Rectal Swabs Research Articles

Comparative evaluation of disease dynamics in wild boar and domestic pigs experimentally inoculated intranasally with the European highly virulent African swine fever virus genotype II strain “Armenia 2007”

Since the reintroduction of African swine fever virus (ASFV) in Europe in 2007 and its subsequent spread to Asia, wild boar has played a crucial role in maintaining and disseminating the virus. There are significant gaps in the knowledge regarding infection dynamics and disease pathogenesis in domestic pigs and wild boar, particularly at the early infection stage. We aimed to compare domestic pigs and wild boar infected intranasally to mimic natural infection with one of the original highly virulent genotype II ASFV isolates (Armenia 2007). The study involved euthanising three domestic pigs and three wild boar on days 1, 2, 3, and 5 post-infection, while four domestic pigs and four wild boar were monitored until they reached a humane endpoint. The parameters assessed included clinical signs, macroscopic lesions, viremia levels, tissue viral load, and virus shedding in nasal and rectal swabs from day 1 post-infection. Compared with domestic pigs, wild boar were more susceptible to ASFV, with a shorter incubation period and earlier onset of clinical signs. While wild boar reached a humane endpoint earlier than domestic pigs did, the macroscopic lesions were comparatively less severe. In addition, wild boar had earlier viremia, and the virus was also detected earlier in tissues. The medial retropharyngeal lymph nodes were identified as key portals for ASFV infection in both subspecies. No viral genome was detected in nasal or rectal swabs until shortly before reaching the humane endpoint in both domestic pigs and wild boar, suggesting limited virus shedding in acute infections.

Detection and Phenotypic Antimicrobial Susceptibility of Salmonella enterica Serotypes in Dairy Cattle Farms in the Po Valley, Northern Italy.

The presence of Salmonella spp. in dairy cattle farms poses a major risk to animal health and welfare. This study focused on Salmonella detection in dairy farms located in the Cremona and Mantua provinces (northern Italy) in samples collected and submitted to laboratories in 2021-2022. A total of 2710 samples from different sources, including calf carcasses/organs (n = 128), rectal swabs (n = 1937), feces (n = 390), bulk milk (n = 93), and overshoes/swabs (n = 127) for environmental sampling, were analyzed for the presence of Salmonella spp. and were included in the present study. Our results indicate that Salmonella was most commonly firstly identified from calf carcasses and organs (61.67%) and that the serotypes most frequently detected in dairies were S. Dublin (38.33%), S. Typhimurium (23.33%), and S. Typhimurium monophasic variant (14.17%). The most common pathological findings in calf carcasses were enteritis, hepatosplenomegaly, and pneumonia. The antimicrobial resistance pattern analyzed using the MIC assay of 51 Salmonella isolates revealed the presence of multi-resistant strains, which pose a major risk to public and animal health.

Characterization of zoonotic hepatitis E virus in domestic pigs and wild boar in Vietnam: Implications for public health

Vietnam's unprecedented demand for meat from livestock, including pigs and farmed wildlife, underscores the importance of understanding zoonotic reservoirs for hepatitis E virus (HEV). This study aimed to identify and characterize circulating zoonotic HEV in domestic pigs and wild boar to understand genotype frequencies, transmission dynamics, and associated human health burdens. Rectal swabs, feces, and liver samples from 415 pigs and 102 wild boars were collected across various farms and slaughterhouses in central and southern Vietnam and screened for HEV RNA using nested PCR. HEV RNA-positive samples underwent sanger sequencing and genotyping. Overall, 10% (n = 54/517) of samples were HEV RNA-positive, with wild boars exhibiting the highest HEV positivity rate at 25%, followed by domestic pigs at 7%. Southern Vietnam showed a higher HEV RNA positivity rate (20%) compared to central Vietnam (7%). Notably, rectal swabs demonstrated the highest positivity rate (15%), followed by feces (8%) and liver (4%). HEV-3a was the predominant genotype at 85%, followed by HEV-4b at 9% and HEV-3f at 6%. While HEV-3a was distributed across both central and southern Vietnam, HEV-3f was exclusively detected in central Vietnam, and HEV-4b was identified in wild boar in southern Vietnam. These findings underscore the substantial prevalence of HEV in wild boars, emphasizing their potential as crucial zoonotic reservoirs alongside domestic pigs. Further investigations involving occupationally exposed individuals in high-prevalence areas are warranted to evaluate the human health impact of zoonotic hepatitis E and inform preventive measures. Regular epidemiological studies are imperative for assessing the prevalence and transmission of zoonotic HEV infections among common reservoirs, thereby aiding in the prevention of spillover events within the community.

