Nosocomial Outbreaks Research Articles

Phylogenetic analyses of antimicrobial resistant Corynebacterium striatum strains isolated from a nosocomial outbreak in a tertiary hospital in China

Corynebacterium striatum is an emerging, multidrug-resistant pathogen that frequently causes nosocomial infections worldwide. This study aimed to investigate phylogenetic relationship and presence of genes responsible for antimicrobial resistance among C. striatum strains associated with an outbreak at the Shanxi Bethune Hospital, China, in 2021. Fecal samples were collected from 65 patients with C. striatum infection at Shanxi Bethune Hospital between February 12, 2021 and April 12, 2021. C. striatum isolates were identified by 16S rRNA and rpoB gene sequencing. E-test strips were used to examine the antimicrobial susceptibility of the isolates. Whole-genome sequencing and bioinformatics analysis were employed to assess the genomic features and identify antimicrobial resistance genes of the isolates. Crystal violet staining was conducted to determine the ability of biofilm formation of each isolate. A total of 64 C. striatum isolates were identified and categorized into 4 clades based on single nucleotide polymorphisms. All isolates were resistant to penicillin, meropenem, ceftriaxone, and ciprofloxacin but susceptible to vancomycin and linezolid. Most isolates were also resistant to tetracycline, clindamycin, and erythromycin, with susceptibility rates of 10.77, 4.62, and 7.69%, respectively. Genomic analysis revealed 14 antimicrobial resistance genes in the isolates, including tetW, ermX, and sul1. Crystal violet staining showed that all isolates formed biofilms on the abiotic surface. Four clades of multidrug-resistant C. striatum spread in our hospitals possibly due to the acquisition of antimicrobial resistance genes.

Whole-genome sequencing rule-out of suspected hospital-onset Rhizopus outbreaks.

Two independent temporal-spatial clusters of hospital-onset Rhizopus infections were evaluated using whole-genome sequencing (WGS). Phylogenetic analysis confirmed that isolates within each cluster were unrelated despite epidemiological suspicion of outbreaks. The ITS1 region alone was insufficient for accurate analysis. WGS has utility for rapid rule-out of suspected nosocomial Rhizopus outbreaks.

Sinks in patient rooms in ICUs are associated with higher rates of hospital-acquired infection: a retrospective analysis of 552 ICUs

Sinks in hospitals are a possible reservoir for healthcare-related pathogens. They have been identified as a source of nosocomial outbreaks in intensive care units (ICU); however, their role in non-outbreak settings remains unclear. To investigate whether sinks in ICU patient rooms are associated with a higher incidence of hospital-acquired infection (HAI). This analysis used surveillance data from the ICU component of the German nosocomial infection surveillance system (KISS) from 2017 to 2020. Between September and October 2021, all participating ICUs were surveyed about the presence of sinks in their patient rooms. The ICUs were then divided into two groups: the no-sink group (NSG) and the sink group (SG). Primary and secondary outcomes were total HAIs and HAIs associated with Pseudomonas aeruginosa (HAI-PA). In total, 552 ICUs (NSG N=80, SG N=472) provided data about sinks, total HAIs and HAI-PA. The incidence density per 1000 patient-days of total HAIs was higher in ICUs in the SG (3.97 vs 3.2). The incidence density of HAI-PA was also higher in the SG (0.43 vs 0.34). The risk of HAIs associated with all pathogens [incidence rate ratio (IRR)=1.24, 95% confidence interval (CI) 1.03-1.50] and the risk of lower respiratory tract infections associated with P.aeruginosa (IRR=1.44, 95% CI 1.10-1.90) were higher in ICUs with sinks in patient rooms. After adjusting for confounders, sinks were found to be an independent risk factor for HAI (adjusted IRR 1.21, 95% CI 1.01-1.45). Sinks in patient rooms are associated with a higher number of HAIs per patient-day in the ICU. This should be considered when planning new ICUs or renovating existing ones.

