Antimicrobial resistance surveillance of Bacteroides fragilis isolated from blood cultures, Europe, 2022 (ReSuBacfrag).

BACKGROUND: Bacteroides fragilis is the most frequent cause of anaerobic bacteraemia. Although recent data suggest a rise in antimicrobial resistance (AMR) of this and other anaerobic bacteria, surveillance remains limited due to a lack of both data availability and comparability. However, a newly introduced standardised method for antimicrobial susceptibility testing (AST) of anaerobic bacteria has made larger scale surveillance possible for the first time. AIM: To investigate phenotypic AMR of Bacteroides fragilis isolates from bacteraemia across Europe in 2022. METHODS: In a multicentre approach, clinical microbiology laboratories in Europe were invited to contribute results of AST for Bacteroides fragilis blood culture isolates (including only the first isolate per patient and year). AST of a selection of four antibiotics was performed locally by participating laboratories in a prospective or retrospective manner, using the new EUCAST disc diffusion method on fastidious anaerobe agar (FAA-HB). RESULTS: A total of 16 European countries reported antimicrobial susceptibilities in 449 unique isolates of Bacteroides fragilis from blood cultures in 2022. Clindamycin demonstrated the highest resistance rates (20.9%, range 0 - 63.6%), followed by piperacillin-tazobactam (11.1%, 0 - 54.5%), meropenem (13.4%, 0 - 45.5%), and metronidazole (1.8%, 0 - 20.0%), all with wide variation between countries. CONCLUSION: Considering that the mean resistance rates across Europe were higher than expected for three of the four anti-anaerobic antibiotics under surveillance, both local AST of clinically relevant isolates of Bacteroides fragilis and continued surveillance on an international level is warranted.

Phenotypic and genotypic analysis of antimicrobial resistance in Nocardia species.

BACKGROUND: Antimicrobial resistance is common in Nocardia species but data regarding the molecular mechanisms beyond their resistance traits are limited. Our study aimed to determine the species distribution, the antimicrobial susceptibility profiles, and investigate the associations between the resistance traits and their genotypic determinants. METHODS: The study included 138 clinical strains of Nocardia from nine Israeli microbiology laboratories. MIC values of 12 antimicrobial agents were determined using broth microdilution. WGS was performed on 129 isolates of the eight predominant species. Bioinformatic analysis included phylogeny and determination of antimicrobial resistance genes and mutations. RESULTS: Among the isolates, Nocardia cyriacigeorgica was the most common species (36%), followed by Nocardia farcinica (16%), Nocardia wallacei (13%), Nocardia abscessus (9%) and Nocardia brasiliensis (8%). Linezolid was active against all isolates, followed by trimethoprim/sulfamethoxazole (93%) and amikacin (91%). Resistance to other antibiotics was species-specific, often associated with the presence of resistance genes or mutations: (1) aph(2″) in N. farcinica and N. wallacei (resistance to tobramycin); (ii) blaAST-1 in N. cyriacigeorgica and Nocardia neocaledoniensis (resistance to amoxicillin/clavulanate); (iii) blaFAR-1 in N. farcinica (resistance to ceftriaxone); (iv) Ser83Ala substitution in the gyrA gene in four species (resistance to ciprofloxacin); and (v) the 16S rRNA m1A1408 methyltransferase in N. wallacei isolates (correlating with amikacin resistance). CONCLUSIONS: Our study provides a comprehensive understanding of Nocardia species diversity, antibiotic resistance patterns, and the molecular basis of antimicrobial resistance. Resistance appears to follow species-related patterns, suggesting a lesser role for de novo evolution or transmission of antimicrobial resistance.

Clinical and molecular features of NDM-producing Acinetobacter baumannii in a multicenter study in Israel.