High prevalence of SARS-CoV-2 antibodies and low prevalence of SARS-CoV-2 RNA in cats recently exposed to human cases

BackgroundThe primary objective of this cross-sectional study, conducted in Québec and Bristish Columbia (Canada) between February 2021 and January 2022, was to measure the prevalence of viral RNA in oronasal and rectal swabs and serum antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) amongst cats living in households with at least one confirmed human case. Secondary objectives included a description of potential risk factors for the presence of SARS-CoV-2 antibodies and an estimation of the association between the presence of viral RNA in swabs as well as SARS-CoV-2 antibodies and clinical signs. Oronasal and rectal swabs and sera were collected from 55 cats from 40 households at most 15 days after a human case confirmation, and at up to two follow-up visits. A RT-qPCR assay and an ELISA were used to detect SARS-CoV-2 RNA in swabs and serum SARS-CoV-2 IgG antibodies, respectively. Prevalence and 95% Bayesian credibility intervals (BCI) were calculated, and associations were evaluated using prevalence ratio and 95% BCI obtained from Bayesian mixed log-binomial models.ResultsNine (0.16; 95% BCI = 0.08–0.28) and 38 (0.69; 95% BCI = 0.56–0.80) cats had at least one positive RT-qPCR and at least one positive serological test result, respectively. No risk factor was associated with the prevalence of SARS-CoV-2 serum antibodies. The prevalence of clinical signs suggestive of COVID-19 in cats, mainly sneezing, was 2.12 (95% BCI = 1.03–3.98) times higher amongst cats with detectable viral RNA compared to those without.ConclusionsWe showed that cats develop antibodies to SARS-CoV-2 when exposed to recent human cases, but detection of viral RNA on swabs is rare, even when sampling occurs soon after confirmation of a human case. Moreover, cats with detectable levels of virus showed clinical signs more often than cats without signs, which can be useful for the management of such cases.

Mycoplasma genitalium's Antibiotic Resistance in Sexually Transmitted Infections Clinics in Israel.

To determine the prevalence of antibiotic resistance rate in Mycoplasma genitalium, and distribution of mutations associated with this resistance, among patients that attended sexually transmitted infections (STI) investigation clinics. This cross-sectional study included M. genitalium-positive samples (urine, vaginal, rectal, and pharyngeal swabs) collected from 170 patients attending two STI investigation clinics, which were subjected to macrolide and quinolone resistance mutations analyses. Data regarding patient age, sex, and material/anatomical site of testing were collected. Macrolide-resistance mutations were identified in 48.8% of samples and were more common among males (p < .0001) and in rectal samples (p < .05). A2059C was the most prevalent macrolide-resistance mutation (18.2%). Quinolone resistance was detected in 23% of the samples, with S83I being the most common (17.1%) mutation. Rate of co-resistance to macrolides and quinolones was 21.2%. The high rate of antibiotic resistance found in the current study, especially to macrolides, underscores the importance of antibiotic resistance monitoring in M. genitalium isolates in cases of persistent or recurrent urethritis/cervicitis, in cases of treatment failure and among specific populations. Such surveillance will improve treatment regimens and cure rates.

Vaginal and rectal microbiome contribute to genital inflammation in chronic pelvic pain

BackgroundChronic pelvic pain (CPP) is a multifactorial syndrome that can substantially affect a patient’s quality of life. Endometriosis is one cause of CPP, and alterations of the immune and microbiome profiles have been observed in patients with endometriosis. The objective of this pilot study was to investigate differences in the vaginal and gastrointestinal microbiomes and cervicovaginal immune microenvironment in patients with CPP and endometriosis diagnosis compared to those with CPP without endometriosis and no CPP.MethodsVaginal swabs, rectal swabs, and cervicovaginal lavages (CVL) were collected among individuals undergoing gynecologic laparoscopy. Participants were grouped based on patients seeking care for chronic pain and/or pathology results: CPP and endometriosis (CPP-Endo) (n = 35), CPP without endometriosis (n = 23), or patients without CPP or endometriosis (controls) (n = 15). Sensitivity analyses were performed on CPP with endometriosis location, stage, and co-occurring gynecologic conditions (abnormal uterine bleeding, fibroids). 16S rRNA sequencing was performed to profile the microbiome, and a panel of soluble immune mediators was quantified using a multiplex assay. Statistical analysis was conducted with SAS, R, MicrobiomeAnalyst, MetaboAnalyst, and QIIME 2.ResultsSignificant differences were observed between participants with CPP alone, CPP-Endo, and surgical controls for body mass index, ethnicity, diagnosis of ovarian cysts, and diagnosis of fibroids. In rectal microbiome analysis, both CPP alone and CPP-Endo exhibited lower alpha diversity than controls, and both CPP groups revealed enrichment of irritable bowel syndrome-associated bacteria. CPP-Endo exhibited an increased abundance of vaginal Streptococcus anginosus and rectal Ruminococcus. Patients with CPP and endometrioma (s) demonstrated increased vaginal Streptococcus, Lactobacillus, and Prevotella compared to other endometriosis sites. Further, abnormal uterine bleeding was associated with an increased abundance of bacterial vaginosis-associated bacteria. Immunoproteomic profiles were distinctly clustered by CPP alone and CPP-Endo compared to controls. CPP-Endo was enriched in TNF⍺, MDC, and IL-1⍺.ConclusionsVaginal and rectal microbiomes were observed to differ between patients with CPP alone and CPP with endometriosis, which may be useful in personalized treatment for individuals with CPP and endometriosis from those with other causes of CPP. Further investigation is warranted in patients with additional co-occurring conditions, such as AUB/fibroids, which add additional complexity to these conditions and reveal the enrichment of distinct pathogenic bacteria in both mucosal sites. This study provides foundational microbiome-immunoproteomic knowledge related to chronic pelvic pain, endometriosis, and co-occurring gynecologic conditions that can help improve the treatment of patients seeking care for pain.

