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Microbiology Spectrum Aug 2022The genus Enterobacter includes species responsible for nosocomial outbreaks in fragile patients, especially in neonatal intensive care units (NICUs). Determining the...
The genus Enterobacter includes species responsible for nosocomial outbreaks in fragile patients, especially in neonatal intensive care units (NICUs). Determining the primary source of infection is critical to outbreak management and patient outcomes. In this investigation, we report the management and control measures implemented during an Enterobacter outbreak of bloodstream infections in premature babies. The study was conducted in a French NICU over a 3-year period (2016 to 2018) and included 20 premature infants with bacteremia. The clinical and microbiological characteristics were identified, and whole-genome sequencing (WGS) was performed on bacteremia isolates. Initially, several outbreak containment strategies were carried out with no success. Next, outbreak investigation pinpointed the neonatal incubators as the primary reservoir and source of contamination in this outbreak. A new sampling methodology during "on" or "in use" conditions enabled its identification, which led to their replacement, thus resulting in the containment of the outbreak. WGS analysis showed a multiclonal outbreak. Some clones were identified in different isolation sources, including patients and neonatal incubators. In addition, microbiological results showed a multispecies outbreak with a high prevalence of Enterobacter bugandensis and Enterobacter xiangfangensis. We conclude that the NICU health care environment represents an important reservoir for Enterobacter transmission and infection. Finally, extracting samples from the neonatal incubator during active use conditions improves the recovery of bacteria from contaminated equipment. This method should be used more frequently to achieve better monitoring of the NICU for HAIs prevention. Neonatal incubators in the NICU can be an important reservoir of pathogens responsible for life-threatening outbreaks in neonatal patients. Traditional disinfection with antiseptics is not sufficient to eradicate the microorganisms that can persist for long periods in the different reservoirs. Identification and elimination of the reservoirs are crucial for outbreak prevention and control. In our investigation, using a new strategy of microbiological screening of neonatal incubators, we demonstrated that these were the primary source of contamination. After their replacement, the outbreak was controlled. This new methodology was effective in containing this outbreak and could be a viable alternative for infection prevention and control in outbreak situations involving incubators as a reservoir.
Topics: Bacteremia; Cross Infection; Disease Outbreaks; Enterobacter; Humans; Incubators; Infant; Infant, Newborn; Neonatal Sepsis
PubMed: 35703554
DOI: 10.1128/spectrum.00964-22 -
Frontiers in Microbiology 2023The Enterobacterales are a group of Gram-negative bacteria frequently exhibiting extended antimicrobial resistance (AMR) and involved in the transmission of resistance...
BACKGROUND
The Enterobacterales are a group of Gram-negative bacteria frequently exhibiting extended antimicrobial resistance (AMR) and involved in the transmission of resistance genes to other bacterial species present in the same environment. Due to their impact on human health and the paucity of new antibiotics, the World Health Organization (WHO) categorized carbapenem resistant and ESBL-producing as critical. Enterobacterales are ubiquitous and the role of the environment in the transmission of AMR organisms or antimicrobial resistance genes (ARGs) must be examined in tackling AMR in both humans and animals under the one health approach. Animal manure is recognized as an important source of AMR bacteria entering the environment, in which resistant genes can accumulate.
METHODS
To gain a better understanding of the dissemination of third generation cephalosporin and fluoroquinolone resistance genes between isolates in the environment, we applied whole genome sequencing (WGS) to Enterobacterales (79 , 1 , 1 , and 1 ) isolated from farm effluents in Ireland before ( = 72) and after ( = 10) treatment by integrated constructed wetlands (ICWs). DNA was extracted using the MagNA Pure 96 system (Roche Diagnostics, Rotkreuz, Switzerland) followed by WGS on a MiSeq platform (Illumina, Eindhoven, Netherlands) using v3 chemistry as 300-cycle paired-end runs. AMR genes and point mutations were identified and compared to the phenotypic results for better understanding of the mechanisms of resistance and resistance transmission.
RESULTS
A wide variety of cephalosporin and fluoroquinolone resistance genes (mobile genetic elements (MGEs) and chromosomal mutations) were identified among isolates that mostly explained the phenotypic AMR patterns. A total of 31 plasmid replicon types were identified among the 82 isolates, with a subset of them ( = 24), identified in isolates. Five plasmid replicons were confined to the isolate and two were confined to the isolate. Virulence genes associated with functions including stress, survival, regulation, iron uptake secretion systems, invasion, adherence and toxin production were identified.
CONCLUSION
Our study showed that antimicrobial resistant organisms (AROs) can persist even following wastewater treatment and could transmit AMR of clinical relevance to the environment and ultimately pose a risk to human or animal health.
