPB abundance and species composition are related to ambient temperature and salinity, with the magnitude of this effect dependent on the particular HPB species. This finding suggests that environmental conditions at fishing sites could affect the risk of human illness from scombrotoxin (histamine) fish poisoning.
Topics: Animals; Male; Humans; Histamine; Gulf of Mexico; RNA, Ribosomal, 16S; Water Quality; Bacteria; Foodborne Diseases
PubMed: 37310253
DOI: 10.1128/spectrum.04720-22 -
Frontiers in Microbiology 2023The role of integrative and conjugative elements (ICEs) in antibiotic resistance in is unknown. This study aimed to determine whether an ICE identified in the genome...
INTRODUCTION
The role of integrative and conjugative elements (ICEs) in antibiotic resistance in is unknown. This study aimed to determine whether an ICE identified in the genome contributed to the polymyxin resistance.
METHODS
Whole-genome sequencing was performed followed by bioinformatics analyses to identify ICEs and antibiotic resistance genes. Conjugation assays were performed to analyze the transferability of a discovered ICE. A drug transporter encoded on the ICE was heterogeneously expressed in , minimum inhibitory concentrations of antibiotics were determined, and a traditional Chinese medicine library was screened for potential efflux pump inhibitors.
RESULTS
An antibiotic resistance-conferring ICE, named ICEMP63, was identified. ICEMP63 was verified to be horizontally transferred among Enterobacteriaceae bacteria. G3577_03020 in ICEMP63 was found to mediate multiple antibiotic resistances, especially polymyxin resistance. However, natural compound glabridin was demonstrated to inhibit polymyxin resistance.
DISCUSSION
Our findings support the need for monitoring dissemination of ICEMP63 in Enterobacteriaceae bacteria. Combined glabridin and polymyxin may have therapeutic potential for treating infections from multi-drug resistant bacteria carrying ICEMP63.
PubMed: 37283918
DOI: 10.3389/fmicb.2023.1188900 -
Microbiology Spectrum Jun 2023An isolate of Morganella morganii (MMOR1) that tested susceptible to 3/4-generation cephalosporins and intermediate to meropenem was characterized as positive for NDM...
An isolate of Morganella morganii (MMOR1) that tested susceptible to 3/4-generation cephalosporins and intermediate to meropenem was characterized as positive for NDM and IMP carbapenemases by NG-Test CARBA 5. Our objective was to further investigate this result, given the inconsistent susceptibility profile and unusual epidemiological profile for our region. The MMOR1 isolate was retested for antimicrobial susceptibilities and characterized for carbapenemase production. MMOR1 tested susceptible to ceftazidime, ceftriaxone, cefepime, aztreonam, and ertapenem, and intermediate to meropenem and imipenem. The isolate tested positive by carbapenem inactivation method (CIM) and CIM+EDTA (eCIM) testing, indicating metallo-β-lactamase production. The isolate tested negative for all carbapenemase genes on Xpert Carba-R, but positive for IMP on repeat testing of NG-Test CARBA 5. Whole-genome sequencing revealed MMOR1 contained , but no other carbapenemase genes. Additional testing with NG-Test CARBA 5 revealed a false-positive NDM band when the assay was overloaded with test inoculum. Supplementary isolates were tested with an overloaded inoculum ( = 6 M. morganii; = 1 P. mirabilis; = 1 IMP-27-producing ; = 1 IMP-1-producing E. coli; = 1 K. pneumoniae), and two non-carbapenemase-producing carbapenem non-susceptible M. morganii also generated a false-positive NDM band; though, this was not universal among this species. A dual IMP+/NDM+ M. morganii is an unusual result that should prompt additional investigation, especially in nonendemic regions and when the susceptibility profile is incompatible. IMP-27 is not detected by Xpert Carba-R but is variably detected by NG-Test CARBA 5. The microorganism inoculum used for NG-Test CARBA 5 must be carefully controlled for accurate results. The detection of carbapenemase-producing carbapenem-resistant Enterobacterales (CP-CRE) is an important function of the clinical microbiology laboratory, where positive identifications have immediate implications for infection control and surveillance strategies in the inpatient setting and can inform appropriate selection of therapy among the various novel anti-CP-CRE agents. NG-Test CARBA 5 is a relatively new lateral flow assay used for detection of carbapenemases in CP-CRE. Here, we describe the characterization of a Morganella morganii isolate that generated a false-positive NDM carbapenemase detection by this assay, and perform bacterial test inoculum experiments with additional isolates to further investigate a cause of false-positive results using the NG-Test CARBA 5. While a lateral flow assay like the NG-Test CARBA 5 is a very desirable test format for clinical laboratories, there are pitfalls to avoid when performing this test and interpreting results, including recognizing an overloaded test assay, which could lead to false-positive results.