Gut colonization by extended-spectrum β-lactamase-producing Escherichia coli in dairy herd in Brazil: successful dissemination of a One Health clone.

The overuse of antimicrobials in livestock has contributed to the emergence and selection of clinically relevant multidrug-resistant bacteria. In Brazil, there is no conclusive information on the occurrence of Escherichia coli producing extended-spectrum β-lactamase (ESβL) in cattle breeding, which is an important sector of agribusiness in this country. Herein, we investigated the presence of ESβL-positive E. coli strains in dairy cattle from a commercial farm with routine practice of therapeutic cephalosporins. Ninety-five rectal swab samples were collected from healthy dairy calves and cows under treatment with ceftiofur. Samples were screened for the presence of ESβL producers, and positive isolates were identified by MALDI-TOF, with subsequent screening for genes encoding ESβL variants by PCR and sequencing. The presence of ESβL (CTX-M-15)-producing E. coli was confirmed in calves, and lactating and dry cows. Most ESβL strains with genetic homologies ≥ 90% were grouped into two major PFGE clusters, confirming the suscessful expansion of clonally related lineages in animals from different lactating cycles, on the same property. Four representatives CTX-M-15-positive E. coli strains had their genomes sequenced, belonging to the clonal complex (CC) 23 and sequence type (ST) 90. A phylogeographical landscape of ST90 was performed revealing a global One Health linkage. Our results highlight the intestinal microbiota of dairy cattle as a hotspot for the spread of critical priority ESβL-producing E. coli and demonstrate that ST90 is an international clone genomically adapted to human and animal hosts, which deserve additional investigation to determine its zoonotic potential and impact in food chain.

Investigation of an Acute Gastrointestinal Illness Outbreak Linked to Drinking Water in a Higher Educational Institute in East Sikkim, India.

Introduction An acute gastrointestinal illness outbreak was reported in a higher educational institution among students and faculties in East Sikkim, India, from January to February 2023. The investigation was conducted to identify the source of the infection and causative pathogens and prevent the spread of the outbreak. Methods We defined a case as three or more loose stools in 24 hours, abdominal pain, or vomiting with the onset of symptoms between January 16 and February 16, 2023. Active surveillance was conducted by reviewing the affected individuals at the campus and patient registers at the dispensary, where cases were treated. Stool samples, rectal swabs, water samples, and suspected food samples were collected for microbiological testing using conventional culture, multiplex polymerase chain reaction (PCR), and kit-based real-time PCR methods. Results Out of 1,850 residents, 106 (5.7%) were affected by gastrointestinal symptoms like diarrhea, vomiting, etc. The attack rate for females was 23 (1.24%) and for males was 83 (4.49%). The most affected individual median age was 21 years (range: 2-51 years). From the laboratory investigations, most of the cases demonstrated polymicrobial etiologies. Gastroenteritis pathogens like Campylobacter, astrovirus, androtavirusdiarrheagenic Escherichia coli (DEC) (EAEC, EIEC, ETEC, EPEC, and EAEC), Shigella,etc., were detected in the suspected samples. The environmental investigation indicated the presence of rusted and leaky water pipes and sewage pipelines, along with ineffective chlorination of the water plant. Conclusions Based on epidemiological and laboratory investigations, it is conjectured that sewage and fecal contamination of drinking water and poor maintenance of the water distribution system most likely caused the outbreak described in this study. Basic treatment modalities, adequate chlorination, and periodic inspection of the water system were suggested, which controlled the outbreak to a greater extent.

Genome analysis of multidrug resistant Enterococcus faecium and Enterococcus faecalis circulating among hospitalized patients in uMgungundlovu District, KwaZulu-Natal, South Africa