BACKGROUND: NDM-producing Acinetobacter baumannii (NDMAb) were reported sporadically worldwide but little is known about the transmission, epidemiology and clinical features of NDMAb-infected patients. The goals of this study were to characterize (1) the epidemiology and clinical features of NDMAb-infected patients; (2) the microbiological and molecular features of NDMAb isolates and (3) the transmission networks of NDMAb within healthcare facilities. METHODS: The study was conducted at the Tel-Aviv Sourasky, Rambam and Sha'are-Zedek Medical centers (TASMC, RMC and SZMC, respectively) in Israel. All cases detected between January 2018 and July 2019 were included. Phylogenetic analysis was based on core genome SNP distances. Clonal transmission was defined according to molecular (≤ 5 SNP) and epidemiological criteria (overlapping hospital stay). NDMAb cases were compared at a ratio of 1:2 with non-NDM carbapenem-resistant A. baumannii (CRAb) cases. RESULTS: The study included 54 NDMAb-positive out of 857 CRAb patients, including 6/179 (3.3%) in TASMC, 18/441 (4.0%) in SZMC and 30/237 (12.6%) in RMC. Patients infected by NDMAb had similar clinical features and risk factors as patients with non-NDM CRAb. The length-of-stay was higher in NDMAb cases (48.5 days vs. 36 days, respectively, p = 0.097) and the in-hospital mortality was similarly high in both groups. Most isolates (41/54, 76%) were first detected from surveillance culture. The majority of isolates harbored the blaNDM-2 gene allele (n = 33), followed by the blaNDM-1 (n = 20) allele and the blaNDM-4 allele (n = 1). The majority of isolates were related within the ST level to other isolates in SZMC and RMC: 17/18 and 27/30 isolates, respectfully. The common ST's were the blaNDM-1 harboring ST-2 (n = 3) and ST-107 (n = 8) in SZMC and the blaNDM-2 harboring ST-103 in SZMC (n = 6) and in RMC (n = 27). All blaNDM alleles were located within a conserved mobile genetic environment flanked by the ISAb125 and IS91 family transposon. Clonal transmission was identified in most hospital-acquired cases in RMC and SZMC. CONCLUSION: NDMAb constitutes a minor part of CRAb cases and are clinically similar to non-NDM CRAb. Transmission of NDMAb occurs mostly by clonal spread.

Whole-Genome Sequencing Reveals Differences among Kingella kingae Strains from Carriers and Patients with Invasive Infections.

As a result of the increasing use of sensitive nucleic acid amplification tests, Kingella kingae is being recognized as a common pathogen of early childhood, causing medical conditions ranging from asymptomatic oropharyngeal colonization to bacteremia, osteoarthritis, and life-threatening endocarditis. However, the genomic determinants associated with the different clinical outcomes are unknown. Employing whole-genome sequencing, we studied 125 international K. kingae isolates derived from 23 healthy carriers and 102 patients with invasive infections, including bacteremia (n = 23), osteoarthritis (n = 61), and endocarditis (n = 18). We compared their genomic structures and contents to identify genomic determinants associated with the different clinical conditions. The mean genome size of the strains was 2,024,228 bp, and the pangenome comprised 4,026 predicted genes, of which 1,460 (36.3%) were core genes shared by >99% of the isolates. No single gene discriminated between carried and invasive strains; however, 43 genes were significantly more frequent in invasive isolates, compared to asymptomatically carried organisms, and a few showed a significant differential distribution among isolates from skeletal system infections, bacteremia, and endocarditis. The gene encoding the iron-regulated protein FrpC was uniformly absent in all 18 endocarditis-associated strains but was present in one-third of other invasive isolates. Similar to other members of the Neisseriaceae family, the K. kingae differences in invasiveness and tropism for specific body tissues appear to depend on combinations of multiple virulence-associated determinants that are widely distributed throughout the genome. The potential role of the absence of the FrpC protein in the pathogenesis of endocardial invasion deserves further investigation. IMPORTANCE The wide range of clinical severities exhibited by invasive Kingella kingae infections strongly suggests that isolates differ in their genomic contents, and strains associated with life-threatening endocarditis may harbor distinct genomic determinants that result in cardiac tropism and severe tissue damage. The results of the present study show that no single gene discriminated between asymptomatically carried isolates and invasive strains. However, 43 putative genes were significantly more frequent among invasive isolates than among pharyngeal colonizers. In addition, several genes displayed a significant differential distribution among isolates from bacteremia, skeletal system infections, and endocarditis, suggesting that the virulence and tissue tropism of K. kingae are multifactorial and polygenic, depending on changes in the allele content and genomic organization. Further analysis of these putative genes may identify genomic determinants of the invasiveness of K. kingae and its affinity for specific body tissues and potential targets for a future protective vaccine.

The use of a diversion tube to reduce blood culture contamination: A "real-life" quality improvement intervention study.