Carbapenem Resistant Acinetobacter baumannii: Current Status of Problem in a Tertiary Care Hospital, Jaipur

ABSTRACT Background: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a serious global health challenge. It is increasingly associated with nosocomial infections and outbreaks in healthcare facilities. This study was conducted in a tertiary care teaching hospital in Jaipur to quantitate the burden of CRAB in our setup, examine the clinico-epidemiological profile of patients infected with this bug, and determine their antibiotic susceptibility pattern. Methods: Clinical specimens collected from patients admitted in various wards and ICUs were processed. Bacterial identification and susceptibility testing were done using standard laboratory techniques and VITEK 2 automated system. Only one isolate per patient was included for study purposes. The data on the sociodemographic and epidemiological profile was collected and analyzed statistically. Results: A total of 4897 clinical samples were received in the department of microbiology during the study period, out of which 1517 exhibited significant growth, sample positivity rate being 31%. Acinetobacter baumannii was the third most common gram-negative isolate (228/1067; 21.3%). Out of the total 228 A. baumannii isolates, 221 (97%) were carbapenem resistant. The maximum number of CRAB isolates were obtained from endotracheal secretions (103), followed by blood (59). All patients were critically ill and needed intensive care. The antibiotic susceptibility testing of these clinical isolates revealed a high level of resistance (99%) against ceftazidime, meropenem, and imipenem with the least resistance against colistin (2%) and tigecycline (9%). Conclusions: CRAB is an important global pathogen contributing to increased morbidity and mortality in hospitalized patients. Viable treatment options that may be used with success against bugs include minocycline, tigecycline, and polymyxins.

Nosocomial outbreak caused by Serratia marcescens in a neonatology intensive care unit in a regional hospital. Analysis and improvement proposals

ObjectivesSerratia marcescens (SM) may cause nosocomial outbreaks in Neonatal Intensive Care Units (NICU). We describe an outbreak of SM in a NICU and propose additional prevention and control recommendations. MethodsBetween March 2019 and January 2020, samples were taken from patients in the NICU (rectal, pharyngeal, axillary and other locations) and from 15 taps and their sinks. Control measures were implemented including thorough cleaning of incubators, health education to staff and neonates’relatives, and use of single-dose containers. PFGE was performed in 19 isolates from patients and in 5 environmental samples. ResultsFrom the first case in March 2019 to the detection of the outbreak, a month elapsed. Finally, 20 patients were infected and 5 colonized. 80% of infected neonates had conjunctivitis, 25% bacteremia, 15% pneumonia, 5% wound infection, and 5% urinary tract infection. Six neonates had two foci of infection. Among the 19 isolates studied, 18 presented the same pulsotype and only one of the isolates from the sinkhole showed a clonal relationship with those of the outbreak. Initial measures established were ineffective to control de outbreak and were implemented with exhaustive cleaning, use of individual eye drops, environmental sampling and changing sinks. ConclusionThis outbreak presented a high number of neonates affected due to its late detection and torpid evolution. The microorganisms isolated from the neonates were related to an environmental isolate. Additional prevention and control measures are proposed, including routine weekly microbiological sampling.

Whole-genome sequencing of carbapenem-resistant Enterobacterales isolates and evaluation of hospital-acquired infections

