Prevalence Of Colonization Research Articles

Neonatal Colonization With Antibiotic-Resistant Pathogens in Low- and Middle-Income Countries: A Systematic Review and Meta-Analysis.

In low- and middle-income countries (LMICs), neonatal bacterial infections are mainly caused by Enterobacterales species and Staphylococcus aureus, which are also the leading causes of mortality directly attributable to antimicrobial resistance. As bacterial colonization often precedes infection, better knowledge of colonization is crucial to prevent antibiotic-resistant neonatal sepsis. To synthesize current evidence on the prevalence of and factors associated with colonization with third-generation cephalosporin-resistant Enterobacterales (3GCRE), carbapenem-resistant Enterobacterales (CRE), and methicillin-resistant S aureus (MRSA) during the first 3 months of life in LMICs. PubMed, Scopus, Web of Science, and the World Health Organization Global Index Medicus were searched for articles published from January 1, 2000, through July 29, 2024. Included studies were conducted in LMICs and reported prevalence rates or factors associated with colonization with 3GCRE, CRE, or MRSA in neonates and infants up to 3 months of age. Outbreak reports were excluded. Data extraction and risk-of-bias assessment using a Joanna Briggs Institute tool were performed by 2 independent reviewers. Pooled prevalence for each pathogen was computed using a random-effects model. Reporting followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guideline. Prevalence of and factors associated with 3GCRE, CRE, and MRSA colonization. Of the 3147 articles identified in the search, 67 studies (51 for 3GCRE and CRE and 16 for MRSA) including 17 152 individuals were eligible. The pooled prevalence of 3GCRE colonization was 30.2% (95% CI, 21.4%-40.7%; τ2 = 1.48; I2 = 95.1%), varying from 18.2% (95% CI, 10.8%-29.1%) in nonhospitalized individuals to 48.2% (95% CI, 36.4%-60.2%) in hospitalized individuals. The prevalence of CRE colonization was 2.6% (95% CI, 0.7%-8.8%; τ2 = 7.79; I2 = 95.6%), while it was 2.7% (95% CI, 1.0%-6.7%; τ2 = 2.58; I2 = 93.5%) for MRSA. Increased risk of colonization with 3GCRE was associated with hospital birth (odds ratio [OR], 1.87; 95% CI, 1.33-2.64), neonatal antibiotic use (OR, 2.96; 95% CI, 1.43-6.11), and prolonged rupture of membranes (OR, 3.86; 95% CI, 2.19-6.84). In this systematic review and meta-analysis of antibiotic-resistant pathogen carriage in individuals aged 0 to 3 months, the pooled prevalence was substantial despite a limited exposure period. Although high heterogeneity between studies limited extrapolation of results, the findings highlight the need for further investigation to identify transmission routes and to design targeted and effective preventive measures.

Comparison of qPCR and chromogenic culture methods for rapid detection of group B streptococcus colonization in Vietnamese pregnant women

IntroductionNeonatal infections can rapidly become severe, with delays in treatment often proving fatal. Streptococcus agalactiae (Group B Streptococcus, GBS) is a common cause, typically transmitted from colonized pregnant women to neonates during childbirth. In Vietnam, routine prenatal care lacks standardized GBS screening protocols. This study aims to compare enhanced qPCR methods with the culture method, evaluate the diagnostic accuracy of these qPCR procedures, and assess the frequency of GBS infection in pregnant Vietnamese women during their final trimester. Materials and methodsPregnant women aged 35 weeks gestation or more were recruited. Rectovaginal swabs were collected and analyzed for GBS using chromogenic culture, a commercial real-time PCR kit, and in-house real-time PCR assays targeting the cfb and sip genes. Clinical diagnostic values were calculated, and GBS prevalence was determined. ResultsThe study included 259 pregnant women with a mean age of 30.2 ± 5.0 years. Of these, 96.6 % had gestational ages of 37 weeks or more at delivery. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of the cfb-based and sip-based qPCR assays were 94.1/92.7, 99.0/99.5, 97.1/98.5, 97.8/97.3, and 97.6 %, respectively. The Kappa values were excellent (0.940 and 0.939), with results available in under 2 h. GBS prevalence was 24.7 % and 25.5 % by cfb-based and sip-based qPCR assays, aligning with the culture method (25.5 %). ConclusionsBoth direct real-time PCR assays demonstrated high accuracy and were comparable to chromogenic culture in diagnosing GBS. A significant prevalence of GBS colonization was found among Vietnamese pregnant women in their final trimester.