PubMed: 37032887
DOI: 10.3389/fmicb.2023.1118264 -
Antimicrobial Agents and Chemotherapy Dec 2023Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant , but carbapenem resistance due to acquisition of...
Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant , but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. carbapenemase () is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn transposon. This means that alongside clonal expansion, can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular -encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian -encoding plasmids. We further estimated the genomic location of incomplete -encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of genomic loci and indicate that multiple, distinct plasmid clusters have contributed to spread and persistence in Canada.
Topics: Humans; Canada; beta-Lactamases; Plasmids; Bacterial Proteins; Klebsiella pneumoniae; Anti-Bacterial Agents; Carbapenems; Genomics; Klebsiella Infections; Microbial Sensitivity Tests
PubMed: 37971242
DOI: 10.1128/aac.00860-23 -
Insects Jul 2022Tardigrades are small micrometazoans able to resist several environmental stresses in any stage of their life cycle. An integrated analysis of tardigrade specimens...
Tardigrades are small micrometazoans able to resist several environmental stresses in any stage of their life cycle. An integrated analysis of tardigrade specimens collected in Tsukuba (Japan) revealed a peculiar morphology and a new sensory field in the cloaca. Molecular taxonomy and phylogenetic analysis on different genes (COI, ITS2, 18S and 28S) confirmed that this population is a new species, sp. nov., belonging to the widespread group. The stress resistance capabilities of sp. nov. have been tested by submitting animals to extreme desiccation, rapid freezing, and high levels of ultraviolet radiations (UVB and UVC). Animals were able to survive desiccation (survivorship 95.71 ± 7.07%) and freezing up to -80 °C (82.33 ± 17.11%). Both hydrated and desiccated animals showed a high tolerance to increasing UV radiations: hydrated animals survived to doses up to 152.22 kJ m (UVB) and up to 15.00 kJ m (UVC), while desiccated specimens persisted to radiations up to 165.12 kJ m (UVB) and up to 35.00 kJ m (UVC). Present data contribute to the discovery of a larger tardigrade biodiversity in Japan, and the tolerance capabilities of sp. nov. show that it could become a new emerging model for stress resistance studies.
PubMed: 35886811
DOI: 10.3390/insects13070634 -
Nature Communications Mar 2024Hospital surfaces can harbour bacterial pathogens, which may disseminate and cause nosocomial infections, contributing towards mortality in low- and middle-income...
Hospital surfaces can harbour bacterial pathogens, which may disseminate and cause nosocomial infections, contributing towards mortality in low- and middle-income countries (LMICs). During the BARNARDS study, hospital surfaces from neonatal wards were sampled to assess the degree of environmental surface and patient care equipment colonisation by Gram-negative bacteria (GNB) carrying antibiotic resistance genes (ARGs). Here, we perform PCR screening for extended-spectrum β-lactamases (bla) and carbapenemases (bla, bla-like and bla), MALDI-TOF MS identification of GNB carrying ARGs, and further analysis by whole genome sequencing of bacterial isolates. We determine presence of consistently dominant clones and their relatedness to strains causing neonatal sepsis. Higher prevalence of carbapenemases is observed in Pakistan, Bangladesh, and Ethiopia, compared to other countries, and are mostly found in surfaces near the sink drain. Klebsiella pneumoniae, Enterobacter hormaechei, Acinetobacter baumannii, Serratia marcescens and Leclercia adecarboxylata are dominant; ST15 K. pneumoniae is identified from the same ward on multiple occasions suggesting clonal persistence within the same environment, and is found to be identical to isolates causing neonatal sepsis in Pakistan over similar time periods. Our data suggests persistence of dominant clones across multiple time points, highlighting the need for assessment of Infection Prevention and Control guidelines.
Topics: Infant, Newborn; Humans; Developing Countries; Neonatal Sepsis; beta-Lactamases; Bacterial Proteins; Hospitals; Anti-Bacterial Agents; Klebsiella pneumoniae; Gram-Negative Bacteria; Microbial Sensitivity Tests
PubMed: 38553439
DOI: 10.1038/s41467-024-46684-z -
Environmental Monitoring and Assessment Aug 2023Lead (Pb) is a non-essential metal with high toxicity, is persistent, is not biodegradable, and has no known biological function. It is responsible for severe health and...