BackgroundVancomycin-resistant enterococci (VRE) are important pathogens categorized as high-priority bacteria in the Global Priority List of Antibiotic-Resistant Bacteria to Guide Research, Discovery, and Development of New Antibiotics published by the World Health Organization. The aim of this study was to determine the risk factors, resistance, virulence, mobilomes associated with multidrug-resistant and clonal lineages of Enterococcus faecium and faecalis circulating among hospitalized patients following the health system in South Africa, using whole genome sequencing (WGS).MethodsA cross-sectional study was conducted during a two-month periods among hospitalized patients in 2017. Rectal swabs were collected from patients admitted to medical and surgical wards in an urban tertiary hospital, and a rural district hospital in uMgungundlovu district, South Africa. Enterococci were screened for vancomycin resistance on bile esculin azide agar supplemented with 6 mg/L of vancomycin and confirmation of VRE was done using ROSCO kits. Conventional and real-time PCR methods were used to ascertain the presence of VanA, VanB, VanC-2/3 and VanC-1 genes. All six multidrug-resistant Enterococcus faecalis and faecium selected were identified using multiplexed paired-end libraries (2 × 300 bp) with the Nextera XT DNA sample preparation kit (Illumina, San Diego, CA, USA) and genome sequencing was done using Illumina MiSeq instrument with 100× coverage at the National Institute of Communicable Diseases Sequencing Core Facility, South Africa. Antibiotic resistance genes, virulence factors, plasmids, integrons and CRISPR were characterized using RAST, ResFinder, VirulenceFinder, PlasmidFinder, PHAST and ISFinder respectively.ResultsSequencing analysis revealed that these strains harbouring numerous resistance genes to glycopeptides (vanC[100%], vex3[100%], vex2[83,33%] and vanG[16,66%]), macrolides, lincosamides, sterptogramine B (ermB[33,32%], Isa[16,66%], emeA[16,66%]) and tetracyclines (tetM[33,32%]) in both district and tertiary hospitals. Multidrug efflux pumps including MATE, MFS and pmrA conferring resistance to several classes of antibiotics were also identified. The main transposable elements observed were in the Tn3 family, specifically Tn1546. Four single sequence types (STs) were identified among E. faecium in the district hospital, namely ST822, ST636, ST97 along with a novel ST assigned ST1386, while one lineage, ST29 was detected in the tertiary hospital.ConclusionThe study reveals the genetic diversity and high pathogenicity of multidrug-resistant Enterococcus faecalis and faecium circulating among hospitalized patients. It underlines the necessity to implement routine screening of admitted patients coupled with infection control procedures, antimicrobial stewardship and awareness should be strengthened to prevent and/or contain the carriage and spread of multidrug resistant E. faecium and E. faecalis in hospitals and communities in South Africa.

Prevalence of GIT Symptoms in Patients of Covid 19

Abstract Background In December 2019, a cluster of patients with pneumonia of undetermined etiology was recognized in Wuhan, Hubei, China. Subsequently, a novel coronavirus (SARS-CoV-2) was identified from lower respiratory tract samples obtained from affected patients. The clinical manifestation of COVID-19 is broad and ranges from asymptomatic and mild upper respiratory tract symptoms to severe illnesses with multiorgan failure and death. Furthermore, it is challenging to predict the clinical course or determine patients at risk of deterioration. Aim of the Work The aim of our study was to assess prevalence of GIT symptoms in patients of covid 19 infected patients Patients and Methods This study was conducted on 100 adult covid 19 patients recently diagnosed by polymerase chain reaction (PCR). All patients were submitted to clinical examination, laboratory testing for ESR, CRP, CBC, and D-dimer. Radiological investigations in the form of CT Chest were be reported by radiologist for all patients. High resolution computed tomography Parenchymal abnormalities on HRCT were assessed. Nasopharyngeal, oropharyngeal and rectal swabs were collected for COVID-19 (PCR) test. All patients received Covid-19 treatment according to protocols of WHO and ministry of health and population, Egypt. Results We found that GI symptoms are prevalent among COVID-19 Egyptian patients (64%). The most common GI symptoms were Nausea, vomiting and diarrhea. We observed that 25 patients (25%) had positive viral RNA in rectal swab. Conclusion Severe COVID-19 was more frequent in older age. Dyspnea and increased respiratory rate were associated with severity of covid 19 infection. Increased CRP and high serum levels of ferritin, d-dimer and lactate dehydrogenase were significantly associated with COVID-19 severity.

Risk factors and molecular epidemiology of intestinal colonization by carbapenem-resistant Gram-negative bacteria in patients with hematological diseases: a multicenter case‒control study.

Patients with hematological diseases are considered to be at high risk for intestinal colonization by carbapenem-resistant Gram-negative bacteria (CR-GNB). However, the epidemiological data regarding risk factors and molecular characteristics of intestinal colonized CR-GNB isolates in this population are insufficient in China. A multicenter case‒control study involving 4,641 adult patients with hematological diseases from 92 hospitals across China was conducted. Following culture of collected rectal swabs, mass spectrometry and antimicrobial susceptibility tests were performed to identify GNB species and CR phenotype. Risk factors were assessed through retrospective clinical information. Whole-genome sequencing was used to analyze the molecular characteristics of CR-GNB isolates. This trial is registered with ClinicalTrials.gov as NCT05002582. Our results demonstrated that among 4,641 adult patients, 10.8% had intestinal colonization by CR-GNB. Of these, 8.1% were colonized by carbapenem-resistant Enterobacterales (CRE), 2.6% were colonized by carbapenem-resistant Pseudomonas aeruginosa (CRPA), and 0.3% were colonized by carbapenem-resistant Acinetobacter baumannii (CRAB). The risk factors for CR-GNB colonization include male gender, acute leukemia, hematopoietic stem cell transplantation, β-lactam antibiotic usage, and the presence of non-perianal infections within 1 week. Compared with CRPA-colonized patients, patients using carbapenems were more likely to be colonized with CRE. NDM was the predominant carbapenemase in colonized CRE. This study revealed a high CR-GNB intestinal colonization rate among adult patients with hematological diseases in China, with CRE being the predominant one. Notably, a significant proportion of CRE exhibited metallo-β-lactamase production, indicating a concerning trend. These findings emphasize the importance of active screening for CR-GNB colonization in patients with hematological diseases.IMPORTANCECarbapenem-resistant Gram-negative bacteria (CR-GNB) has emerged as a significant threat to public health. Patients with hematological diseases are at high risk of CR-GNB infections due to their immunosuppressed state. CR-GNB colonization is an independent risk factor for subsequent infection. Understanding the risk factors and molecular characteristics of CR-GNB associated with intestinal colonization in patients with hematological diseases is crucial for empirical treatment, particularly in patients with febrile neutropenia. However, the epidemiology data are still insufficient, and our study aims to determine the intestinal colonization rate of CR-GNB, identify colonization risk factors, and analyze the molecular characteristics of colonized CR-GNB isolates.