High prevalence of colonization with extended-spectrum β-lactamase-producing and multidrug-resistant Enterobacterales in the community in Addis Ababa Ethiopia: risk factors, carbapenem resistance, and molecular characterization

BackgroundGlobally, extended-spectrum beta-lactamase-producing and carbapenem-resistant Enterobacterales are major causes of hospital-acquired infections and there are increasing concerns about their role in community-acquired infections.ObjectiveWe aimed to investigate the prevalence of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and Carbapenemase-producing-Carbapenemresistant-Enterobacterales (CP-CRE) and associated factors in community settings in Gulele sub city, Addis Ababa, Ethiopia.MethodsA cross-sectional study was conducted among 261 healthy individuals. Stool samples were collected and processed using standard microbiological methods. Antimicrobial susceptibility and phenotypic ESBL and carbapenemase tests were performed. Antibiotic resistance genes were detected by Polymerase Chain Reaction (PCR).ResultsThe colonization rate of ESBL-PE and CP-CRE were 31.4% (82/261, 95% CI: 25.91–37.48) and 0.8% (2/261, 95% CI: 0.13–3.1), respectively by phenotypic method. Molecular detection of genes for ESBL-PE was 27.9% (73/261, 95% CI:22.7–33.9), and for CP-CRE was 0.8% (2/261, 95% CI: 0.13–3.1). The most prevalent genes were blaTEM [76.7% (56/73)] and blaCTX-M [45.2% (33/73)]. Previous antibiotic use (AOR:2.04, 95%CI: 1.35–4.41, P:0.041) and age between 42 and 53 years old (AOR:3.00, 95%CI:1.12–7.48, P:0.019) were significantly associated with ESBL-PE colonization.ConclusionIntestinal colonization by ESBL-PE harboring the associated antibiotic resistance genes was substantially high but with low CP-CRE. Continued surveillance of community-level carriage of antimicrobial resistance Enterobacterales is warranted.

Role of Xpert PCR kit in assessing MRSA colonization in medical and surgical units of a tertiary care teaching hospital

Background and rationaleMethicillin resistant Staphylococcus aureus (MRSA) colonization increases the risk of MRSA infection. Detecting MRSA colonization can influence postoperative outcomes and prolong hospital stay. The conventional standard culture method for detecting MRSA colonization has limitations in terms of sensitivity and turnaround time. Hence, we sought out use of Xpert PCR kit for prompt evaluation of MRSA colonization to support MRSA prevention in a tertiary care hospital in Karachi, Pakistan.Materials and methodsDuring 1st April-31st December 2022, 290 nasal and skin swab samples were collected from 257 patients and processed using routine culture (as gold standard method) and PCR-based MRSA detection assay (MRSA Xpert).ResultsA total of two hundred and ninety (290) swab samples from 257 patients were obtained, 33 of which were paired. The overall prevalence of MRSA colonization was 12% by both methods, with 90% of cases classified as community-associated (CA-MRSA) whereas 10% as hospital-acquired (HA-MRSA). The colonized group showed a higher subsequent MRSA infection rate (11% vs. 3.5%) compared to the noncolonized group. Culture identified 11% of screening samples as MRSA positive, Xpert MRSA assay showed 100% sensitivity and 95% specificity. The cost of a single MRSA Xpert assay was $50 while MRSA culture cost around $7.50.ConclusionOur study findings suggest that the presence of MRSA colonization in our cohort of patients is consistent with the existing trends in hospital epidemiology. Both conventional culture and Xpert MRSA methods showed comparable efficacy for detection of MRSA colonization. Larger-scale studies are recommended to validate these findings conclusively.

Prevalence and factors associated with human colonisation and vancomycin minimum inhibitory concentration of <em>Staphylococcus aureus</em> in Colombo, Sri Lanka

Introduction: Staphylococcus aureus is known to cause a wide variety of diseases of varying severity in humans. The objectives of this study were to determine the prevalence of S. aureus and methicillin resistant S. aureus (MRSA) colonisation, assess factors associated with MRSA colonisation, identify antibiotic susceptibility patterns of MRSA isolates, determine distribution of vancomycin minimum inhibitory concentrations (MIC) of S. aureus and factors associated with high vancomycin MIC values (≥2 µg/ml). Methods: A descriptive cross sectional study was conducted among 341 participants aged 18 to 84 years selected randomly from the Colombo district from 11th December 2018 to 10th April 2019. Samples were collected from the nose, axilla, groin of participants and identification and sensitivity testing of S. aureus were performed based on standard operation procedures given in the Laboratory manual in microbiology published by the Sri Lanka College of Microbiologists (2011). Results: Prevalence of S. aureus and MRSA colonisation in the sample population was 34.6% and 13.78% respectively. All MRSA isolates were susceptible to linezolid. MRSA susceptibility to gentamicin (86%), co-trimoxazole (88 %), and chloramphenicol (80%) was high. Erythromycin had the lowest susceptibility (20%). Inducible clindamycin resistance was demonstrated in 31% of isolates. Meat consumption and consumption of antibiotics within the previous six months showed a significant association with MRSA colonisation. Vancomycin MIC of S. aureus ranged from ≤ 0.5 to 2 µg/ml. Conclusion: As prevalence of MRSA colonisation is 13.78%, more attention should be paid when managing patients with suspected S. aureus infections presenting from the community. Further research on associated factors and environmental triggers are warranted with a larger sample size and different study design to formulate national regulations and guidelines.

Prevalence and Molecular Epidemiology of Intestinal Colonization by Multidrug-Resistant Bacteria among Hematopoietic Stem-Cell Transplantation Recipients: A Bulgarian Single-Center Study.