BACKGROUND: Blood culture contamination is associated with health care costs and potential patient harm. Diversion of the initial blood specimen reduces blood culture contamination. We report results of the "real-life" clinical implementation of this technique. METHODS: Following an educational campaign, use of a dedicated diversion tube was recommended prior to all blood cultures. Blood culture sets taken from adults using a diversion tube were defined as "diversion sets," those without, "non-diversion" sets. Blood culture contamination and true positive rates were compared for diversion and nondiversion sets and to nondiversion historical controls. A secondary analysis investigated efficacy of diversion by patient age. RESULTS: Out of 20,107 blood culture sets drawn, the diversion group included 12,774 (60.5%) and the nondiversion group 8,333 (39.5%) sets. The historical control group included 32,472 sets. Comparing nondiversion to diversion, contamination decreased by 31% (5.5% [461/8333] to 3.8% [489/12744], P < .0001]. Contamination was also 12% lower in diversion than historical controls [3.8% (489/12744) vs 4.3% (1,396/33,174) P = .02)]. The rate of true bacteremia was similar. In older patients, contamination rate was higher, and the relative reduction associated with diversion decreased (54.3% amongst 20-40-year-olds vs 14.5% amongst >80-year-olds). CONCLUSIONS: Use of a diversion tube in the ED reduced blood culture contamination in this large real life observational study. Efficacy decreased with increasing age, which requires further investigation.

Molecular features and transmission of NDM-producing Enterobacterales in Israeli hospitals.

OBJECTIVES: NDM-producing Enterobacterales (NDME) account for 34.9% of new carbapenemase-producing Enterobacterales cases in Israeli hospitals. The goals of this study were to characterize the genomic composition of NDME isolates and mobile genetic elements (MGEs) and to identify NDME transmission events (TEs). METHODS: The study was conducted at the Tel-Aviv Sourasky, Rambam and Sha'are-Zedek Medical Centers (TASMC, RMC and SZMC, respectively). All NDME isolates detected between January 2018 and July 2019 were included.Phylogenetic analysis was based on core-genome SNP distances. Core-genome distance of ≤5 SNPs between isolates from patients with overlapping hospitalization periods was suggestive of a potential TE. MGEs were classified by comparison of the blaNDM gene flanking regions. RESULTS: The study included 212 NDME isolates from 203 patients, including 104 isolates from TASMC, 30 isolates from RMC and 78 isolates from SZMC. The majority of isolates (n = 157; 74%) harboured the blaNDM-1 gene, followed by the blaNDM-5 (n = 48) and blaNDM-15 genes (n = 7). The most common NDME species were Klebsiella pneumoniae (n = 67), Escherichia coli (n = 65) and Enterobacter cloacae (n = 45), all showing a highly diverse clonal structure. Most blaNDM-1-harbouring isolates (134/157; 85%) were divided into nine different MGE modules, variably distributed across species and hospitals.The numbers of post-admission acquisition cases (n = 118) that could be linked to other cases by both molecular and epidemiological criteria were 13/58 (24.2%), 3/48 (6.3%) and 4/12 (33.3%) in TASMC, SZMC and RMC, respectively. CONCLUSIONS: The study depicted a complex and diverse population structure, suggesting that NDME had not spread via clonal expansion.

Non-typhoidal Salmonella bacteremia: comparison of adults and children in a single medical center.

Introduction. Non-typhoidal Salmonella (NTS) bacteremia can cause significant morbidity and mortality. There is high incidence of Salmonellosis in the Middle East, including Israel, but there is a paucity of data on the clinical and epidemiological features of children in comparison to adults.Hypothesis/Gap Statement. Previous studies describing the differences between paediatric and adult populations with Salmonella bacteremia are sparse.Aim. This study's aim was to describe the differences between adults and children with NTS bacteremia.Methodology. All records of patients with NTS bacteremia between 1 January 1998 and 31 July 2020 were reviewed. Data regarding clinical manifestations and laboratory results were extracted from the medical records; records of children (aged <18 years) were compared with those of adults.Results. Records for 137 cases of Salmonella bacteremia (69 adults and 68 children, aged 2 days to 98 years) were reviewed. Seventy nine (58 %) patients had concomitant gastrointestinal symptoms. Fifty-eight (84 %) adults and 13 (19 %) children had underlying conditions (P<0.001). Eighteen patients died, none of whom was a child. Over the study period, most of the children (n=46, 67 %) but only five adults were discharged from the emergency department on their first visit to the ED.Conclusions. The main characteristics of NTS bacteremia in children compared to adults, are higher rates of prior discharge from emergency department, higher rate of gastrointestinal symptoms and better prognosis.

