Search Results (20)

Brucella intermedia, a gram-negative, non-lactose-fermenting, aerobic, rod-shaped bacterium, is found in environmental sources (e.g., soil and water). In 2020, Ochrobactrum was reclassified as Brucella. We conducted a genomic analysis of B. intermedia from hospital wastewater samples in western Ghana. A hybrid genome assembly was constructed integrating short-read data from DNA Nanoball sequencing with long-read sequences generated by Oxford Nanopore MinION technology. Identification and antimicrobial susceptibility profiles were determined using MicroScan autoSCAN-4 based on Clinical and Laboratory Standard Institute documents. ResFinder and CARD Resistance Gene Identifier (RGI) were used to identify antimicrobial resistance (AMR) genes, and BLAST and VFDB datasets were used to identify virulence factor genes. The complete genome had two chromosomes, no plasmid, and a high average nucleotide identity value (98.05%) with B. intermedia. Resistance to trimethoprim-sulfamethoxazole was revealed, the first report in this species. CARD RGI revealed the presence of AMR genes, including ANT(9)-Ic and adeF. Local BLAST analysis revealed Cgs, a B. melitensis virulence factor. B. intermedia is an opportunistic human pathogen clinically isolated several times, suggesting the importance of accurately identifying multidrug resistance. B. intermedia may possess virulence factors similar to those of B. melitensis. Further study is needed to fully elucidate its pathogenesis. Full article

Colistin resistance poses a significant clinical challenge, particularly in Gram-negative bacteria. This study investigates the occurrence of plasmid-mediated colistin resistance among Enterobacterales isolates (Escherichia coli, Klebsiella pneumoniae, and Enterobacter spp.) and non-fermentative rods (Acinetobacter baumannii and Pseudomonas aeruginosa). We analyzed 114 colistin-resistant isolates that were selected, based on resistance phenotypes, and isolated between 2019 and 2023. To achieve this, we used the rapid immunochromatographic test, NG-Test^® MCR-1; multiplex PCR for mcr-1 to mcr-8, and real-time PCR for mcr-1 and mcr-2. One E. coli isolate was identified as carrying the mcr-1 gene, confirmed by NG-Test^® MCR-1, multiplex PCR and whole-genome sequencing. This strain, belonging to ST69, harbored four plasmids, harboring different antimicrobial resistance genes, with mcr-1 being located on a 33,304 bp circular IncX4 plasmid. No mcr-2 to mcr-8-positive isolates were detected, prompting further investigation into alternative colistin resistance mechanisms. This is the first report of a mcr-1-positive, colistin-resistant E. coli isolated from a human clinical sample in the North-East of Romania. Full article

Pseudomonas jordanii strain G34 is a moderately halophilic endophytic bacterium isolated from the root tissue of durum wheat plants growing in the saline environment of the Jordan Valley’s Ghor Sweimeh region. Microscopic and biochemical analyses of P. jordanii strain G34 revealed that it is a Gram-negative, non-motile rod. It also exhibits capsule formation, catalase and oxidase positive reactions, indole positivity, citrate utilization, and non-glucose fermenting capability. Pseudomonas jordanii strain G34 showed growth-promoting effects on durum wheat seedlings grown under severe salinity stress conditions up to a 200 mM NaCl concentration. The draft genome of P. jordanii strain G34 comprises 5,142,528 base pairs (bp) and possesses a G + C content of 64.0%. It contains 57 RNA coding genes and is predicted to encode a total of 4675 protein-coding genes. Putative genes linked to various aspects of the bacterial endophyte lifestyle were identified including ion transport, motility, secretion, adhesion, delivery systems, and plant cell wall modification. Performing a comprehensive phylogenomic analysis identified P. jordanii as a new species, with its closest relative being P. argentinensis LMG 22563, sharing only around 40.2% digital DNA-DNA hybridization identity. Pseudomonas jordanii strain G34 holds great potential for future use as a biofertilizer in saline environments. Full article