Background/Objectives: Intestinal colonization by multidrug-resistant (MDR) bacteria is considered one of the main risk factors for invasive infections in the hematopoietic stem-cell transplant (HSCT) setting, associated with hard-to-eradicate microorganisms. The aim of this study was to assess the rate of intestinal colonization by MDR bacteria and their microbial spectrum in a group of post-HSCT patients to study the genetic determinants of beta-lactam and glycopeptide resistance in the recovered isolates, as well as to determine the epidemiological relation between them. Methods: The intestinal colonization status of 74 patients admitted to the transplantation center of University Hospital "St. Marina"-Varna in the period January 2019 to December 2021 was investigated. Stool samples/rectal swabs were screened for third-generation cephalosporin and/or carbapenem-resistant Gram-negative bacteria, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and Stenotrophomonas maltophilia. Identification and antimicrobial susceptibility testing were performed by Phoenix (BD, Sparks, MD, USA) and MALDI Biotyper sirius (Bruker, Bremen, Germany). Molecular genetic methods (PCR, DNA sequencing) were used to study the mechanisms of beta-lactam and glycopeptide resistance in the collected isolates, as well as the epidemiological relationship between them. Results: A total of 28 patients (37.8%) were detected with intestinal colonization by MDR bacteria. Forty-eight non-duplicate MDR bacteria were isolated from their stool samples. Amongst them, the Gram-negative bacteria prevailed (68.8%), dominated by ESBL-producing Escherichia coli (30.3%), and followed by carbapenem-resistant Pseudomonas sp. (24.2%). The Gram-positive bacteria were represented exclusively by Enterococcus faecium (31.2%). The main beta-lactam resistance mechanisms were associated with CTX-M and VIM production. VanA was detected in all vancomycin-resistant enterococci. A clonal relationship was observed among Enterobacter cloacae complex and among E. faecium isolates. Conclusions: To the best of our knowledge, this is the first Bulgarian study that presents detailed information about the prevalence, resistance genetic determinants, and molecular epidemiology of MDR gut-colonizing bacteria in HSCT patients.

Multidrug Resistant Group B Streptococcus Isolates from Pregnant Women in Delta State, Nigeria.

&lt;b&gt;Background and Objective:&lt;/b&gt; Group B &lt;i&gt;Streptococci&lt;/i&gt; (GBS) are globally recognized as a major risk factor for neonatal infections and various obstetric complications. More so, biofilm formation has been suggested to be important for GBS pathogenesis. The aim of this study was to determine the prevalence and antibiotic susceptibility pattern of GBS among pregnant women and their capacity to form biofilm. &lt;b&gt;Materials and Methods:&lt;/b&gt; A total of 87 pregnant women at 34 to 37 weeks' gestation aged 17-45 years were recruited from 3 healthcare centres in Delta State, Nigeria. Cultures for the isolation of GBS were carried out using recto-vaginal swabs, according to standard microbiological methods. All strains isolated were used for susceptibility tests to various antibiotics as recommended by CLSI using the disk-diffusion method. &lt;b&gt;Results:&lt;/b&gt; The overall prevalence of GBS colonization among pregnant women was 43.6% (38/87). The &lt;u&gt;<&lt;/u&gt;30 age group had the highest rate of GBS colonization. Resistance to erythromycin and vancomycin was 48.2 and 66.4%, respectively. The fluoroquinolones had the lowest resistant rates with no isolate showing resistance to ofloxacin. Multidrug resistance (MDR) (&lt;u&gt;>&lt;/u&gt;3 drug classes) was detected in 73.7% (28/38) of the GBS isolates. All GBS isolated in this study were either strong, moderate or weak biofilm producers. However, most 28 (73.7%) were strong biofilm producers. Resistance of GBS isolates to erythromycin and vancomycin, drugs used for treating GBS infection was high. &lt;b&gt;Conclusion:&lt;/b&gt; This suggested the importance of testing antimicrobial susceptibilities in GBS colonized pregnant women in order to guide antibiotic therapy and minimize newborn infection and co-morbidity.

The prevalence and risk factors of methicillin-resistant Staphylococcus aureus among pediatric populations: a systematic review and meta-analysis.

Future research should build on these findings by emphasizing ongoing efforts to combat MRSA in pediatric settings and implementing targeted interventions. • Methicillin-resistant Staphylococcus aureus (MRSA) is considered a threat to public health. It is noteworthy to mention that the prevalence of MRSA strains has not been adequately quantified in many countries, especially in the pediatric population. The pediatric population is a pivotal source of MRSA and may play a central role in its distribution in both community and healthcare settings. A notable study underscores the gravity of the situation, estimating a tenfold increase in the incidence of MRSA infection among children in the USA between 1999 and 2008. • Here we present the first global systematic review and meta-analysis to investigate the prevalence and risk factors of MRSA among the pediatric population. A total of 124 studies encompassing 44 million participants were included in this analysis. The overall pooled estimated global prevalence of MRSA colonization in the pediatric population was 5% [95% CI 4-5%]. The prevalence was the highest in Asia and lowest in Europe. Female sex, recent surgery, recent hospitalization, and antibiotic use were significantly associated with higher odds of MRSA colonization.