Rate and Risk Factors for Carbapenem Resistant Acinetobacter baumannii Clinical Infections in Colonized Patients.

BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAB) is an important cause of nosocomial infections. Active surveillance for CRAB carriage to identify and isolate colonized patients is used to reduce transmission. OBJECTIVES: To assess the rate and risks of clinical infection among CRAB-carrier and non-carrier patients. METHODS: Hospitalized patients from whom CRAB screening-cultures were obtained between January and June 2018 were identified retrospectively. All CRAB-carriers were compared to a convenient sample of non-carriers and were followed to detect development of CRAB clinical infection during admission. RESULTS: We compared 115 CRAB carriers to 166 non-carriers. The median age in the study group was 76 years (IQR 71-87) vs. 65 years (55-79) in the non-carriers group (P < 0.001). Residence in a nursing facility, debilitated state, and admission to medical wards vs. intensive care units were more frequent among CRAB-carriers (P < 0.001). Mechanically ventilated patients included 51 CRAB carriers (44%) and 102 non-carriers (61%). Clinical infection developed in 49 patients (17%), primarily CRAB pneumonia. Of the CRAB-carriers and non-carriers, 26/115 (23%) and 23/166 (14%), respectively, developed a clinical infection (P = 0.05). One-third of the ventilated patients were infected. Debilitated state and antibiotic treatment during hospitalization were linked to higher infection rates (P = 0.01). Adjusted analysis showed that mechanical ventilation and CRAB colonization were strongly associated with clinical infection (P < 0.05). CONCLUSIONS: The rate of CRAB infection among carriers was high. Mechanical ventilation and CRAB colonization were associated with CRAB clinical infection, primarily pneumonia.

The NICU flora: An effective technique to sample surfaces.

OBJECTIVE: Environmental surface sampling in healthcare settings is not routinely recommended. There are several methods for environmental surface sampling, however the yield of these methods is not well defined. The aim of the present study is to compare two methods of environmental surface sampling, to characterize the neonatal intensive care unit (NICU) flora, compare it with rates of infection and colonization and correlate it with the workload. DESIGN AND SETTING: First, the yield of the swab and the gauze-pad methods were compared. Then, longitudinal surveillance of environmental surface sampling was performed over 6 months,once weekly, from pre-specified locations in the NICU. Samples were streaked onto selective media and bacterial colonies were identified using matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF). RESULTS: The number of colonies isolated using the gauze pad method was significantly higher compared with the swab method. Overall, 87 bacterial species of 30 different bacterial genera were identified on the NICU environmental surfaces. Of these, 18% species were potential pathogens, and the other represent skin and environmental flora. In 20% of clinical cultures and in 60% of colonization cultures, the pathogen was isolated from the infant's environment as well. The number of bacteria in environmental cultures was negatively correlated with nurse/patient ratio in the day prior to the culture. CONCLUSION: The gauze pad method for environmental sampling is robust and readily available. The NICU flora is very diverse and is closely related with the infants' flora, therefore it may serve as a reservoir for potential pathogens.

Colistin-resistant Klebsiella pneumoniae bloodstream infection: old drug, bad bug.

Multi-drug-resistant (MDR) Enterobacteriaceae pose a global threat to hospitalized patients. We report a series of colistin-resistant Klebsiella pneumoniae blood isolates from Israel and explore their resistance mechanisms using whole genome sequencing (WGS). Patients with colistin-resistant K. pneumoniae bloodstream infection (BSI) were identified during the period between 2006 and 2018. Demographic and clinical data were collected, and antibiotic susceptibility testing (AST) was performed using three commercial platforms. Long and short read sequencing were performed on a PacBio RS II (Pacific Biosciences) and an Illumina Miseq (Illumina), respectively. Thirteen patients with colistin-resistant K. pneumoniae BSI were identified, and seven isolates from seven different patients were successfully revived. Patient records indicated that five of the patients were previously treated with colistin. AST indicated that six of the seven isolates were colistin resistant and four of these isolates were resistant to carbapenems. WGS assigned the isolates to four distinct clusters that corresponded to in silico-derived multi-locus sequence types (MLST). Three isolates carried blaKPC-3 on two different plasmids and one carried blaOXA-48 on a novel IncL/M plasmid. All colistin-resistant isolates carried a variety of different mutations that inactivated the mgrB gene. We report the first comprehensive analysis of a series of colistin-resistant K. pneumoniae from Israel. A diverse set of isolates were obtained and colistin resistance was found to be attributed to different mechanisms that ablated the mgrB gene. Notably, carbapenemase genes were identified in four isolates and were carried on novel plasmids.