Two isolates of Roseateles were discovered in soil samples collected from Uiwang-si, Gyeonggi-do, Republic of Korea. These isolates exhibited rod-shaped morphology and were facultatively anaerobic, non-motile, and tested positive for oxidase and catalase. Designated as strains R3-3^T and R3-11, their growth was hindered by NaCl concentrations exceeding 0.5%, while their optimal growth conditions were observed at temperatures ranging from 25 °C to 30 °C and pH levels between 7.0 and 9.0. Both strains exhibited positive results for the hydrolysis of Tween 80 and DNA, but tested negative for starch, casein, chitin, and gelatin hydrolysis. Additionally, they assimilated L-Arabinose, D-mannitol, and D-Maltose, while exhibiting negative results for the fermentation of D-glucose, esculin ferric citrate, D-mannose, N-acetyl-glucosamine, potassium gluconate, capric acid, adipic acid, trisodium citrate, and phenylacetic acid. The DNA G+C content of strain R3-3^T was measured at 67.5 mol%. Comparative analysis revealed that the average nucleotide identity (ANI) values between R3-3^T and the Roseateles type strains ranged from 75.14% to 78.30% while the digital DNA-DNA hybridization (dDDH) values ranged from 20.70% to 22.70%. Consequently, based on comprehensive genomic, chemotaxonomic, phenotypic, and phylogenomic evaluations, the isolated strains have been designated as a new species within the genus Roseateles, named Roseateles agri sp. nov. (with type strain R3-3^T = KACC 23678^T = NBRC 116681^T). Full article

The impact of bacterial pneumonia on patients with COVID-19 infection remains unclear. This prospective observational monocentric cohort study aims to determine the incidence of bacterial community- and hospital-acquired pneumonia (CAP and HAP) and its effect on mortality in critically ill COVID-19 patients admitted to the intensive care unit (ICU) at University Hospital Olomouc between 1 November 2020 and 31 December 2022. The secondary objectives of this study include identifying the bacterial etiology of CAP and HAP and exploring the capabilities of diagnostic tools, with a focus on inflammatory biomarkers. Data were collected from the electronic information hospital system, encompassing biomarkers, microbiological findings, and daily visit records, and subsequently evaluated by ICU physicians and clinical microbiologists. Out of 171 patients suffering from critical COVID-19, 46 (27%) had CAP, while 78 (46%) developed HAP. Critically ill COVID-19 patients who experienced bacterial CAP and HAP exhibited higher mortality compared to COVID-19 patients without any bacterial infection, with rates of 38% and 56% versus 11%, respectively. In CAP, the most frequent causative agents were chlamydophila and mycoplasma; Enterobacterales, which were multidrug-resistant in 71% of cases; Gram-negative non-fermenting rods; and Staphylococcus aureus. Notably, no strains of Streptococcus pneumoniae were detected, and only a single strain each of Haemophilus influenzae and Moraxella catarrhalis was isolated. The most frequent etiologic agents causing HAP were Enterobacterales and Gram-negative non-fermenting rods. Based on the presented results, commonly used biochemical markers demonstrated poor predictive and diagnostic accuracy. To confirm the diagnosis of bacterial CAP in our patient cohort, it was necessary to assess the initial values of inflammatory markers (particularly procalcitonin), consider clinical signs indicative of bacterial infection, and/or rely on positive microbiological findings. For HAP diagnostics, it was appropriate to conduct regular detailed clinical examinations (with a focus on evaluating respiratory functions) and closely monitor the dynamics of inflammatory markers (preferably Interleukin-6). Full article