Containment of a KPC-CRE Outbreak Associated with Premise Plumbing in a Long-Term Care Facility— Minnesota, 2022-2023

Background: On March 23, 2022, the Minnesota Department of Health (MDH) was notified of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella oxytoca isolated from a resident’s urine in long-term care facility A (LTCF-A). Carbapenem-resistant Enterobacterales (CRE) are reportable statewide with required isolate submission to MDH Public Health Laboratory (MDH-PHL), where carbapenemase production and mechanism identification is confirmed. Methods: MDH partnered with LTCF-A on a containment response, including infection prevention and control (IPC) measures, KPC-CRE education, and colonization screening. Rectal swabs were screened for carbapenemase genes by real-time PCR (Cepheid Xpert Carba-R), with positive specimens undergoing culture, isolation, and whole genome sequencing (WGS). MDH-PHL conducted WGS including multilocus sequence typing (MLST) and single nucleotide polymorphism (SNP) analysis to describe genetic relationships among isolates. When screening indicated a potential environmental source, due to species diversity and ongoing resident transmission, an environmental screening plan was developed including collection of premise plumbing samples from room faucets, aerators, sinks, toilets, and shared shower drains. Results: KPC-CRE was detected in 23 residents (urine, n=2; rectal swab, n=21) during March 2022–November 2023. 21 isolates comprising 10 Enterobacterales species were cultured from KPC-positive screening specimens. SNP analysis performed on bacteria of the same species demonstrated 5 distinct clusters of relatedness comprising 2-3 residents per cluster (Cluster 1: Klebsiella oxytoca, n=3; Cluster 2: Klebsiella oxytoca, n=3; Cluster 3: Escherichia coli, n=2; Cluster 4: Klebsiella pneumoniae, n=2; Cluster 5: Raoultella planticola, n=2). 7 KPC-positive resident specimens did not yield a culturable organism. KPC-CRE was detected throughout the premise plumbing including 8 of 9 shared shower room drains and 6 of 75 resident room sink drains. WGS and SNP analysis suggest relatedness among resident and environmental KPC-CRE isolates. Gaps in IPC measures including hand hygiene, use of personal protective equipment (PPE), environmental cleaning and disinfection, and sink hygiene practices were observed during onsite assessments. Use of an EPA-registered biofilm disinfectant in facility drains and repeated environmental sampling has demonstrated a decrease in KPC-harboring bacteria within the premise plumbing, but not complete elimination. Conclusion: Containing the spread of KPC-CRE within LTCF-A has been challenging due to environmental reservoirs of KPC-CRE along with insufficient implementation of IPC practices. Continued colonization screening has been necessary to detect newly colonized residents and reinforce efforts to increase IPC compliance. Strict implementation and adherence to IPC measures, including those that minimize the spread of KPC-CRE from facility premise plumbing, are needed to fully halt KPC-CRE transmission within LTCF-A.

Epidemiology of Extrapulmonary Nontuberculous Mycobacterial Disease – 4 Emerging Infection Program Sites, 2021

Background: Extrapulmonary nontuberculous mycobacteria (ENTM) infections are difficult to treat and often require prolonged therapy or surgery. Few population-based studies describe ENTM epidemiology, though well-known healthcare-associated outbreaks have occurred. Using the first year of multi-site ENTM surveillance, we characterized rates and how frequently ENTM infections may be related to healthcare. Methods: CDC’s Emerging Infections Program conducted active, laboratory- and population-based surveillance for ENTM cases in 4 sites (Colorado [5 counties], Minnesota [statewide], New York [1 county], and Oregon [statewide]) in 2021. An incident ENTM case was NTM isolation from a non-pulmonary specimen, excluding stool or rectal swabs, in a resident of the surveillance area without either medical record documentation of prior ENTM infection or isolation of ENTM in the prior 12 months. Demographic, clinical, information on selected healthcare and community exposures, and laboratory data were collected via medical record review. We calculated incidence per 100,000 population using U.S. Census population estimates and performed descriptive analyses. Results: A total of 180 incident ENTM cases were reported in 2021. The crude annual incidence rate was 1.3 per 100,000 persons. Incidence increased with age (from 0.95 per 100,000 among 0–17 year-olds to 2.65 per 100,000 among persons ≥65), ranged from 0.8 among non-Hispanic Asian persons to 1.6 per 100,000 in non-Hispanic Black persons, and was similar among males (1.3 per 100,000) and females (1.4 per 100,000; Figure 1). Mycobacterium avium complex (64 [35.6%]) was the most frequently isolated species group, followed by Mycobacterium chelonae complex (31 [17.2%]). Skin and soft tissue infections were the most frequent infection type (37 [20.6%]); 27 cases (15.0%) were associated with disseminated and/or only bloodstream infection, and 56 cases (31.1%) had no infection type documented. Among 93 cases with localized ENTM infections (i.e., infections that were not disseminated and/or only bloodstream infections), 38.7% had only healthcare-related exposures, 14% had only community-related exposures and 6.5% had both exposure types at the site of infection (Figure 2). Healthcare-related exposures at the infection site included surgery (23.7%), injection/infusion (21.5%), and medical devices (18.3%). The most frequent community-related exposure at the infection site was trauma (17.2%). Only one case was part of a known outbreak, which was healthcare-associated. Conclusions: ENTM infections are relatively rare, but nearly half of patients with localized ENTM infections had prior healthcare-related exposures. This indicates that the burden of ENTM infections related to healthcare may be much larger than what has been suggested from reported outbreaks.