Quantitative real-time PCR in Borrelia persica tick-borne relapsing fever demonstrates correlation with the Jarisch-Herxheimer reaction.

The purpose of this study is to explore whether a correlation exists between the bacterial load of Borrelia persica in tick-borne relapsing fever (TBRF), established by quantitative real-time PCR, and the development of Jarisch-Herxheimer reaction (JHR) after the initiation of antibiotic treatment. Forty-two blood samples were included in our study. The mean bacterial load, as established by real-time PCR, in patients who developed JHR was significantly greater than in those patients who did not develop JHR (443,293 copies vs. 140,598, p = 0.035). Accordingly, real-time PCR may assist clinicians in identifying patients at higher risk of JHR.

Misidentification of Candida dubliniensis isolates with the VITEK MS.

The phylogenetic relatedness of Candida dubliniensis and C. albicans may lead to misidentification of C. dubliniensis and underestimation of its clinical significance. We evaluated the performance of VITEK-MS in identifying C. dubliniensis isolates following growth on different culture media. Correct identification was documented in 98% of the isolates grown on blood agar media whereas only 44% were correctly identified from SDA or CHROMagar. The use of non-manufacturer validated media for identifying C. dubliniensis with VITEK-MS, may result in misidentification of these isolates as C. albicans. This finding calls for reassessing the accuracy of fungal isolates identification in local workflows using non-validated culture media.

Nontuberculous mycobacteria infections of peritoneal dialysis patients: A multicenter study.

OBJECTIVES: Nontuberculous mycobacteria (NTM) infections pose a diagnostic challenge in peritoneal dialysis (PD) patients. In this study, we sought to identify findings that are suggestive of NTM infection in PD adult patients. METHODS: All patients with NTM exit-site infection (ESI) with/without tunnel infection and peritonitis identified during the last decade in eight medical centers in Israel were included. Clinical, microbiological, and outcome data were collected and analyzed. RESULTS: Thirty patients were identified; 16 had ESI (53%) and 14 had peritonitis (47%). Median age was 65 years (interquartile range 52-76). Abdominal pain and cloudy PD fluid were reported in all patients with peritonitis, whereas exit-site discharge and granulation tissue were common in patients with ESI. Fourteen patients (47%) had negative cultures prior NTM diagnosis, and isolation of diphtheroids or Corynebacterium spp. was reported in 9 of 30 patients (30%). Antimicrobial treatment prior to diagnosis was documented in 13 of 30 patients (43%). Delayed diagnosis was frequent. Treatment regimens and duration of therapy varied widely. In 26 of 30 (87%) patients, catheter was removed and 19 of 30 patients (63%) required permanent transition to hemodialysis. Two patients with peritonitis (2 of 14, 14%) and seven with ESI (7 of 16, 44%) were eligible for continuation of PD. CONCLUSIONS: Culture negative peritonitis, isolation of diphtheroids or Corynebacterium spp., previous exposure to antibiotics, and/or a refractory infection should all prompt consideration of PD-related NTM infection and timely workup. Catheter removal is recommended aside prolonged antimicrobial therapy. In select patients with ESI, continuation of PD may be feasible.

False-positive galactomannan antigen testing in pulmonary nocardiosis.

Early diagnosis of invasive aspergillosis (IA) is facilitated by detection of galactomannan (GM) in serum and bronchoalveolar lavage fluid (BALF) using an enzyme-linked immunosorbent assay (ELISA). Although accurate, false positive results have been reported with these tests in numerous contexts. We report for the first time the occurrence of false positive GM ELISA due to nocardiosis, initially in a clinical sample of BALF from a patient with pulmonary nocardiosis, and subsequently corroborated by in vitro reactivity of 26% of tested isolates. Since patients at risk for IA are also at risk for nocardiosis, this finding has important clinical implications. LAY SUMMARY: Early diagnosis of aspergillosis has been facilitated by the routine use of antibody-based detection of galactomannan in various bodily fluids. We report for the first time the occurrence of false positive results of this assay in the context of nocardiosis.