Multidrug-Resistant Bacteria in Immunocompromised Patients.

The increasing incidence of antibiotic resistance in bacteria is a major problem in terms of therapeutic options, especially in immunocompromised patients, such as patients from intensive care units (ICUs), HIV-positive patients, patients with malignancies or transplant patients. Commensal bacteria, especially anaerobes, serve to maintain microbial stability by preventing overpopulation with pathogenic bacteria. In immunocompromised patients, microbiota imbalance caused by antibiotic therapy and decreased host immunity favors intestinal overpopulation with pathogenic species, leading to increased bacterial translocation and susceptibility to systemic infections. Infections with multidrug-resistant (MDR) bacteria pose major challenges to the establishment of appropriate treatment and lead to increased mortality. Asymptomatic colonization with MDR bacteria usually precedes infection and tends to persist for long periods of time, and in immunocompromised patients, colonization with MDR bacteria is a risk factor for systemic infections. This review aims to assess the relation between colonization and infection with MDR bacteria in immunocompromised patients such as ICU patients, HIV-positive patients and cancer patients and to identify the prevalence and patterns of MDR bacterial colonization and infection in this category of patients.

Clostridioides difficile Infections in Children: What Is the Optimal Laboratory Diagnostic Method?

The diagnosis of Clostridioides difficile infection (CDI) in the pediatric population is complicated by the high prevalence of asymptomatic colonization, particularly in infants. Many laboratory diagnostic methods are available, but there continues to be controversy over the optimal laboratory testing approach to diagnose CDI in children. We evaluated commonly used C. difficile diagnostic commercial tests in our pediatric hospital population at Sidra Medicine in Doha, Qatar. Between June and December 2023, 374 consecutive stool samples from pediatric patients aged 0-18 years old were tested using: Techlab C. diff Quik Chek Complete, Cepheid GeneXpert C. difficile, QIAstat-Dx Gastrointestinal Panel, and culture using CHROMagar C. difficile. The results of these tests as standalone methods or in four different testing algorithms were compared to a composite reference method on the basis of turnaround time, ease of use, cost, and performance characteristics including specificity, sensitivity, negative predictive value, and positive predictive value. Our study showed variability in test performance of the different available assays in diagnosing CDI. In our population, a testing algorithm starting with Cepheid GeneXpert C. difficile PCR assay or QIAstat-Dx Gastrointestinal panel as a screening test followed by toxin immunoassay for positive samples using the Techlab C. diff Quik Chek Complete kit showed the best performance (100% specificity and 100% positive predictive value) when combined with clinical review of the patient to assess risk factors for CDI, clinical presentation, and alternative causes of diarrhea.

Nanopore R10.4 metagenomic detection of blaCTX-M/blaDHA antimicrobial resistance genes and their genetic environments in stool

The increasing prevalence of gut colonization with CTX-M extended-spectrum β-lactamase- and/or DHA plasmid-mediated AmpC-producing Escherichia coli is a concern. Here, we evaluate Nanopore-shotgun metagenomic sequencing (Nanopore-SMS) latest V14 chemistry to detect blaCTX-M and blaDHA genes from healthy stools. We test 25 paired samples characterized with culture-based methods (native and pre-enriched). Antimicrobial resistant genes (ARGs) are detected from reads and meta-assembled genomes (MAGs) to determine their associated genetic environments (AGEs). Sensitivity and specificity of native Nanopore-SMS are 61.1% and 100%, compared to 81.5% and 75% for pre-enriched Nanopore-SMS, respectively. Native Nanopore-SMS identifies only one sample with an AGE, whereas pre-enriched Nanopore-SMS recognizes 9/18 plasmids and 5/9 E. coli chromosomes. Pre-enriched Nanopore-SMS identifies more ARGs than native Nanopore-SMS (p < 0.001). Notably, blaCTX-Ms and blaDHAs AGEs (plasmid and chromosomes) are identified within 1 hour of sequencing. Furthermore, microbiota analyses show that pre-enriched Nanopore-SMS results in more E. coli classified reads (47% vs. 3.1%), higher differential abundance (5.69 log2 fold) and lower Shannon diversity index (p < 0.0001). Nanopore-SMS has the potential to be used for intestinal colonization screening. However, sample pre-enrichment is necessary to increase sensitivity. Further computational improvements are needed to reduce the turnaround time for clinical applications.