Medical complications during pregnancy have been frequently reported from Western Africa with a particular importance of infectious complications. Placental tissue can either become the target of infectious agents itself, such as, e.g., in the case of urogenital schistosomiasis, or be subjected to contamination with colonizing or infection-associated microorganisms of the cervix or the vagina during vaginal delivery. In the retrospective cross-sectional assessment presented here, the quantitative dimension of infection or colonization with selected resistant or pathogenic bacteria and parasites was regionally assessed. To do so, 274 collected placental tissues from Ivory Coastal and Ghanaian women were subjected to selective growth of resistant bacteria, as well as to molecular screening for beta-lactamase genes, Schistosoma spp. and selected bacterial causative agents of sexually transmitted infections (STI). Panton–Valentine-negative methicillin-resistant Staphylococcus aureus (MRSA) was grown from 1.8% of the tissue samples, comprising the spa types t008 and t688, as well as the newly detected ones, t12101 (n = 2) and t12102. While the culture-based recovery of resistant Enterobacterales and nonfermentative rod-shaped Gram-negative bacteria failed, molecular assessments confirmed beta-lactamase genes in 31.0% of the samples with multiple detections of up to four resistance genes per sample and bla_CTX-M, bla_IMP, bla_GES, bla_VIM, bla_OXA-58-like, bla_NDM, bla_OXA-23-like, bla_OXA-48-like and bla_KPC occurring in descending order of frequency. The beta-lactamase genes bla_OXA-40/24-like, bla_{NMC_A/IMI}, bla_BIC, bla_SME, bla_GIM and bla_DIM were not detected. DNA of the urogenital schistosomiasis-associated Schistosoma haematobium complex was recorded in 18.6% of the samples, but only a single positive signal for S. mansoni with a high cycle-threshold value in real-time PCR was found. Of note, higher rates of schistosomiasis were observed in Ghana (54.9% vs. 10.3% in Ivory Coast) and Cesarean section was much more frequent in schistosomiasis patients (61.9% vs. 14.8% in women without Schistosoma spp. DNA in the placenta). Nucleic acid sequences of nonlymphogranuloma-venereum-associated Chlamydia trachomatis and of Neisseria gonorrhoeae were recorded in 1.1% and 1.9% of the samples, respectively, while molecular attempts to diagnose Treponema pallidum and Mycoplasma genitalium did not lead to positive results. Molecular detection of Schistosoma spp. or STI-associated pathogens was only exceptionally associated with multiple resistance gene detections in the same sample, suggesting epidemiological distinctness. In conclusion, the assessment confirmed considerable prevalence of urogenital schistosomiasis and resistant bacterial colonization, as well as a regionally expected abundance of STI-associated pathogens. Continuous screening offers seem advisable to minimize the risks for the pregnant women and their newborns. Full article

Antiseptics, disinfectants, and hand hygiene products can act as reservoirs of Gram-negative bacteria causing healthcare-associated infections. This problem is rarely documented in low- and middle-income countries, particularly in sub-Saharan Africa. In a cross-sectional survey, we assessed the bacterial contamination of antiseptics, disinfectants, and hand hygiene products in two university hospitals in Burkina Faso and Benin. During ward visits and staff interviews, in-use products were cultured for the presence of Gram-negative bacteria. The growth of Gram-negative bacteria was absent or rare in alcohol-based products, povidone iodine, and Dakin solution. Contamination was highest (73.9% (51/69)) for liquid soap products (versus antiseptic/disinfectants (4.5%, 7/157) (p < 0.0001)), mostly used in high-risk areas and associated with high total bacterial counts (>10,000 colony-forming units/mL). Contaminating flora (105 isolates) included Enterobacterales and the Vibrio non-cholerae/Aeromonas group (17.1%) and non-fermentative Gram-negative rods (82.8%). Multidrug resistance was present among 9/16 Enterobacterales (Klebsiella and Enterobacter spp.) and 3/12 Acinetobacter spp., including carbapenem resistance (Acinetobacter baumannii: NDM, Pseudomonas stutzeri: VIM). The risk factors for contamination included the type of product (cleaning grade and in-house prepared liquid soap), use of recycled disposable containers and soft drink bottles, absence of labeling, topping-up of containers, dilution with tap water (pharmacy and ward), and poor-quality management (procurement, stock management, expiry dates, and period after opening). Full article

The respiratory tract of lung transplant recipients (LTR) is likely to be colonized with non-fermentative Gram-negative rods. As a consequence of the improvements in molecular sequencing and taxonomy, an increasing number of bacterial species have been described. We performed a review of the literature of bacterial infections in LTR involving non-fermentative Gram-negative rods with exclusion of Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Achromobacter spp. and Burkholderia spp. Overall, non-fermenting GNR were recovered from 17 LTR involving the following genera: Acetobacter, Bordetella, Chryseobacterium, Elizabethkinga, Inquilinus, and Pandoraea. We then discuss the issues raised by these bacteria, including detection and identification, antimicrobial resistance, pathogenesis, and cross-transmission. Full article