Topics: Meropenem; Morganella morganii; Escherichia coli; Bacterial Proteins; beta-Lactamases; Imipenem; Carbapenems; Microbial Sensitivity Tests; Anti-Bacterial Agents
PubMed: 37199652
DOI: 10.1128/spectrum.00793-23 -
Infectious Diseases Now Oct 2023Secondary infection is a frequent complication after bites by Bothrops atroxin French Guiana or B. lanceolatus in Martinique. Knowledge of the bacteria present in snake...
Antibiotic susceptibility of cultivable microbiota from the oral cavity of captive Bothrops atrox and Bothrops lanceolatus: Implications for the treatment of snakebite-associated infections in the French departments of America.
INTRODUCTION
Secondary infection is a frequent complication after bites by Bothrops atroxin French Guiana or B. lanceolatus in Martinique. Knowledge of the bacteria present in snake mouths is a valuable aid for determining probabilistic antibiotherapy after Bothrops bite. The objectives of this study were to describe the cultivable bacteria of the oral microbiota of the specimens of B. atrox and B. lanceolatus kept in captivity, and to study their susceptibility to antibiotics.
METHODS
Fifteen B. atrox and 15 B. lanceolatus were sampled. Bacterial cultures were performed and each morphotype on plates was identified using MALDI-TOF mass spectrometry. Antibiotic susceptibility was studied using the agar disk diffusion method, with possible determination of the MICs.
RESULTS
One hundred and twenty-two isolates were identified: 52 isolates and 13 species in B. atrox, 70 isolates and 23 species in B. lanceolatus. The main species were Providencia rettgeri, Morganella morganii, Pseudomonas aeruginosa, Staphylococcus xylosus, and Paeniclostridium sordellii (only in B. lanceolatus mouths). For B. atrox, 96% of isolates were susceptible to piperacillin/tazobactam, cefepime, imipenem and meropenem, 94% to ciprofloxacin and 76% to cefotaxime and ceftriaxone. For B. lanceolatus, 97% of isolates were susceptible to meropenem, 96% to cefepime, 93% to imipenem and piperacillin/tazobactam, 80% to ciprofloxacin, and 75% to cefotaxime and ceftriaxone. Many isolates were resistant towards amoxicillin/clavulanate.
CONCLUSION
Among currently recommended antibiotics, cefepime and piperacillin/tazobactam seem more suitable than cefotaxime or ceftriaxone in the event of a Bothrops bite. Ciprofloxacin may also be considered for B. atrox.
PubMed: 37196810
DOI: 10.1016/j.idnow.2023.104721 -
Cells Apr 2023Maes et al. (2008) published the first paper demonstrating that major depressive disorder (MDD) is accompanied by abnormalities in the microbiota-gut-brain axis, as...
Maes et al. (2008) published the first paper demonstrating that major depressive disorder (MDD) is accompanied by abnormalities in the microbiota-gut-brain axis, as evidenced by elevated serum IgM/IgA to lipopolysaccharides (LPS) of Gram-negative bacteria, such as and . The latter aberrations, which point to increased gut permeability (leaky gut), are linked to activated neuro-immune and oxidative pathways in MDD. To delineate the profile and composition of the gut microbiome in Thai patients with MDD, we examined fecal samples of 32 MDD patients and 37 controls using 16S rDNA sequencing, analyzed α- (Chao1 and Shannon indices) and β-diversity (Bray-Curtis dissimilarity), and conducted linear discriminant analysis (LDA) effect size (LEfSe) analysis. Neither α- nor β-diversity differed significantly between MDD and controls. , , , , and were significantly enriched in MDD, while Gracillibacteraceae family, , and , , , , and were enriched in controls. Contradictory results have been reported for all these taxa, with the exception of , which is depleted in six different MDD studies (one study showed increased abundance), many medical disorders that show comorbidities with MDD, and animal MDD models. Our results may suggest a specific profile of compositional gut dysbiosis in Thai MDD patients, with increases in some pathobionts and depletion of some beneficial microbiota. The results suggest that depletion of may be a more universal biomarker of MDD that may contribute to increased enteral LPS load, LPS translocation, and gut-brain axis abnormalities.
Topics: Humans; Depressive Disorder, Major; Gastrointestinal Microbiome; Ruminococcus; Lipopolysaccharides; Southeast Asian People; Biomarkers
PubMed: 37174640
DOI: 10.3390/cells12091240 -
Antibiotics (Basel, Switzerland) Apr 2023The Enterobacteriaceae , , , , , and (CESPM group) produce numerous urinary tract infections (UTIs) which are difficult to treat due to their high multiresistance rate....