Prevalence, serotype distribution, and antimicrobial susceptibility profile of Streptococcus pneumoniae in Sea Nomad children under 5 years of age in Wakatobi, Southeast Sulawesi, Indonesia: A cross-sectional study

ObjectiveIndonesia commenced the nationwide introduction of pneumococcal conjugate vaccine (PCV) in 2022. Pre-vaccine Streptococcus pneumoniae data from across the country could be critical to enable vaccine impact evaluation in the future. This study evaluates colonization prevalence, factors associated with colonization, serotype distribution, and the antimicrobial susceptibility profile of S. pneumoniae. MethodsChildren under 5 years of age were enrolled from Bajau tribe settlements in Wakatobi, southeast Sulawesi, Indonesia, from October 2018 to February 2019. Nasopharyngeal swab specimens were analysed by culture, and isolates were serotyped using sequential multiplex polymerase chain reaction. Antibiotic susceptibility was performed by the disk diffusion method. Multivariable logistic regression was performed for risk factor analysis. ResultsA total of 499 NP swab specimens were collected; 61.9% were colonized with S. pneumoniae and 48.9% of the isolates were of PCV13-vaccine type. The most common serotypes were 23F, 6B, 19F, and 6A at 13.2%, 9.8%, 8.9%, and 8.0%, respectively. Exposure to cigarette smoke in the household and runny nose were significant risk factors for colonization, with aORs of 1.6 (95% confidence interval: 1.1–2.3) and 2.1 (95% confidence interval: 1.4–3.3), respectively. ConclusionsThe findings of this study may contribute to baseline pre-vaccine data in Indonesia that would be critical for the impact evaluation of vaccines.

Prevalence of group B Streptococcus colonisation in mother–newborn dyads in low-income and middle-income south Asian and African countries: a prospective, observational study

Rectovaginal group B Streptococcus (GBS) colonisation in pregnant individuals at the time of labour is a major risk factor for invasive GBS disease by age 7days (early-onset disease). We aimed to investigate the prevalence of rectovaginal GBS colonisation at the time of labour among pregnant women and vertical transmission to their newborns across selected low-income and middle-income African and south Asian countries. This prospective, observational study was undertaken at 11maternity and obstetric care facilities based in Ethiopia, Kenya, Mozambique, Nigeria, Mali, South Africa, Bangladesh, India, and Bhutan. HIV-negative pregnant women aged 18-45years who were in the early stages of labour and at least 37weeks' gestation were eligible for inclusion. Lower vaginal and rectal swabs and urine were collected from the women, and swabs of the umbilicus, outer ear, axillary fold, rectum, and throat were obtained from their newborns, for GBS culture. Standardised sampling and culture using direct plating and selective media broth for detection of GBS colonisation was undertaken at the sites. Serotyping of GBS isolates was done in South Africa. The primary outcome was the prevalence of rectovaginal GBS among pregnant women, analysed in participants with available data. This study is registered with the South African National Clinical Trials Register, number DOH-27-0418-4989. 6922pregnant women were enrolled from Jan 10, 2016, to Dec 11, 2018, of whom 6514 (94·1%; 759-892per country) were included in the analysis; data from Bhutan were not included in the study due to issues with specimen collection and processing. Overall, the prevalence of maternal GBS colonisation was 24·1% (95% CI 23·1-25·2; 1572of 6514); it was highest in Mali (41·1% [37·7-44·6]; 314of 764) and lowest in Ethiopia (11·6% [9·5-14·1]; 88of 759). Theoverall rate of vertical transmission of GBS from women with rectovaginal GBS colonisation was 72·3% (70·0-74·4; 1132of 1566); it was highest in Mozambique (79·2% [73·3-84·2]; 168of 212) and lowest in Bangladesh (55·8%, 47·5-63·8; 77of 138). The five most common GBS colonising serotypes were Ia (37·3% [34·9-39·7]; 586of 1572), V(28·5% [26·3-30·8]; 448of 1572), III (25·1% [23·0-27·3]; 394of 1572), II (9·2% [7·8-10·7]; 144of 1572), and Ib(6·5% [5·4-7·8]; 102of 1572). There was geographical variability in serotype proportion distribution; serotype VIIwas the third most common serotype in India (8·6% [5·3-13·7]; 15of 174) and serotype VI was mainly identified in Bangladesh (5·8% [3·0-11·0]; eight of 138) and India (5·7% [3·2-10·3]; ten of 174). Our study reported a high prevalence of GBS colonisation in most settings, with some geographical variability even within African countries. Our findings suggest that serotypes not included in current multivalent capsular-polysaccharide GBS vaccines prevail in some regions, so vaccine efficacy and post-licensure effectiveness studies should assess the effect of vaccination on maternal GBS colonisation given the potential for replacement by non-vaccine serotypes. Bill & Melinda Gates Foundation.

An Unusual High Prevalence of Cryptococcus (Naganishia) diffluens Colonization in Neonates Hospitalized in a Referral Neonatal Intensive Care Unit.