Lead (Pb) is a non-essential metal with high toxicity, is persistent, is not biodegradable, and has no known biological function. It is responsible for severe health and environmental issues that need appropriate remediation. Therefore, microbes have thrived in a lead-contaminated environment without exhibiting any negative impacts. The present study aimed to examine the toxic effects of lead on animals and the isolation, identification, and characterization of lead-resistant bacterial strains and their biodegradation potential. After oral administration of lead for 4 weeks, mice showed an elevated level of leukocytes and a decrease in TEC, Hb, PCV, MCV, MCH, and MCHC levels. However, a decline in body weight and inflammation and oxidative stress was observed in liver tissues. To remediate toxic heavy metal, lead-resistant bacterial strains were isolated, among which Enterobacter exhibited maximum degradation potential at high lead concentrations. It was identified by molecular basis and after 16S rRNA sequencing, and 99% resemblance was observed with Enterobacter cloacae. FT-IR analysis of the bacteria illustrated the presence of functional groups, including hydroxyl, carboxyl group, sulfide, and amino groups, on the bacterial cell surface involved in the adsorption of lead. Moreover, electron microscopy (SEM) revealed the morphological and physiochemical changes in the bacterial cell after biosorption, indicating the interaction of Cu ions with functional groups. To summarize, the findings show the highly toxic effects of lead on animals and humans and its effective biodegradation by the bacterial strains in the lead-contaminated environment. This biological strategy can be an ideal alternative to remediate heavy metals from contaminated sites to clean up the environment.
Topics: Humans; Animals; Mice; Lead; Biodegradation, Environmental; RNA, Ribosomal, 16S; Spectroscopy, Fourier Transform Infrared; Environmental Monitoring; Metals, Heavy
PubMed: 37589892
DOI: 10.1007/s10661-023-11632-9 -
Surgery Open Science Dec 2023Ventilator-associated pneumonias (VAPs) are a complication of mechanical ventilation in the intensive care unit (ICU) that increase length of stay, morbidity, and...
INTRODUCTION
Ventilator-associated pneumonias (VAPs) are a complication of mechanical ventilation in the intensive care unit (ICU) that increase length of stay, morbidity, and mortality. While identifying and treating infections early is paramount to improving patient outcomes, more and more data demonstrate limited courses of antibiotics improve outcomes. Prolonged (10-14 day) courses of antibiotics have remained the standard of care for pneumonia due to gram-negative bacilli (GNR). We aimed to review our GNR VAPs to assess risk factors for recurrent GNR infections.
METHODS
We reviewed trauma patients who developed VAP from 02/2019 through 05/2022. Demographics, injury characteristics, and outcomes were reviewed with a focus on pneumonia details including the cultured pathogen(s), antibiotic(s) used, treatment duration, and presence of recurrent infections. We then compared single episode VAPs to multiple episode VAPs among patients infected by GNRs.
RESULTS
Eleven of the fifty trauma patients admitted to the ICU suffered a VAP caused by a GNR. Of these eleven patients, six experienced a recurrent infection, four of which were caused by and two of which were caused by . Among the patients who received ten days of antibiotic treatment, half suffered a recurrence. Although, there was no difference in the microbiology or antibiotic duration between the recurrences and single episodes.
CONCLUSION
Despite prolonged use of antibiotics, we found that the risk of recurrent or persistent infections was high among patients with VAP due to GNB. Further study is needed to determine optimal treatment to minimize the risk of these recurrences.
KEY MESSAGE
Ventilator-associated pneumonia due to gram-negative bacilli is a rare but high morbidity complication in intensive care units. Despite prolonged duration of therapy, these infections still appear to account for many recurrent infections and further study into optimal therapy is warranted.
PubMed: 37789948
DOI: 10.1016/j.sopen.2023.09.014 -
Journal of Pediatric Urology Aug 2023Persistent cloaca, defined as confluence of the rectum, the vagina and the urethra into a single common channel, has an estimated incidence of 1/50,000 live births. We...
INTRODUCTION
Persistent cloaca, defined as confluence of the rectum, the vagina and the urethra into a single common channel, has an estimated incidence of 1/50,000 live births. We describe the buccal mucosa graft vaginoplasty for a 11 year old female with cloaca, who underwent at the age of 11 months a Peña repair. We performed the vaginoplasty after the onset of uterine pain due to the beginning of menstruation.
MATERIAL AND METHODS
We accessed the lower lip for superficial dissection to harvest the graft. The donor site has been kept with as much submucosal fat as possible to avoid damage to the buccinatoria muscles. A second graft was further obtained from the cheek. Both grafts were submitted to multiple small sections to produce a mesh graft and increase its size. A arciform incision anterior to the anal canal and posterior to the urethra was performed followed by consecutive dissection with eletrocautery to gain profundity. The mesh-graft was placed over the neovaginal cavity and sutured with 4.0 PDS monofilament suture used to suture and then quilt the graft in place. The vaginal capacity was confirmed by ease of a two-digit insertion. Haemostasis was confirmed before the insertion of a soft vaginal mold. The patient remained with an indwelling urinary catheter. The mold was equivalent to 24Fr and had 13 cm of profundity and Foley tube were removed after 14 days postoperatively.
RESULTS
Patient had an excellent postoperative course and had been instructed to perform vaginal dilatation every 3 h during the day. Current follow up is 10 months.