Background: Multidrug-resistant organisms (MDROs) are increasingly implicated in nosocomial outbreaks worldwide. We evaluated whole-genome sequencing (WGS) as an adjunctive epidemiological tool to identify infection clusters and MDRO transmission in the healthcare setting. Methods: Clinical isolates of carbapenem-resistant Enterobacterales (CRE) from July 1, 2021, to June 30, 2022, underwent Illumina WGS. Assembled genomes were taxonomically classified with GTDB-Tk software and were typed using multilocus sequence typing (MLST). Average nucleotide identity (ANI) was calculated between genomes. Numbers of differences among core single-nucleotide polymorphisms (SNPs) were calculated for pairs within taxonomic groups, and the data were evaluated in the context of patient dates and locations of care obtained from the electronic medical record. Results: In total, 39 CRE isolates underwent WGS (Fig. 1). Klebsiella pneumoniae represented the largest number of isolates (n = 18). Using MLST, 2 distinct groups of K. pneumoniae were identified (ST307 and ST258) with 5 and 4 isolates, respectively (Fig. 2). Within ST307, SNP differences ranged between 8 and 115. 3 isolates (CRE8, CRE10, and CRE12) were collected within 4 weeks of each other and had ≤26 pairwise SNP differences. Notably, CRE8 and CRE10 were located on the same unit at the same time and used the same MRI scanner on the same day. CRE35 had >95 SNP differences and was admitted 8 months prior to others in ST307 but had surgery in the same OR as CRE8. Within ST258, pairwise comparison of samples revealed 139–588 SNP differences. CRE21, CRE31, and CRE33 had SNP differences of ≤150. These patients were in the same hospital room (CRE33 and CRE21) and unit (CRE31 and CRE33), but they did not overlap temporally. CRE37 had >580 SNP differences, with no overlap in hospitalization dates or locations with other patients. Conclusions: Two closely related K. pneumoniae isolate populations were identified using WGS. Strong temporal and spatial commonalities were identified among isolates with few SNP differences. Isolate pairs with intermediate SNP differences shared spatial commonalities, suggesting possible indirect transmission between patients. No common exposures were identified for pairs with large numbers of SNP differences. WGS is an evolving tool to detect outbreak clonal populations of MDRO not identified through traditional epidemiologic techniques. WGS can provide insight into transmission patterns and the role of environmental contamination in propagating these nosocomial infections. More studies are needed to define the role and clinical significance of isolates with intermediate SNP differences in transmission of these pathogens between hosts and the healthcare environment.Disclosures: None

Outbreaks by Klebsiella oxytoca in neonatal intensive care units: Analysis of an outbreak in a tertiary hospital and systematic review

ObjectiveKlebsiella oxytoca can cause nosocomial infections, affecting vulnerable newborns. There are few studies describing nosocomial outbreaks in the neonatal intensive care units (NICU). In this study, a systematic review of the literature was carried out to know the main characteristics of these outbreaks and the evolution of one is described. MethodsWe conducted a systematic review in the Medline database up to July 2022, and present a descriptive study of an outbreak with 21 episodes in the NICU of a tertiary hospital, between September 2021 and January 2022. Results9 articles met the inclusion criteria. The duration of outbreaks was found to be variable, of which 4 (44.4%) lasted for a year or more. Colonization (69%) was more frequent than infections (31%) and the mortality rate was 22.4%. In studies describing sources, the most frequent was the environmental origin (57.1%). In our outbreak there were 15 colonizations and 6 infections. The infections were mild conjunctivitis without sequelae. Molecular typing analysis made it possible to detect 4 different clusters. ConclusionsThere is an important variability in the evolution and results of the published outbreaks, highlighting a greater number of colonized, use of PFGE (pulsed-field gel electrophoresis) techniques for molecular typing and implementation of control measures. Finally, we describe an outbreak in which 21 neonates were affected with mild infections, resolved without sequelae and whose control measures were effective.

Polyclonal Burkholderia cepacia complex outbreak caused by contaminated chlorhexidine gluconate solution

Background:Burkholderia cepacia complex is an opportunistic environmental pathogen that has been linked to nosocomial outbreaks. We describe an outbreak of bacteremia caused by Burkholderia cenocepacia from a contaminated chlorhexidine gluconate solution. Methods: The hospital infection control team carried out an outbreak investigation on February 21, 2021, when 3 adult hemodialysis patients developed B. cenocepacia bacteremia. Patient demographics and clinical profile were reviewed retrospectively. Potential sources of infection were identified, and environmental screening was performed in several units. Processes of catheter care in the hemodialysis unit were reviewed. Water samples from the hemodialysis unit, and samples of solutions used in patient care were sent for culture. Isolates from patients and from environmental samples were sent for 16S rRNA gene sequencing to determine genetic relatedness. Results: In total, 16 patients, 8 of whom were male, developed B. cenocepacia bacteremia during the investigated period. The median age was 68 years (range, 19–83), and 15 of 16 had at least 1 comorbidity. All patients used a central venous catheter (CVC) for hemodialysis, and 11 (70%) of these 16 were temporary. Chlorhexidine gluconate solution was routinely used as part of CVC care and 1 bottle was shared among 4 hemodialysis stations. On suspicion of contamination, all identified chlorhexidine bottles were recalled on February 26, 2021, and random samples from 15 opened and 19 unopened bottles were sent for culture from the following units: hemodialysis (n = 2), ICU (n = 14), wards (n = 6), and 4 each from transplant surgery, and delivery suites. O0f 34 sampled bottles, 17 grew B. cenocepacia: 8 opened and 9 unopened bottles. The Bayesian inference tree (Fig. 1) supports the hypothesis that patient samples and the samples from the chlorhexidine solutions were most probably related to each other based on the 16S rRNA sequences. However, the individual identities of the specific sample sequences could not be determined using the analyzed region of the gene, possibly due to low quality of the sequences received. No new cases of B. cenocepacia were identified after recall of the chlorhexidine solution, and the outbreak was deemed resolved on March 24, 2021. Conclusions: Medical solutions routinely used in patient care can cause outbreaks and should be suspected as a potential source of infection by infection control teams.Disclosures: None