Serratia marcescens Burden in a Neonatal Intensive Care Unit: Colonization Rate, Clinical Infections and Strain Relatedness

Background: Serratia marcescens (S. marcescens) is an environmentally associated organism known for causing healthcare associated infections and outbreaks in neonatal intensive care units (NICUs). The colonization or infection rates in NICU settings remain uncertain. This study aims to evaluate the rate of baseline colonization and clinical infection and relatedness of S. marcescens isolates. Methods: Prospective surveillance of rectal colonization and clinical infection of S. marcescens was conducted on patients admitted to the NICU at Mount Sinai Hospital in Toronto, Ontario, from March 1, 2023, to September 30, 2023. The NICU is a 57 bed unit with all private rooms. Monthly point prevalence assessments by rectal screening were performed, alongside active surveillance for clinical infections associated with S. marcesens. Isolates from screening or clinical samples underwent assessment for relatedness using pulse field gel electrophoresis (PFGE). Results: Over the 7 month study period, 12 different patients (5.4%) were colonized/infected with S. marcescens. Among these, 10 patients (4.5%) were identified through rectal screening (316 rectal swabs were collected from 224 patients) and two patients (0.9%) exhibited positive clinical specimens (urine and endotracheal aspirate) in association with pyelonephritis and ventilator-associated pneumonia, respectively. Of the two clinical cases, one case showed a negative preceding rectal swab and the other detected through a clinical sample before the point prevalence date. The age at which a positive S. marcescens swab or positive clinical specimen was identified ranged from 4 to 66 days (median=18 days, IQR 5-38.8) (Figure 1). Sixty seven infants had repeated screening. Three out of 67 (4.5%) were colonized with S. marcescens, the timing and sequence of positive and negative testing are presented in Figure 2. Females demonstrated a higher positivity rate compared to males [9.1% (9/99) vs 2.4% (3/125), p=0.04, respectively]. PFGE analysis of all 12 (100%) isolates revealed a polyclonal pattern. Most cases were detected from March to May in 9/12 cases (75%). Ten different strains were identified. Notably, two strains demonstrated clusters of two cases each, one during March and the other during May (Figure 3). No mortality was reported among the cases. Conclusions: The study highlights the polyclonal nature of S. marcesens and raises questions about the utility of point prevalence in anticipating clinical cases or patient-to-patient transmission, especially in patients with clinical infection where there were no preceding positive screening tests.

Isolamento e sensibilidade antimicrobiana de Staphylococcus sp. e Escherichia coli de peixe-boi-da-amazônia (Trichechus inunguis) em cativeiro

ABSTRACT: The Amazonian manatee (Trichechusinunguis) is an aquatic mammal threatened with extinction. However, few studies have investigated the pathogens in this species, which may affect both animal and human health. This study aimed to evaluate the frequency, distribution, and patterns of antimicrobial susceptibility of Staphylococcus spp. and Escherichiacoli colonizing the nasal and rectal cavities of Amazonian manatees kept in captivity at the National Institute for Amazonian Research (INPA) in the state of Amazonas, Brazil. Rectal and nasal swabs from 44 manatees of different ages were used in this study. The genus Staphylococcus was isolated from the nasal swabs of 32 (72.7%) animals, with two individuals harboring more than one species of Staphylococcus. S. sciuri was the most commonly isolated species. Resistance to penicillin was observed in 13 (40.6%) isolates, more frequent than the other antimicrobials tested (P = 0.01). E. coli was isolated from the rectal swabs of all animals, with phylogroup B1 being the most frequent among the strains obtained (P = 0.0008). Four isolates (6.8%) were positive for virulence factors, three of which were classified as enterotoxigenicE. coli (ETEC) and one as enteropathogenicE. coli (EPEC). To our knowledge, this is the first study to evaluate Staphylococcus spp. and E. coli in Amazonian manatee samples. This study revealed nasal colonization by Staphylococcus spp., mainly S. sciuri, and diarrheagenicE. coli isolates, including antimicrobial-resistant strains.