The Enterobacteriaceae , , , , , and (CESPM group) produce numerous urinary tract infections (UTIs) which are difficult to treat due to their high multiresistance rate. The objectives of this study were to carry out a systematic review of antibiotic resistances by UTIs and to determine changes over time in urine cultures from a reference hospital in southern Spain. The literature was searched for European data on the resistance rates of each microorganism, and a retrospective cross-sectional descriptive study was performed in samples with suspicion of UTI from patients in Virgen de las Nieves University Hospital (Granada, Spain) between 2016 and the first half of 2021. Among 21,838 positive urine cultures, 1.85% were caused by , 0.77% by , 0.65% by , 0.46% by , 0.29% by , and 0.25% by The lowest resistance rates by microorganism were: to amikacin (3.47%) and imipenem (5.28%); to piperacillin-tazobactam (1.79%), cefepime (4.76%), and tobramycin (7.74%); to tobramycin (3.55%), gentamicin (4.25%), trimethoprim-sulfamethoxazole (4.96%), imipenem (5.75%), and cefepime (6.43%); to imipenem (no resistance), nitrofurantoin (1.96%), fosfomycin (2.80%), and ertapenem (6.12%); to cefepime (3.28%) and ceftazidime (3.28%); and to gentamicin (1.8%), ciprofloxacin (3.64%), cefepime (3.70%), piperacillin-tazobactam (3.70%), and trimethoprim-sulfamethoxazole (5.45%). In our setting, CESMP Enterobacteriaceae showed the lowest resistance to piperacillin-tazobactam, cefepime, imipenem, gentamicin, and colistin, which can therefore be recommended for the empirical treatment of UTIs. The COVID-19 pandemic may have had a clinical impact in relation to the increased resistance of and to some antibiotics.
PubMed: 37107092
DOI: 10.3390/antibiotics12040730 -
3 Biotech May 2023a non-negligent opportunistic pathogen of the family enlisted recently in the global priority pathogens by WHO for its swift propensity to acquire drug-resistant...
UNLABELLED
a non-negligent opportunistic pathogen of the family enlisted recently in the global priority pathogens by WHO for its swift propensity to acquire drug-resistant genes, engendering enhanced death rates. A combination of diverse antimicrobials could be recycled to overcome the ongoing acquisition of resistance mechanisms by . Herein, we investigated the in vitro synergistic effect of colistin with meropenem, rifampicin, minocycline and linezolid against three intrinsic colistin-resistant strains collected from critical departments of tertiary care hospitals. The strains were identified and tested for antimicrobial susceptibility by VITEK 2 automated system. The 16S rRNA sequencing was used to reconfirm the species identification. Minimum inhibitory concentrations (MICs) of colistin, meropenem, rifampicin, minocycline and linezolid were determined by the broth microdilution method. Synergistic interactions were studied by checkerboard and time-kill assay. The VITEK 2 identification and 16S rRNA sequencing confirmed that the strains were . The automated antimicrobial susceptibility test revealed that all three isolates were multi-drug resistant. The checkerboard analysis demonstrated the synergy of all four combinations with FICI values ranging from 0.06 to 0.31 in all three isolates. These results suggest a potential role of meropenem as an adjuvant for treating infections. The current work presented the first evidence of synergy between colistin and other antibiotics against infection, which needs validation through in vitro and in vivo studies using a larger number of isolates.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s13205-023-03551-w.
PubMed: 37064006
DOI: 10.1007/s13205-023-03551-w -
Scientific Reports Apr 2023Although polymerase chain reaction (PCR) amplification and sequencing of the bacterial 16S rDNA region has numerous scientific applications, it does not provide DNA...
Although polymerase chain reaction (PCR) amplification and sequencing of the bacterial 16S rDNA region has numerous scientific applications, it does not provide DNA methylation information. Herein, we propose a simple extension for bisulfite sequencing to investigate 5-methylcytosine residues in the bacterial 16S rDNA region from clinical isolates or flora. Multiple displacement amplification without DNA denaturation was used to preferentially pre-amplify single-stranded bacterial DNA after bisulfite conversion. Following the pre-amplification, the 16S rDNA region was analyzed using nested bisulfite PCR and sequencing, enabling the simultaneous identification of DNA methylation status and sequence data. We used this approach (termed sm16S rDNA PCR/sequencing) to identify novel methylation sites and a methyltransferase (M. MmnI) in Morganella morganii and different methylation motifs among Enterococcus faecalis strains from small volumes of clinical specimens. Further, our analysis suggested that M. MmnI may be correlated to erythromycin resistance. Thus, sm16S rDNA PCR/sequencing is a useful extension method for analyzing the DNA methylation of 16S rDNA regions in a microflora, providing additional information not provided by conventional PCR. Given the relationship between DNA methylation status and drug resistance in bacteria, we believe this technique can be effectively applied in clinical sample testing.
Topics: DNA, Ribosomal; DNA, Bacterial; Bacteria; Sequence Analysis, DNA; DNA Methylation; RNA, Ribosomal, 16S
PubMed: 37029177
DOI: 10.1038/s41598-023-28706-w