Although the Candida species continue to be the most frequent colonizer of neonatal skin, a clear increase of colonization due to rare yeast-like fungi has been reported. In this study, we report an unusual high prevalence of Cryptococcus diffluens colonization in neonates admitted to the neonatal intensive care unit (NICU) over a 1-month period. From January 2020 to June 2021, the study included all neonates who were admitted to the NICU of Bu Ali Sina Hospital at least 28 days old. Skin swabs from different anatomical areas were collected. Sampling was done 3 times/week. Each sample was inoculated into Sabouraud Dextrose Agar containing chloramphenicol and CHROMagar Candida, separately. The plates were incubated at 30 °C and 35 °C, respectively. Identification of the isolates was molecularly confirmed. In vitro antifungal susceptibility testing of the isolates was performed against different antifungal agents using the Clinical Laboratory Standards Institute protocol. Among 1026 samples collected from 78 neonates, 213 yeast isolates were recovered, of which the Candida species were the most common (77.5%), followed by C. diffluens (16.9%). During the study, 55 isolated yeasts were collected from December 26, 2020, to January 26, 2021, of which 65.5% were C. diffluens, while Candida spp. constituted 100% and 98.3% of the isolates before and after this period, respectively. The most frequent sources of C. diffluens were genital regions (27.8%). Of 36 C. diffluens isolates, 13.9%, 22.2%, 52.8%, and 83.3% were non-wild type to fluconazole, amphotericin B, itraconazole and 5-flucytosine, respectively. We reported for the first time an unusual high prevalence of C. diffluens colonization in neonates hospitalized in NICU. Our findings also showed the high minimum inhibitory concentration of amphotericin B and 5-flucytosine against C. diffluens.

Temporal decreases in pathogen colonization and infection among hospitalized neonates following routine skin antisepsis with chlorhexidine gluconate: Botswana 2022 – 2023

Background: Multidrug-resistant Gram-negative bacteria are a major cause of sepsis among hospitalized neonates globally. Aqueous chlorhexidine gluconate (CHG) skin antisepsis has been shown to be safe for use in infants; however, its sustained effectiveness in preventing Gram-negative pathogen colonization, bloodstream infection (BSI), and mortality is unclear. Methods: We conducted a period prevalence survey, with 26 sampling events over 12 months (18 October 2022 – 31 October 2023) at a 33-bed neonatal unit in a tertiary public hospital in Botswana where ESBL-producing Klebsiella pneumoniae and carbapenem-resistant Acinetobacter baumannii are leading causes of BSI. Perirectal and periumbilical skin swabs were collected every two weeks from all inpatients. Swabs were inoculated onto chromogenic media selective and differential for extended-spectrum beta-lactamase producing Enterobacterales (ESBL-E) and Acinetobacter spp. (CHROMagar™ ESBL, Acinetobacter). Colonization status was determined based on culture growth and colony morphology. Contemporaneous data on all-cause mortality and BSI were abstracted from routine surveillance records. Pre- and post-CHG prevalences were compared using a simple Chi-square test. During the surveillance period, an outbreak of K. pneumoniae linked to contaminated multi-use vials was detected, thus BSIs and deaths during the outbreak period (2 February–6 April, 2023) were excluded. In February 2023, the hospital infection prevention and control (IPC) team introduced twice-weekly whole-body cleansing with commercially available 2% aqueous CHG, performed by caregivers and healthcare workers on neonates &gt;24 hours old and weighing ≥1 kg until discharge. Results: There were significant decreases in ESBL-E and Acinetobacter skin and perirectal colonization following the CHG intervention (Table 1; Figure 1). After the CHG intervention, the incidence of Acinetobacter BSIs declined significantly and there was a trend toward a decline in other BSIs and mortality. No adverse events associated with CHG were reported. Conclusions: Twice-weekly CHG application was temporally associated with significant reductions in neonatal ESBL-E and Actinetobacter skin and perirectal colonization and Acinetobacter BSI. This analysis was limited by a short pre-intervention surveillance period and thus may have been influenced by confounders such as seasonality, and intensified IPC efforts following the outbreak. Analysis of the routine CHG use in other settings and over longer surveillance periods are needed to better understand its effectiveness as an IPC strategy in settings where neonatal sepsis incidence is high. Table 1. Colonization prevalence, BSI incidence, and mortality surrounding introduction of CHG skin cleansing in a neonatal unit, 18 October 2022 – 31 October 2023.

Whole Genome Sequencing for the Identification of a Streptococcus agalactiae Outbreak in Neonatal Intensive Care Unit