Investigation of a Donor-derived Carbapenamase-producing Carbapenem-resistant Enterobacterales Hospital Outbreak

Carbapenamase-producing carbapenem-resistant Enterobacterales (CP-CRE) is an urgent public health threat for healthcare facilities. Solid organ transplant (SOT) recipients carry an increased risk for CRE infection and colonization due to prolonged exposures to antimicrobials, healthcare facilities and immunosuppression. CRE infection in SOT patients is associated with an increase in morbidity and mortality. Here, we describe a hospital outbreak investigation of three cases of New Delhi metallo-beta-lactamase (NDM) - CRE that led to novel findings with implications for further interdisciplinary investigations. An NDM-CRE infection in a critically-ill patient was identified during passive surveillance and prompted an investigation. Previous CP-CRE passive surveillance cases were reviewed. Rectal screening was performed for potentially exposed patients. 403 rectal swabs were tested for carbapenemase genes in active surveillance. Patients identified to have a new NDM-CRE isolate on active or passive surveillance were considered cases and underwent in-depth chart review including possible patient-to-patient exposures, hospital locations, procedures, devices, and consultations. NDM-CRE isolates were sent to the Minnesota Department of Health (MDH) for whole genome sequencing (WGS) to assess relatedness. Five NDM-CRE cases were identified, with all isolates harboring blaNDM including three NDM-Klebsiella pneumoniae (NDM-KP) cases (Figure 1). The first NDM-KP case, patient 1, developed mediastinal infection following lung transplantation. Review of United Network for Organ Sharing revealed that respiratory specimens from patient 1’s donor grew NDM-KP and a bronchial wash at the time of transplant yielded NDM-KP. The second NDM-KP case (patient 3) developed ventilator-associated pneumonia and was found to have used sequentially the same ventilator as patient 1. The third NDM-KP case (patient 4) was detected via rectal swab in active surveillance and shared wound care personnel in common with patients 1 and 3 (Figure 2). WGS demonstrated two single nucleotide polymorphisms (SNP) among all three isolates, strongly suggesting relatedness (Figure 3). Best practices for infection prevention were reviewed with wound care personnel. To date, no further NDM-KP isolates have been identified. Investigation was facilitated by in-depth chart review and WGS via the Central Region Antimicrobial Resistance Laboratory Network at MDH. Detection of the NDM-KP from a lung donor specimen appears genetically linked to clinical isolates in other patients, raising the possibility of a donor-derived hospital outbreak. This investigation is the first to describe a donor-derived NDM outbreak in a healthcare facility. Communication between organ procurement agencies, transplant centers, and infection prevention must be optimized to prevent CRE-associated morbidity in SOT receipts and CRE hospital outbreaks.

Rapid Genomic Characterization of High-Risk, Antibiotic Resistant Pathogens Using Long-Read Sequencing to Identify Nosocomial

Background: Current epidemiological methods have limitations in identifying transmission of bacteria causing healthcare-associated infections (HAIs). Recent whole genome sequencing (WGS) studies found that genetically related strains can cause HAIs without meeting standard epidemiologic definitions, but these results could not provide data in a timely fashion needed for intervention. Given recent advances in Oxford Nanopore Technologies (ONT) sequencing, we sought to establish a validated ONT pipeline capable of providing accurate WGS-based comparisons of clinical pathogens within a short time frame that would allow for infection control interventions. Method: Using electronic medical record data, we identified potential healthcare acquisition of methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and carbapenem-resistant gram-negative rods. Bacterial genomic DNA was directly extracted from clinical microbiology lab plates. Sequencing was conducted with the ONT MinION sequencer and R10.4.1 flow cell. MINTyper for single nucleotide polymorphism (SNP) calling and Ridom SeqSphere+ for core genome MLST were used to determine genetic relatedness. The main outcome was time from pathogen identification to completed genetic analysis. Result: The weekly workflow, from genomic DNA extraction to complete data analysis, averaged 2.6 days with a standard deviation of 1.3 days. (range: 1 to 6 days). Starting in August 2023, we have sequenced a total of 177 bacterial isolates from 156 unique patients. Isolates came from blood (38%), tissue/wound/body fluid (24%), urinary tract (20%), respiratory tract (16%), and rectal swab (2%). To date, six genetically related clusters have been identified. Three clusters involved ST117 vancomycin-resistant Enterococcus faecium (VREfm), comprising a total of 13 unique patients distributed as 2, 3, and 8 patients in each group, with pairwise SNP differences of 20, 11, and 14. Patients within the same clusters showed epidemiological links through overlapping admissions and temporally shared ICU stays. Additionally, another cluster consisted of five genetically related ST633 Pseudomonas aeruginosa isolates, with a pairwise SNP difference of 57.5. Each patient in this cluster had potential epidemiological links through overlapping admission times, despite the absence of identified shared spaces. The last two clusters involved Klebsiella pneumoniae and Escherichia coli (two cases each), with pairwise SNP differences of 18 and 9, respectively. In both cases, each patient showed potential epidemiological links through overlapping admission times. Conclusion: Our stand-alone ONT pipeline was able to rapidly and accurately detect genetically related AMR pathogens, aligning closely with epidemiological data. Our approach has the potential to assist in the efficient detection and deployment of preventative measures against healthcare-associated infection transmission.