Serratia marcescens Colonization in a Neonatal Intensive Care Unit Has Multiple Sources, with Sink Drains as a Major Reservoir.

Compelling evidence suggests a contribution of the sink environment to the transmission of opportunistic pathogens from the hospital environment to patients in neonatal intensive care units (NICU). In this study, the distribution of the opportunistic pathogen Serratia marcescens in the sink environment and newborns in a NICU was investigated. More than 500 sink drain and faucet samples were collected over the course of five sampling campaigns undertaken over 3 years. Distribution and diversity of S. marcescens were examined with a modified MacConkey medium and a high-throughput short-sequence typing (HiSST) method. Sink drains were an important reservoir of S. marcescens, with an average of 44% positive samples, whereas no faucet sample was positive. The genotypic diversity of S. marcescens was moderate, with an average of two genotypes per drain, while the spatial distribution of S. marcescens was heterogeneous. The genotypic profiles of 52 clinical isolates were highly heterogeneous, with 27 unique genotypes, of which 71% of isolates were found in more than one patient. S. marcescens acquisition during the first outbreaks was mainly caused by horizontal transmissions. HiSST analyses revealed 10 potential cases of patient-to-patient transmission of S. marcescens, five cases of patient-to-sink transmission, and one bidirectional transfer between sink and patient. Environmental and clinical isolates were found in sink drains up to 1 year after the first detection, supporting persisting drain colonization. This extensive survey suggests multiple reservoirs of S. marcescens within the NICU, including patients and sink drains, but other external sources should also be considered. IMPORTANCE The bacterium Serratia marcescens is an important opportunistic human pathogen that thrives in many environments, can become multidrug resistant, and is often involved in nosocomial outbreaks in neonatal intensive care units (NICU). We evaluated the role of sinks during five suspected S. marcescens outbreaks in a NICU. An innovative approach combining molecular and culture methods was used to maximize the detection and typing of S. marcescens in the sink environment. Our results indicate multiple reservoirs of S. marcescens within the NICU, including patients, sink drains, and external sources. These results highlight the importance of sinks as a major reservoir of S. marcescens and potential sources of future outbreaks.

Prevalence of Methicillin Resistant Staphylococcus aureus Carriage Amongst Healthcare Workers of Critical Care Units in Tertiary Hospitals of Jashore, Bangladesh

Staphylococcus aureus is responsible for numerous mild to severe diseases in humans in both hospital and community settings. This problem is getting even worse for multi-drug resistant S. aureus. Healthcare workers (HCWs) are in a threat of MRSA carriage and can serve as reservoirs. Therefore, this can lead to subsequent infection and cause a nosocomial outbreak of MRSA. This cross-sectional study involved 85 healthcare workers (HCWs) from surgery units and critical care units of five different tertiary hospitals at Jashore, Bangladesh. Nasal swab samples were collected and inoculated on selective Mannitol Salt Agar (MSA) media. S. aureus was confirmed by selective growth on MSA and detection of the presence of the femA gene. Antibiotic susceptibility pattern was determined for all S. aureus isolates. Methicillin resistance was detected using both disc diffusion assay and gene specific polymerase chain reaction. S. aureus specific staphylococcal protein A (Spa) typing was also done by sequence analyses of PCR products. Among the 85 enrolled HCW personnel, 34 (40%) were carrying S. aureus followed by the S. intermedius (N=32). An overall prevalence of MRSA was found to be 3.53% (3/85). However, all the strains were susceptible to vancomycin. Additionally, 100% sensitivity was found against Trimethoprim/sulfamethoxazole and Linezolid. Sequence analysis of Spa PCR product revealed that all S. aureus isolates were of t304 spa type. None of the S. aureus was a biofilm former. This study was only a survey on the prevalence of MRSA among HCWs. Integrated surveillance for MDR MRSA carriage among HCWs is warranted to control bursts of nosocomial infections effectively. It is strongly recommended to maintain good microbiological and personal hygiene practices by HCWs.
 Bangladesh J Microbiol, Volume 39, Number 2, December 2022, pp 60-66