DISCUSSION
Buccal mucosal grafting has advantages over the use of keratinized skin flaps and intestinal flaps. Buccal mucosa is ideal for female genital reconstruction, given its color, texture, lack of hair and mild mucous production. In our particular case, we connected the neovagina after two months of adequate healing to the native 1⁄3 through laparoscopic approach.
CONCLUSIONS
BMG vaginoplasty is a viable alternative to treat females with cloaca at adolescence.
Topics: Adolescent; Humans; Female; Infant; Child; Mouth Mucosa; Plastic Surgery Procedures; Vagina; Surgical Flaps; Rectum
PubMed: 37120365
DOI: 10.1016/j.jpurol.2023.03.036 -
International Journal of... 2022Pesticides are widely used for managing pathogens and pests for sustainable agricultural output to feed around seven billion people worldwide. After their targeted role,...
Pesticides are widely used for managing pathogens and pests for sustainable agricultural output to feed around seven billion people worldwide. After their targeted role, residues of these compounds may build up and persist in soils and in the food chain. This study evaluated the efficiency of bacterial strains capable of plant growth promotion and biodegradation of profenofos. To execute this, bacteria were isolated from an agricultural area with a history of repeated application of profenofos. The profenofos degrading bacterial strains with growth-promoting characteristics were identified based on biochemical and molecular approaches through partial 16S ribosomal rRNA gene sequencing. The results revealed that one strain, MUG75, degraded over 90% profenofos after 9days of incubation. Similarly, plant growth was significantly increased in plants grown in profenofos (100mg L) contaminated soil inoculated with the same strain. The study demonstrated that inoculation of profenofos degrading bacterial strains increased plant growth and profenofos degradation. Pesticides are extensively applied in the agriculture sector to overcome pest attacks and to increase food production to fulfill the needs of the growing world population. Residues of these pesticides can persist in the environment for long periods, may enter the groundwater reservoirs and cause harmful effects on living systems highlighting the need for bioremediation of pesticide-contaminated environments. Microbes can use pesticides as a source of carbon and energy and convert them into less toxic and non-toxic products. Application of profenofos degrading rhizobacteria in interaction with the plants in the rhizosphere can remediate the pesticide-contaminated soils and minimize their uptake into the food chain. Hence, this approach can improve soil health and food quality without compromising the environment.
Topics: Biodegradation, Environmental; Humans; Solanum lycopersicum; Organothiophosphates; Rhizosphere; Soil Microbiology; Soil Pollutants
PubMed: 34304658
DOI: 10.1080/15226514.2021.1952927 -
Journal of Pediatric Urology Jun 2021'Persistent Cloaca' refers to one of the major groups of anorectal anomalies in the female when a single perineal orifice is located at the normal site of the urethra...
BACKGROUND
'Persistent Cloaca' refers to one of the major groups of anorectal anomalies in the female when a single perineal orifice is located at the normal site of the urethra draining both urogenital and alimentary tracts. However, 'posterior cloaca' is a new term developed by Pena to describe a unique defect in females in which a common urogenital sinus is deviated posteriorly to open into normally located anorectum (type A) or in the perineum slightly anterior to the anus (type B).
METHODS
The study included seven girls diagnosed as posterior cloaca. Their age at presentation ranged from 1 to 108 months (median 12 months). The main presentation was abnormal external genitalia, while two cases underwent colostomy (±vaginostomy) at birth. Surgical reconstruction varied according to the degree of deviation from normal anatomy. Partial urogenital sinus mobilization (PUM) was used to correct minor forms; while at the other end of the spectrum (absent urinary bladder), continent urinary diversion was performed. Due to the high incidence of renal and urological anomalies, regular follow up at paediatric nephrology/urology clinics was advised for affected cases.
RESULTS
All seven cases had a common urogenital confluence characteristically deviated posteriorly. The degree of backward deviation of the common urogenital orifice was variable ranging from mild to severe posterior displacement. In six cases (85%), the common urogenital orifice was shifted backwards in the perineum approaching the anal verge (type B). In one case, the common urogenital orifice opened internally into the anorectum (type A). Major urinary tract anomalies were quite common (5 of 7 cases; 71%): absent urinary bladder (2 cases); single kidney (2 cases); crossed ectopic kidney (1 case); hydroureteronephrosis (2 cases).
CONCLUSION
Posterior cloaca is a rare anomaly in the female essentially affecting the lower urogenital tract with a high incidence of associated renal anomalies. Management should be tailored according to the degree of developmental defect.
Topics: Anal Canal; Anorectal Malformations; Child; Child, Preschool; Cloaca; Female; Humans; Infant; Infant, Newborn; Urogenital Abnormalities; Urogenital System
PubMed: 33549475
DOI: 10.1016/j.jpurol.2021.01.014