When a Root Is the Cause of Infection.

BACKGROUND: Sinorhizobium meliloti is a phytobacterium found in the root nodules of plants, where it is involved in fixing nitrogen for delivery to the roots in exchange for a photosynthate carbon source. There have been no reported cases of S. meliloti infection in humans. We conducted a retrospective review of clinical records and diagnostic tests. CASE DESCRIPTION: An 81-year-old woman who presented to the emergency department with a 1-day history of progressive decline in her level of consciousness following a head injury and deep scalp laceration. Her medical history was significant for a ventriculoperitoneal shunt due to normal pressure hydrocephalus. Imaging studies revealed hydrocephalus and a tear in the shunt catheter. Cerebrospinal fluid analysis was not suggestive for meningitis. Cerebrospinal fluid culture revealed an unfamiliar organism, identified as S. meliloti following sequencing of its entire genome, which was considered a contaminant. The patient subsequently developed peritonitis, and the same pathogen was detected in the peritoneal fluid, suggesting distal shunt infection. Symptoms resolved after shunt removal and antibiotic treatment. Thorough history taking revealed that the patient had fallen and struck her head against a flowerpot. CONCLUSIONS: S. meliloti is a phytopathogen that should not be easily disregarded as a contaminant when isolated from human sterile fluids or tissues. Aggressive management including removal of infected hardware, if present, is required to ensure resolution of infection. It emphasizes the importance of thorough history taking.

The utility of MALDI-TOF MS for outbreak investigation in the neonatal intensive care unit.

Our aim was to evaluate the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), routinely used in the microbiology laboratory for bacterial identification, for bacterial typing in the setting of extended spectrum beta-lactamase producing Klebsiella pneumoniae (ESBL-KP) outbreak in the neonatal intensive care unit (NICU). Isolates from a 2011 outbreak in the NICU were retrieved from frozen stocks and analyzed by MALDI-TOF. The MALDI typing was compared with core genome multilocus sequence typing (cg-MLST). MALDI typing divided the 33 outbreak isolates into 2 clones: sequence type (ST)-290 and 405. These results were in complete agreement with cg-MLST results. The differentiation of the outbreak isolates into two clones correlated with the patients' location in the NICU, but also with their place of residence.Conclusion: Here, we show that MALDI-TOF MS, which has been integrated into the microbiology laboratory workflow for microbial species identification, can be secondarily used for epidemiological typing at no added cost. What is Known: • Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is now routinely used in the microbiology laboratory for bacterial identification What is New: • MALDI typing was used for outbreak investigation in the NICU and divided the outbreak isolates into two clones • MALDI-TOF MS may be secondarily used for epidemiological typing at no added cost.

The spectrum of bacteria and mechanisms of resistance identified from the casualties treated in the Israeli field hospital after the earthquake in Nepal, 2015: A retrospective analysis.

BACKGROUND: On the April 25, 2015, a 7.8 magnitude earthquake struck Nepal. Soon-after, the Israel Defense Force (IDF) dispatched a tertiary field-hospital to Kathmandu. The field-hospital was equipped with a clinical laboratory with microbiology capabilities. Limited data exists regarding the spectrum of bacteria isolated from earthquake casualties. We aimed to identify the spectrum of bacteria and their mechanisms of resistance in-order to allow preparedness of antibiotic treatment protocols for future disaster scenarios. METHODS: - The field-laboratory phenotypically processed cultures from sterile and non-sterile sites as needed clinically. Later-on, the isolates were brought to Israel for quality control, definite identification and molecular characterization including mechanisms of resistance. RESULTS: A total of 82 clinical pathogens were isolated from 56 patients; 68% of them were Gram negative bacilli. The most common isolates were Enterobacteriaceae (55%) -36% carried bla-NDM and 33% produced Extended-spectrum beta-lactamase (ESBL), mostly blaCTX-M-15. Enterococcus spp were the main Gram positive bacteria isolated (22 isolates), yet, none were vancomycin resistant. The overall level of resistance was 27% MDR and 23% extensively drug resistant (XDR) bacteria. CONCLUSIONS: - Gram negative bacteria were the predominant organism cultured from the casualties, of them 77% were MDR or XDR. NDM was the most common resistance mechanism. The Antibiotic inventory of a field-hospital should be set to cover a wide and unexpected spectrum of bacteria, including resistant organisms. This report adds important information to the scarce reports of bacterial resistance in Nepal.