Background: While Streptococcus agalactiae (Group B Streptococcus [GBS]) infections in infants usually result from maternal transmission, healthcare-associated cases, particularly in the neonatal intensive care unit (NICU), can occur. Whole genome sequencing (WGS) can aid in investigating GBS outbreaks among infants in hospital settings. The aim of the study is to describe the investigation of GBS infections in NICU using WGS. Methods: Infection prevention and control (IPAC) at our hospital monitors the occurrence of late-onset GBS disease (LOD) in our 57-bed NICU, which consists of all private rooms. The occurrence of 2 cases of LOD within 2 weeks triggered an investigation, including WGS of the two isolates and isolates causing invasive GBS during the last 6 months in the unit. GBS isolates underwent WGS using Illumina at Canada’s National Microbiology Laboratory. All affected patients underwent chart-review. Outbreak description and investigation: In August 2023, two NICU neonates (patients 2,3) experienced LOD two weeks apart, one with bacteremic meningitis and the other with two bacteremic episodes three weeks apart. While WGS was pending two additional cases of late-onset GBS bacteremia (patients 4,5) occurred. Isolates from Pts 2,3 and 5 were indistinguishable from each other and from an isolate from an infant admitted to the NICU with early onset bacteremia on July 27, 2023 (day 1 of life) (patient 1). Weekly point prevalence for throat and rectal colonization over 3 weeks identified five infants colonized with unrelated strains. An additional long-stay infant (patient 6) developed GBS conjunctivitis due to a strain indistinguishable from (patient 4) by pulse field gel electrophoresis, WGS for the second cluster is pending. IPAC interventions: Lapses in IPAC practices were observed, with no commonalities among cases other than similar geographic location within the unit. We hypothesized transmission was due to horizontal transmission between babies due to these lapses. Basic IPAC measures, including hand hygiene and environmental cleaning, were reinforced; Additional Precautions were not used due to private rooms’ unit structure. No environmental samples were taken due to lack of an obvious environmental point or common source. Point prevalence monitoring persisted until no new cases related to the outbreak strains were further identified in three consecutive weekly point prevalence. Conclusions: Increased awareness of healthcare-associated transmission is crucial in NICU as LOD GBS emerges. WGS plays a key role in identifying transmission. Detecting a multi-strain outbreak can appropriately redirect investigations. Legend: Figure 1: Timeline of stay at NICU and infection timing for patients 1-6

Long-term impact of 10-valent pneumococcal conjugate vaccine in Kenya: Nasopharyngeal carriage among children in a rural and an urban site six years after introduction

BackgroundKenya introduced Synflorix™ (GlaxoSmithKline, PCV10-GSK), a 10-valent pneumococcal conjugate vaccine, in 2011, using three primary doses and, in select areas, catch-up campaigns. Surveys conducted 1–2 years post-introduction showed a stable prevalence of pneumococcal colonization, with declines in vaccine-type carriage. However, little is known about the long-term impact of PCV10-GSK in Kenya. MethodsWe conducted a cross-sectional survey of pneumococcal carriage among children aged <5 years in November–December 2017 in Kibera (Nairobi informal settlement, no catch-up) and Asembo (rural western Kenya, 2-dose catch-up for children 1–4 years), using the same methods and settings as prior annual surveys from 2009 to 2013. Participants were randomly selected from an ongoing population-based surveillance platform. Nasopharyngeal swabs were frozen in skim milk-tryptone-glucose-glycerin media within 4 h and underwent culture with broth enrichment for pneumococcus. Isolates were serotyped by polymerase chain reaction and Quellung. ResultsWe enrolled 504 children, including 252 from each site; >90 % of participants had received 3 doses of PCV10-GSK. Pneumococcal colonization was detected in 210 (83.3 %) participants in Kibera and 149 (59.1 %) in Asembo, which was significantly lower than the prevalence observed in 2013 (92.9 % and 85.7 %, respectively). PCV10-GSK serotypes were detected in 35/252 (13.9 %) participants in Kibera and 23/252 (9.1 %) in Asembo, respectively; these prevalences were lower, but not statistically different, from vaccine-type carriage prevalences in 2013 (17.3 % and 13.3 %, respectively). In 2017 in both sites, serotypes 3, 6A, 19A, 19F, and 35B were among the most common serotypes. ConclusionSix years post-PCV10-GSK introduction, the prevalence of pneumococcal carriage among children has decreased, and the impact of PCV10-GSK on vaccine-type carriage has plateaued. Kenya recently changed from PCV10-GSK to Pneumosil™ (Serum Institute of India), a 10-valent PCV that includes serotypes 6A and 19A; these data provide historical context for interpreting changes in vaccine-type carriage following the PCV formulation switch.

MDRO Colonization Among Nursing Homes Patients: A Risk Classification Tool for Early Identification

Background: Nursing homes (NHs) have high prevalence of multi-drug resistant organisms (MDROs) with rates exceeding those in hospitals. This study proposes quantifying patients’ risk of MDRO colonization and creating a risk profile for the NH patient populations to assist in reducing MDRO burden in health care facilities. Methods: We assessed a risk classification model using data from a prospective cohort study (2018 Pathways study). Patient sample included 783 newly admitted patients followed for up to 180 days and 9,587 samples collected from patients during 2,089 visits. Individual risk factors of MDRO colonization were assessed using unadjusted logistic regression, and patients were risk classified based on number of risk factors. Multivariate regression was performed to obtain odds of MDRO colonization for patient risk groups adjusting for patient age, sex, race, and length of NH stay (LOS). The risk classification tool developed using Pathways data was also tested among a sample of NH residents from Veterans Administration (N=190). Results: The patient sample (Pathways data) was 43.2% male, 37.2% Black with a mean age 74 years. 69.3% were colonized with a MDRO during the study. In unadjusted regression, recent antibiotic use (p&lt;.001), open wounds (p&lt;.05), use of urinary catheter or feeding tube (p&lt;.001), functional disability (p&lt;.001), diabetes (p&lt;.01), and preadmission hospital stay over 14 days (p&lt;.001) were associated with colonization, while Charlson comorbidity score, age, sex, and race were not. In adjusted analysis (c-statistic=0.75), a patient’s colonization risk increased with the number of risk factors (Figure 1), with 47.2% expected colonization among patients with none of the risk factors and 86.7% expected colonization among patients with four or more risk factors. The risk classification model had similar performance among male and female patients, and among Black and White patients (Figure 2). Secondary analysis using data obtained from separate, Veterans Administration facilities provided preliminary validation of the risk scoring tool. The model had acceptable fit (c-statistic=0.71). Veterans with four or more risk factors had 87.8% expected probability of MDRO colonization compared with 39.6% colonization among those without any risk factors. Veterans with less than four risk factors also had higher colonization, but these differences were not statistically significant. Conclusions. Despite system-wide efforts to reduce MDRO burden, prevalence of MDRO colonization remains high in NHs. The risk classification tool can assist in early identification of most vulnerable NH patients to direct targeted interventions such as education, enhanced environmental cleaning, and active surveillance.Disclosure: Lona Mody: NIH, VA, CDC, Kahn Foundation; Honoraria: UpToDate; Contracted Research: Nano-Vibronix