Brote nosocomial causado por Serratia marcescens en una unidad de cuidados intensivos neonatal de un hospital regional. Análisis y propuestas de mejora

ObjectivesSerratia marcescens may cause nosocomial outbreaks in neonatal intensive care units. We describe an outbreak of Serratia marcescens in a neonatal intensive care unit and propose additional prevention and control recommendations. MethodsBetween March 2019 and January 2020, samples were taken from patients in the neonatal intensive care unit (rectal, pharyngeal, axillary and other locations) and from 15 taps and their sinks. Control measures were implemented including thorough cleaning of incubators, health education to staff and neonates’ relatives, and use of single-dose containers. PFGE was performed in 19 isolates from patients and in 5 environmental samples. ResultsFrom the first case in March 2019 to the detection of the outbreak, a month elapsed. Finally, 20 patients were infected and 5 colonized. Eighty percent of infected neonates had conjunctivitis, 25% bacteremia, 15% pneumonia, 5% wound infection, and 5% urinary tract infection. Six neonates had 2 foci of infection. Among the 19 isolates studied, 18 presented the same pulsotype and only one of the isolates from the sinkhole showed a clonal relationship with those of the outbreak. Initial measures established were ineffective to control the outbreak and were implemented with exhaustive cleaning, use of individual eye drops, environmental sampling and changing sinks. ConclusionThis outbreak presented a high number of neonates affected due to its late detection and torpid evolution. The microorganisms isolated from the neonates were related to an environmental isolate. Additional prevention and control measures are proposed, including routine weekly microbiological sampling.

Brotes por Klebsiella oxytoca en unidades de cuidados intensivos neonatales: análisis de un brote en un hospital de tercer nivel y revisión sistemática

ObjectivesKlebsiella oxytoca can cause nosocomial infections, affecting vulnerable newborns. There are few studies describing nosocomial outbreaks in the neonatal intensive care units (NICU). In this study, a systematic review of the literature was carried out to know the main characteristics of these outbreaks and the evolution of one is described. MethodsWe conducted a systematic review in the Medline database up to July 2022, and present a descriptive study of an outbreak with 21 episodes in the NICU of a tertiary hospital, between September 2021 and January 2022. ResultsNine articles met the inclusion criteria. The duration of outbreaks was found to be variable, of which 4 (44.4%) lasted for a year or more. Colonization (69%) was more frequent than infections (31%) and the mortality rate was 22.4%. In studies describing sources, the most frequent was the environmental origin (57.1%). In our outbreak there were 15 colonizations and 6 infections. The infections were mild conjunctivitis without sequelae. Molecular typing analysis made it possible to detect 4 different clusters. ConclusionsThere is an important variability in the evolution and results of the published outbreaks, highlighting a greater number of colonized, use of pulsed-field gel electrophoresis (PFGE) techniques for molecular typing and implementation of control measures. Finally, we describe an outbreak in which 21 neonates were affected with mild infections, resolved without sequelae and whose control measures were effective.

Evaluation of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Molecular Typing of Acinetobacter baumannii in Comparison with Orthogonal Methods.