Bacterial contamination of surgical scrubs in the operating theater.

BACKGROUND: Measures for the prevention of postsurgical infections include issuing special scrubs for the operating room (OR) and prohibiting walking out of the OR complex wearing these scrubs. The aim of this study was to provide further data on bacterial contamination of surgical scrubs. METHODS: Specimens were collected at the entrance to the OR from surgical scrubs worn by surgeons. Participants completed a questionnaire regarding the times, places, and activities in which they were involved during the time interval they were wearing the scrubs. RESULTS: Among the 133 surgeons who participated, the median colony-forming unit (CFU) count was higher (39 CFU/plate) for their scrubs than for clean scrubs worn by the control group (3 CFU/plate; n = 11; P < .001), but there was no significant difference between the study and control groups in the rate of carriage of pathogenic bacteria (13% and 9%, respectively). The majority of the bacteria isolated were considered commensals. Fifty-five (41%) of the surgeons stated that before sampling they took part in medical activities, and 45 (34%) participated in non-medical activities. Practicing these activities was associated with a higher number of CFUs compared to not being involved in such activities (P < .05). CONCLUSIONS: Our data show that, even in less than optimal situations when scrubs are worn outside the OR, surgical scrubs are contaminated with a low bacterial load and only a small number of pathogenic bacteria.

Modification of Blood Test Draw Order to Reduce Blood Culture Contamination: A Randomized Clinical Trial.

BACKGROUND: Blood culture contamination leads to unnecessary interventions and costs. It may be caused by bacteria in deep skin structures unsusceptible to surface decontamination. This study was designed to test whether diversion of blood obtained at venipuncture into a lithium heparin tube prior to aspiration of blood culture reduces contamination. METHODS: The order of blood draws for biochemistry and blood cultures was randomized. Following standard disinfection and venipuncture, blood was either aspirated into a sterile lithium heparin tube before blood culture bottles (diversion group) or blood cultures first and then lithium heparin tube (control group). All study personnel were blinded with the exception of the phlebotomist. RESULTS: After exclusions, 970 blood culture/biochemistry sets were analyzed. Contamination occurred in 24 of 480 (5.0%) control vs 10 of 490 (2.0%) diversion group cultures (P = .01). True pathogens were identified in 26 of 480 (5.4%) control vs 18 of 490 (3.7%) diversion cultures (P = .22). Despite randomization, demographic differences were apparent between the 2 groups. A post hoc analysis of 637 cultures from 610 medical patients admitted from home neutralized demographic differences. Culture contamination remained more frequent in the control vs diversion group (17/312 [5%] vs 7/325 [2%]; P = .03). Fewer diversion group patients were admitted to hospital (control: 200/299 [66.9%] vs diversion: 182/311 [58.5%]; P = .03), and length of stay was shorter (control: 30 hours [interquartile range {IQR}, 6-122] vs diversion: 22 [IQR, 5-97]; P = .02). CONCLUSIONS: Use of lithium heparin tubes for diversion prior to obtaining blood cultures led to a 60% decrease in contamination. This technique is easy and inexpensive and might decrease overall hospital length of stay. CLINICAL TRIALS REGISTRATION: NCT03966534.

A Cluster of Bacillus cereus Infections in the Neonatal Intensive Care Unit: Epidemiologic and Whole-genome Sequencing Analysis.

Bacillus cereus isolates causing an outbreak in the neonatal intensive care unit were investigated using whole-genome sequencing. The outbreak coincided with construction work performed adjacent to the neonatal intensive care unit and ceased after strict sealing of the construction area. We found the outbreak to be polyclonal, however, the clonality did not correlate with the virulence in vivo. Genotypically similar isolates were associated with both lethal/severe infection and colonization/environmental contamination. Environmental bacterial load may be a major determinant of infection, especially in high-risk patients. Clinicians should be alert to unusual increase in B. cereus isolations from clinical cultures to facilitate early recognition and investigations of Bacillus outbreaks and pseudo-outbreaks. The integration of genomics into the classical infectious disease work can augment our understanding of pathogen transmission and virulence, and can rapidly assist our response to unusual disease trends.