This scoping review addresses bacterial contamination of antiseptics, low-level disinfectants, and hand hygiene products in healthcare settings in high-income countries. Over 70 years, 114 articles were found: 68 outbreaks, 13 pseudo-outbreaks and 33 cross-sectional surveys. Outbreaks affected median 29 (1–151) patients, extended for 26 (1–156) weeks and had a case fatality of 0.0% (0.0–60.0%). Most (72.8%) (pseudo-)outbreaks were caused by water-based chlorhexidine (CHG), quaternary ammonium compounds (QUAT) and the combination CHG–QUAT. Contaminating bacteria were nonfermentative Gram-negative rods (87.6% (pseudo-)outbreaks), mainly Burkholderia cepacia, Pseudomonas aeruginosa and Achromobacter spp.) and Enterobacterales (29.6%, 24/81), mostly Serratia spp.). Risk factors were at the level of the bacteria (natural resistance to CHG and QUAT), containers (design and functioning, presence of cork and cotton, biofilm formation), preparation (nonsterile water, overdilution) and practices (too long expiry dates, inappropriate container reprocessing, topping up of containers and deviation from procedures). Transmission occurred through direct contact (antiseptics), contact with semicritical items (disinfectants) and were handborne (soaps). During recent decades, reports of soap contaminated with Enterobacterales emerged and nationwide outbreaks of intrinsically contaminated CHG occurred. Outstanding issues comprise intrinsic contamination, implementation of antiseptic stewardship, the role of unit doses and sterile products, transmission studies, biofilm control and understanding healthcare providers’ perceptions. Full article

We conducted a systematic review of healthcare-associated outbreaks and cross-sectional surveys related to the contamination of antiseptics, disinfectants, and hand hygiene products in healthcare settings in low- and middle-income countries (PROSPERO CRD42021266271). Risk of bias was assessed by selected items of the ORION and MICRO checklists. From 1977 onwards, 13 outbreaks and 25 cross-sectional surveys were found: 20 from Asia and 13 from Africa. Products most associated with outbreaks were water-based chlorhexidine, chlorhexidine-quaternary ammonium compound combinations (7/13), and liquid soap products (4/13). Enterobacterales (including multidrug-resistant Enterobacter cloacae, Klebsiella pneumoniae, and Serratia marcescens) and non-fermentative Gram-negative rods were found in 5 and 7 outbreaks and in 34.1% and 42.6% of 164 isolates, respectively, from cross-sectional surveys. Risk factors included preparation (place, utensils, or tap water high and incorrect dilutions), containers (reused, recycled, or inadequate reprocessing), and practices (topping-up or too long use). Potential biases were microbiological methods (neutralizers) and incomplete description of products’ identity, selection, and denominators. External validity was compromised by low representativeness for remote rural settings and low-income countries in sub-Saharan Africa. Outstanding issues were water quality, biofilm control, field-adapted containers and reprocessing, in-country production, healthcare providers’ practices, and the role of bar soap. A list of “best practices” to mitigate product contamination was compiled. Full article

The clinical aspects of persistent bacteremia (PB) caused by gram-negative rods (GNRs) in terms of antimicrobial resistance (AMR) and PB clearance status are unclear. This secondary analysis of a retrospective cohort study investigated differences in PB caused by Enterobacterales and glucose non-fermentative GNRs (NF-GNRs) based on AMR and PB clearance. We retrospectively surveyed medical records at Tohoku University Hospital. Patients for whom blood cultures were performed between January 2012 and December 2021 were recruited. PB cases were grouped based on AMR and PB clearance; the characteristics of PB due to each bacterial pathogen were examined. The main outcome variable was mortality. The late (30–90-day) mortality rate was significantly higher in the multidrug-resistant (MDR) group than in the non-MDR group for Enterobacterales. However, no significant difference was noted in mortality rates between NF-GNRs with and without AMR. Mortality rates tended to be higher in the non-PB-clearance group than in the clearance group for both Enterobacterales and NF-GNRs. Since the mortality rate was higher in the MDR group in the case of Enterobacterales PB, more careful management is necessary for this condition. Follow-up blood cultures and confirming the clearance of PB are useful for improving the survival rate. Full article

Gram-negative fermenting and non-fermenting bacteria are important etiological factors of nosocomial and community infections, especially those that produce carbapenemases. Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa are the most frequently-detected carbapenemase-producing microorganisms. The predominant type of resistance is metallo-β-lactamase (MBL). These bacteria are predominantly isolated from bronchial alveolar lavage, urine, and blood. Carbapenemase-producing Enterobacterales (CPE) strains are always multi-drug-resistant. This significantly limits the treatment options for this type of infection, extends the time of patient hospitalization, and increases the risk of a more severe and complicated disease course. Preventing the transmission of these microorganisms should be a major public health initiative. New antibiotics and treatment regimens offer hope against these infections. Full article