Colonization and subsequent health care-associated infection (HCAI) with Acinetobacter baumannii are a concern for vulnerable patient groups within the hospital setting. Outbreaks involving multidrug-resistant strains are associated with increased patient morbidity and mortality and poorer overall outcomes. Reliable molecular typing methods can help to trace transmission routes and manage outbreaks. In addition to methods deployed by reference laboratories, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) may assist by making initial in-house judgments on strain relatedness. However, limited studies on method reproducibility exist for this application. We applied MALDI-TOF MS typing to A. baumannii isolates associated with a nosocomial outbreak and evaluated different methods for data analysis. In addition, we compared MALDI-TOF MS with whole-genome sequencing (WGS) and Fourier transform infrared spectroscopy (FTIR) as orthogonal methods to further explore their resolution for bacterial strain typing. A related subgroup of isolates consistently clustered separately from the main outbreak group by all investigated methods. This finding, combined with epidemiological data from the outbreak, indicates that these methods identified a separate transmission event unrelated to the main outbreak. However, the MALDI-TOF MS upstream approach introduced measurement variability impacting method reproducibility and limiting its reliability as a standalone typing method. Availability of in-house typing methods with well-characterized sources of measurement uncertainty could assist with rapid and dependable confirmation (or denial) of suspected transmission events. This work highlights some of the steps to be improved before such tools can be fully integrated into routine diagnostic service workflows for strain typing. IMPORTANCE Managing the transmission of antimicrobial resistance necessitates reliable methods for tracking outbreaks. We compared the performance of MALDI-TOF MS with orthogonal approaches for strain typing, including WGS and FTIR, for Acinetobacter baumannii isolates correlated with a health care-associated infection (HCAI) event. Combined with epidemiological data, all methods investigated identified a group of isolates that were temporally and spatially linked to the outbreak, yet potentially attributed to a separate transmission event. This may have implications for guiding infection control strategies during an outbreak. However, the technical reproducibility of MALDI-TOF MS needs to be improved for it to be employed as a standalone typing method, as different stages of the experimental workflow introduced bias influencing interpretation of biomarker peak data. Availability of in-house methods for strain typing of bacteria could improve infection control practices following increased reports of outbreaks of antimicrobial-resistant organisms during the COVID-19 pandemic, related to sessional usage of personal protective equipment (PPE).

Serratia marcescens Meningitis: Neonatal Case

Serratia marcescens belongs to the Enterobacteriaceae family, commonly found in water, soil, animals, insects, plants. Although Serratia marcescens has low virulence, it causes nosocomial infections and outbreaks in extremely immunocompromised or critically ill patients, particularly in intensive care units, particularly neonatal units. This pathogen causes a wide range of clinical symptoms in newborns, including keratitis, conjunctivitis, urinary tract infections, pneumonia, surgical site infections, sepsis, bloodstream infection, and meningitis. The bloodstream is the most commonly infected location, followed by the respiratory tract and the gastrointestinal tract. Serratia marcescens strains implicated in epidemic events have often proven to be multiresistant. Indeed, this species has an inherent resistance to multiple antibiotic families. Often, the particular source of infection cannot be determined. However, infected hands of healthcare professionals are thought to be a key vector for its spread. Infection of the central nervous system by this bacterium in the neonatal period leads to serious neurological sequelae with high mortality interest of early and adequate management. Through our work we report the clinical presentation, the positive diagnosis as well as the therapeutic management and the evolution of a newborn having presented a meningitis with Serratia marcescens complicated by ventriculitis.

Invasive fusariosis in acute leukaemia patients-An outbreak in the haematology ward.

Fusarium, a common fungus, emerges as a pathogen in severely immunocompromised patients. We present a series of patients who developed invasive fusariosis (IF) during admission to an acute leukaemia ward: an outbreak of 12 cases in June and July 2018, followed by four sporadic cases until 2021. No case was reported earlier. All patients were clustered in the same location with indoor air and water installations found to be contaminated with Fusarium spp. thus a nosocomial outbreak was assumed. Following the water installation replacement, the number of Fusarium cases dramatically dropped to one or two isolated instances per year in the same location. All 16 patients had acute leukaemia and developed IF during severe neutropenia following induction therapy. IF diagnosis was based on positive blood cultures (14 patients) and/or on tissue biopsies (3 patients). The median time from admission to the IF onset was 20 days, and from the first day of severe neutropenia (≤500/mm3) was 11.5 days. All patients were febrile, eight had moderate-to-severe myalgias, eight had respiratory involvements: lung lesions and/or sinusitis and seven had characteristic skin lesions. Follow-up: 12 out of 16 (75%) were alive on Day 90; nine out of 15 (60%) were alive on Month 6. All with intractable neutropenia died. In severely neutropenic febrile patients, the triad of respiratory involvement/skin lesions/severe myalgia may suggest Fusarium aetiology. The ability to recover from neutropenia is critical to surmount IF. The indoor environment in immunocompromised dedicated settings must be constantly controlled.