Carbapenem-Resistant Enterobacteriaceae Colonization or Infection Was Not Associated with Post-Liver Transplant Graft Failure: An Observational Cohort Study

Introduction: Carbapenem-resistant Enterobacteriaceae (CRE) epidemiology among liver transplant (LT) recipients is variable. We studied the impact of CRE colonization and infection on LT recipients’ outcomes. Methods: This observational cohort study included consecutive adult LT recipients between January 2019 and December 2020 at Curry Cabral Hospital, Lisbon, Portugal. Primary exposures were CRE colonization (rectal swabs under a screening program) and infection within 1 year of index LT. Primary endpoint was graft failure within 1 year of the index LT. Results: Among 209 patients, the median (interquartile range [IQR]) age was 57 (47–64) years and 155 (74.2%) were male. CRE colonization was identified in 28 (13.4%) patients during the first year posttransplant (median [IQR] number of rectal swabs per patient of 4 [2–7]). CRE resistance genes identified were OXA48 in 8 (3.6%) patients, KPC in 19 (67.9%) patients, and VIM in 1 (3.6%) patient. Any bacterial/fungal and CRE infections were diagnosed in 88 (42.1%) and 6 (2.9%) patients, respectively, during the first year posttransplant. After adjusting for confounders, neither CRE colonization (aOR [95% CI] = 1.83 [0.71–4.70]; p = 0.21) nor infection (aOR [95% CI] = 1.35 [0.17–11.06]; p = 0.78) was associated with graft failure within 1 year of index LT. Discussion/Conclusion: Under a screening program, CRE colonization and infection prevalence was low and neither was associated with graft failure.

Modeling the transmission of antibiotic-resistant Enterobacterales in the community: A systematic review

BackgroundAntibiotic-resistant Enterobacterales (ARE) are a public health threat worldwide. Dissemination of these opportunistic pathogens has been largely studied in hospitals. Despite high prevalence of asymptomatic colonization in the community in some regions of the world, less is known about ARE acquisition and spread in this setting. As explaining the community ARE dynamics has not been straightforward, mathematical models can be key to explore underlying phenomena and further evaluate the impact of interventions to curb ARE circulation outside of hospitals. MethodsWe conducted a systematic review of mathematical modeling studies focusing on the transmission of AR-E in the community, excluding models only specific to hospitals. We extracted model features (population, setting), formalism (compartmental, individual-based), biological hypotheses (transmission, infection, antibiotic impact, resistant strain specificities) and main findings. We discussed additional mechanisms to be considered, open scientific questions, and most pressing data needs. ResultsWe identified 18 modeling studies focusing on the human transmission of ARE in the community (n=11) or in both community and hospital (n=7). Models aimed at (i) understanding mechanisms driving resistance dynamics; (ii) identifying and quantifying transmission routes; or (iii) evaluating public health interventions to reduce resistance. To overcome the difficulty of reproducing observed ARE dynamics in the community using the classical two-strains competition model, studies proposed to include mechanisms such as within-host strain competition or a strong host population structure. Studies inferring model parameters from longitudinal carriage data were mostly based on models considering the ARE strain only. They showed differences in ARE carriage duration depending on the acquisition mode: returning travelers have a significantly shorter carriage duration than discharged hospitalized patient or healthy individuals. Interestingly, predictions across models regarding the success of public health interventions to reduce ARE rates depended on pathogens, settings, and antibiotic resistance mechanisms. For E. coli, reducing person-to-person transmission in the community had a stronger effect than reducing antibiotic use in the community. For Klebsiella pneumoniae, reducing antibiotic use in hospitals was more efficient than reducing community use. ConclusionsThis study raises the limited number of modeling studies specifically addressing the transmission of ARE in the community. It highlights the need for model development and community-based data collection especially in low- and middle-income countries to better understand acquisition routes and their relative contribution to observed ARE levels. Such modeling will be critical to correctly design and evaluate public health interventions to control ARE transmission in the community and further reduce the associated infection burden.