An accurate and reliable susceptibility testing method for polymyxins is urgently needed not only for the clinical laboratory but also for new polymyxin-like lipopeptide development. Reference broth microdilution (rBMD), which was the recommended method by CLSI-EUCAST in clinics, has been proven not to be ideal, while the agar dilution (AD) method that was widely used in new antibiotics discovery has been neglected. In the present study, the AD method was compared with rBMD and broth macrodilution (BMAD) in susceptibility testing of polymyxin B and colistin against >200 Gram-negative isolates. AD showed strong agreement with BMAD for colistin (except for Klebsiella aerogenes and Pseudomonas aeruginosa); however, its performance was poor for polymyxin B or compared to rBMD. MICs of AD method were not affected when different types of Petri dishes were used, while glass-bottom microtiter plates could lower the MIC of polymyxins 2–8 times compared to tissue-culture-treated polystyrene plates when using rBMD, which demonstrated that tissue-culture-treated plates were not suitable. It was then validated with non-tissue-culture-treated plates. The culture volume was another influencing factor of accuracy for rBMD, and 200 μL seemed to be the most suitable volume for MIC detection of polymyxins. Additionally, no lack of growth phenomenon (skipped well) was observed for AD when it frequently occurred for both BMAD and rBMD. As for strains carrying mcr-1 gene, 100% of AD results were in essential agreement (EA) and categorical agreement (CA) with both rBMD and BMAD. Overall, rBMD is convenient and widely accepted for susceptibility testing of polymyxins. Although it may be too early to say that AD is superior compared to rBMD and BMAD, it did show some advantages in repeatability and anti-interference ability. Full article

Levofloxacin is considered an alternative treatment option of Stenotrophomonas maltophilia infections to trimethoprim/sulfamethoxazole. The fluoroquinolone resistance in S. maltophilia is usually caused by an overproduction of efflux pumps. In this study, the contribution of efflux systems to levofloxacin resistance in S. maltophilia clinical isolates was demonstrated using phenotypic (minimal inhibitory concentrations, MICs, of antibiotics determination ± efflux pump inhibitors, EPIs) and molecular (real-time polymerase-chain-reaction and sequencing) methods. Previously, the occurrence of genes encoding ten efflux pumps was shown in 94 studied isolates. Additionally, 44/94 isolates demonstrated reduction in susceptibility to levofloxacin. Only 5 of 13 isolates (with ≥4-fold reduction in levofloxacin MIC) in the presence of EPIs showed an increased susceptibility to levofloxacin and other antibiotics. The overexpression of smeD and smeV genes (in five and one isolate, respectively) of 5 tested efflux pump operons was demonstrated. Sequencing analysis revealed 20–35 nucleotide mutations in local regulatory genes such as smeT and smeRv. However, mutations leading to an amino acid change were shown only in smeT (Arg123Lys, Asp182Glu, Asp204Glu) for one isolate and in smeRv (Gly266Ser) for the other isolate. Our data indicate that the overproduction of the SmeVWX efflux system, unlike SmeDEF, plays a significant role in the levofloxacin resistance. Full article

An increase of nosocomial infections caused by Stenotrophomonas maltophilia strains has recently been observed all over the world. The isolation of these bacteria from the blood is of particular concern. In this study we performed the phenotypic and genotypic characterization of 94 S. maltophilia isolates, including isolates from patients hospitalized in a tertiary Warsaw hospital (n = 79) and from outpatients (n = 15). All isolates were found to be susceptible to trimethoprim-sulfamethoxazole and minocycline, while 44/94 isolates demonstrated a reduction in susceptibility to levofloxacin. A large genetic variation was observed among the isolates tested by pulsed-field gel electrophoresis. A clonal relationship with 100% similarity was observed between isolates within two sub-pulsotypes: the first included nine bloodstream isolates and the second involved six. Multilocus sequence typing showed two new sequence types (ST498 and ST499) deposited in public databases for molecular typing. Moreover, the presence of genes encoding ten different efflux pumps from the resistance-nodulation-division family and the ATP-binding cassette family was shown in the majority of the 94 isolates. The obtained knowledge about the prevalence of efflux pump genes in clinical S. maltophilia strains makes it possible to predict the scale of the risk of resistance emergence in strains as a result of gene overexpression. Full article