Pseudo-outbreak of Mycobacterium lentiflavum at a general hospital in Japan.

Mycobacterium lentiflavum is a slow-growing nontuberculous mycobacterium that is widely distributed in soil and water systems, but it is sometimes pathogenic to humans. Although cases of M. lentiflavum infections are rare, 22 isolates of M. lentiflavum were identified at a single hospital in Japan. We suspected a nosocomial outbreak; thus, we conducted transmission pattern and genotype analyses. Cases of M. lentiflavum isolated at Kushiro City General Hospital in Japan between May 2020 and April 2021 were analyzed. The patient samples and environmental culture specimens underwent whole-genome sequencing (WGS). Additionally, we retrospectively collected clinical data from patient medical records. Altogether, 22 isolates of M. lentiflavum were identified from sputum and bronchoalveolar lavage samples. Clinically, the instances with M. lentiflavum isolates were considered contaminants. In the WGS analysis, 19 specimens, including 18 patient samples and 1 environmental culture from the hospital's faucet, showed genetic similarity. The frequency of M. lentiflavum isolation decreased after we prohibited the use of taps where M. lentiflavum was isolated. WGS analysis identified that the cause of M. lentiflavum pseudo-outbreak was the water used for patient examinations, including bronchoscopy.

First nosocomial outbreak of SME-4-producing Serratia marcescens in South America

Carbapenemase-producing-Serratia marcescens isolates, although infrequent, are considered important nosocomial pathogens due to their intrinsic resistance to polymyxins, which limits therapeutic options. We describe a nosocomial outbreak of SME-4-producing S. marcescens in Buenos Aires city which, in our knowledge, represents the first one in South America.

Improving the Detection of Epidemic Clones in Candida parapsilosis Outbreaks by Combining MALDI-TOF Mass Spectrometry and Deep Learning Approaches.

Identifying fungal clones propagated during outbreaks in hospital settings is a problem that increasingly confronts biologists. Current tools based on DNA sequencing or microsatellite analysis require specific manipulations that are difficult to implement in the context of routine diagnosis. Using deep learning to classify the mass spectra obtained during the routine identification of fungi by MALDI-TOF mass spectrometry could be of interest to differentiate isolates belonging to epidemic clones from others. As part of the management of a nosocomial outbreak due to Candida parapsilosis in two Parisian hospitals, we studied the impact of the preparation of the spectra on the performance of a deep neural network. Our purpose was to differentiate 39 otherwise fluconazole-resistant isolates belonging to a clonal subset from 56 other isolates, most of which were fluconazole-susceptible, collected during the same period and not belonging to the clonal subset. Our study carried out on spectra obtained on four different machines from isolates cultured for 24 or 48 h on three different culture media showed that each of these parameters had a significant impact on the performance of the classifier. In particular, using different culture times between learning and testing steps could lead to a collapse in the accuracy of the predictions. On the other hand, including spectra obtained after 24 and 48 h of growth during the learning step restored the good results. Finally, we showed that the deleterious effect of the device variability used for learning and testing could be largely improved by including a spectra alignment step during preprocessing before submitting them to the neural network. Taken together, these experiments show the great potential of deep learning models to identify spectra of specific clones, providing that crucial parameters are controlled during both culture and preparation steps before submitting spectra to a classifier.

Microbial profile and antibiotic resistance pattern of water supply in a tertiary care hospital of Uttarakhand.

In healthcare settings, hospital water and water-related devices can act as a reservoir for waterborne infections. Potable water, sinks, faucet aerators, showers, tub immersion, toilets, dialysis water, water baths, eyewash stations, and dental-unit water stations have all been linked to nosocomial outbreaks. This study aimed to determine the microbial profile and pattern of antibiotic resistance in the water supply of a tertiary care hospital in Uttarakhand. This is a 1-year prospective study which was carried out by the Department of Microbiology and Immunology at Sri Mahant Indersh Hospital (SMIH), Dehradun. A total of 154 water samples were collected from the AC outlets, ventilators in the Intensive care unit (ICUs), Operation theatre (OTs), and High dependency unit (HDUs), scrub stations, pantry, and blood bank, patient's bathroom, private ward, septic ward, labour room, transplant unit, laboratory, scope rinse water, the dialysis unit and tank throughout the hospital, including tap water (pre and post flush [25%]), tap swabs (24%), drinking water (9%), AC outlets (13%), and other areas (3%). 30 of the 154 (19.5%) water samples tested were culture-positive. The most contaminated water samples were tap swabs (27%, n = 8/30). A total of nine organisms were isolated, of which the most predominant was Pseudomonas aeruginosa (40%; 12/30), followed by Legionella pneumophila (13%; 4/30), Acinetobacter baumanii (10%; 3/30), Klebsiella pneumoniae (10%; 3/30), Escherichia coli (7%; 2/30), Enterococcus faecalis (7%; 2/30), Aspergillus flavus (7%; 2/30), Stenotrophomonas (3%; 1/30), and Fusarium spp. (3%; 1/30). Gram-negative bacilli and non-lactose fermenting (GNB and NLF) showed a high rate of contamination, 53.3% (n = 16/30). P. aeruginosa showed resistance to gentamicin and amikacin (42%), imipenem (50%), levofloxacin (58%), and colistin (25%), while Acinetobacter baumanii showed resistance to gentamicin and amikacin (67%), minocycline (63%), and levofloxacin, imipenem and colistin (33%). The study's findings show that a variety of microorganisms are contaminating hospital water supplies and can be a source of hospital-acquired infections. A suitable and robust surveillance program for hospital water supplies, as well as strict adherence to infection control practices, is strongly advised.

Overestimation of Amphotericin B Resistance in Candida auris with Sensititre YeastOne Antifungal Susceptibility Testing: a Need for Adjustment for Correct Interpretation.

Significant variation in minimal inhibitory concentrations (MIC) has been reported for amphotericin B (AMB) and C. auris, depending on the antifungal susceptibility testing (AFST) method. Although the Sensititre YeastOne (SYO) is widely used in routine laboratory testing, data regarding its performance for the AFST of C. auris are scarce. We tested AMB against 65 C. auris clinical isolates with the SYO and the reference methodology by the Clinical and Laboratory Standards Institute (CLSI). The essential agreement (EA, ±1 dilution) between the two methods and the categorical agreement (CA) based on the Centers for Disease Control and Prevention (CDC)'s tentative breakpoint of MIC ≥ 2 mg/L were determined. The SYO wild type upper limit value (WT-UL) was determined using the ECOFFinder. The modal (range) CLSI growth inhibitory MIC was lower than the SYO colorimetric MIC [1(0.25-1) versus 2(1-8) mg/L, respectively]). The CLSI-colorimetric SYO EA was 29% and the CA was 11% (89% major errors; MaE). MaE were reduced when the SYO WT-UL of 8 mg/L was used (0% MaE). Alternatively, the use of SYO growth inhibition endpoints of MIC-1 (75% growth inhibition) or MIC-2 (50% growth inhibition) resulted in 88% CA with 12% MaE and 97% CA with 3% MaE, respectively. In conclusion, SYO overestimated AMB resistance in C. auris isolates when colorimetric MICs, as per SYO instructions and the CDC breakpoint of 2 mg/L, were used. This can be improved either by using the method-specific WT-UL MIC of 8 mg/L for colorimetric MICs or by determining growth inhibition MIC endpoints, regardless of the color. IMPORTANCE Candida auris is an emerging and frequently multidrug-resistant fungal pathogen that accounts for life-threatening invasive infections and nosocomial outbreaks worldwide. Reliable AF is important for the choice of the optimal treatment. Commercial methods are frequently used without prior vigorous assessment. Resistance to AMB was over-reported with the commercial colorimetric method Sensititre YeastOne (SYO). SYO produced MICs that were 1 to 2 twofold dilutions higher than those of the reference CLSI method, resulting in 89% MaE. MaE were reduced using a SYO-specific colorimetric wild type upper limit MIC value of 8 mg/L (0%) or a 50% growth inhibition endpoint (3%).