Longitudinal Follow Up of Patients Colonized with Clostridioides difficile: a Retrospective Cohort Study

Background: Patients colonized with Clostridioides difficile are at risk of transmitting C. difficile to other patients, and of developing C. difficile infection (CDI). Known risk factors for carriage include previous hospitalization, gastric acid suppression and previous CDI. Data regarding duration of carriage and its predictors are lacking but could be useful to better understand the natural evolution of carriage and better estimate the likelihood of transmission or progression to CDI. Methods: We performed a retrospective cohort study of C. difficile colonized patients with &gt; = 1 admission to a tertiary academic institution between November 2013 and January 2017. Colonization status was determined upon hospital admission by detection of TcdB gene by polymerase chain reaction on a rectal screening swab, as part of a systematic screening program. Overall duration of carriage and predictors of prolonged carriage were explored using Kaplan-Meier methods and Cox regression. Results: There were 134 patients, who after having a positive initial screening test (and therefore identified as colonized with C. difficile), had subsequent testing. The median age was 77 years (IQR, 66 to 85), and 53.6% of the patients were female. After hospital discharge, 26 (19.4%) colonized patients progressed to CDI. Mean duration of follow up was 269 days, with a median of 179 days. Median duration of carriage was 211 days, (95% confidence interval (CI) [157, 264]). Predictors associated with decreased duration of C. difficile colonization included younger age (HR per unit decrease (year), 1.013; 95% CI, 1.025 to 1.001; p=0.03), and receipt of antibiotics in the 3 months prior to first admission (mean days to clearance of patients with and without recent antibiotic use, 252 days vs 372 days, respectively; HR, 1.55; 95% CI, 1.01 to 2.36; p &lt; 0 .04). By contrast, the presence of comorbidities (e.g. heart failure, diabetes, cancer, and chronic kidney disease), the use of proton-pump inhibitors (PPIs), the receipt of antibiotics during the first admission, and the duration of first hospitalization were not associated with significant differences in duration of carriage. Conclusion: This study is the largest cohort of C. difficile carriers with longitudinal follow up of their colonization status. It highlights the extended duration of carrier status especially in older patients and identifies predictors of prolonged carriage. Further studies are needed to understand the underlying relationship with the predictors identified in this study.

Carbapenem Versus Non-carbapenem Therapy in Hematology Patients: Extended-Spectrum Beta-Lactamase Positive Enterobacteriaceae Colonization Impact.

Extended-spectrum beta-lactamase-producing Enterobacteriacea (ESBL-E) infections are a major source of mortality and morbidity in patients with hematologic cancers. One of the most significant risk factors for bacterial illness is prior colonization with resistant germs. Empiric usage of carbapenems is recommended for the treatment of infections in patients with a positive colonization history. We aimed to determine the outcome of empirical carbapenem (de-escalation) versus non-carbapenem (escalation) therapy in adult hematology patients who have rectal extended-spectrum beta-lactamase positive ESBL-Ecolonization. Two hundred three rectal swab cultures were collected from 130 patients, admission or during hospitalization between June 2014andMay 2015. Patients were followed till January 2016 for future infections due to ESBL-E. Empirical antibiotic treatment was started according to the patient's medical condition without consideration of previous colonization status. Stable patients received empirical escalation therapy. All-cause and early mortality of infections are analyzed. Seventy-three (36%) swabs were positive for ESBL-E. Patients with rectal ESBL-E colonization were defined as cases; patients without colonization were defined as controls. Prospective infection due to ESBL-E in the case and control group was 6.8% and 2.3%, respectively. No statistically significant relation was found between colonization and prospective infection due to ESBL-E (p=0.110). There was no all-cause or early mortality in prospective infections with ESBL-E.Among case patients, one patient each died from all-cause mortality in the escalation (n=55) and de-escalation (n=3) group.The all-cause mortality in the antibiotic switch group (n=30) was eight, including five patients in the early mortality group although the bacteriologic agents were susceptible to the given antibiotics. In our institution, rectal colonization with ESBL-E was high, but contracting an infection due to ESBL-E was surprisingly low. Colonization with ESBL-E may not necessarily end with an infection in some situations. In stable patients, disregarding colonization features before empirical therapy did not seem to be inappropriate.

Impact of Transitioning to Single-Patient Rooms on Prevention of Multidrug-Resistant Organisms in a Resource-Limited Facility

Background: Healthcare-associated infections (HAI) substantially increase hospital costs and lead to poor patient outcomes, particularly when caused by multidrug-resistant organisms (MDRO). To decrease MDRO transmission, isolation of colonized or infected patients in single rooms is recommended. However, single-patient isolation rooms are expensive to build and often unavailable in resource-limited hospitals. In 2023, an intensive care unit (ICU) at a large Brazilian tertiary hospital relocated from a space with an open floor plan to a newly built location with single-patient rooms. We evaluated the impact of this transition on acquisition of carbapenem-resistant Enterobacterales (CRE) colonization, HAI, and compliance with Hand Hygiene (HH) and Contact Precaution (CP) activities. Methods: We compared rates of CRE colonization acquisition, CRE colonization pressure, HAI, and compliance with HH and CP between pre- (March 1, 2022 – Feb 28, 2023) and post-implementation of single-rooms (March 1, 2023 - October 31, 2023) in a 12-bed surgical ICU. All patients were screened for CRE colonization on admission to the unit and weekly until discharge using rectal swab cultures. Colonization pressure was defined as the ratio of CRE-positive patient-days (PDs) to the total number of PDs. Rates of central-line associated blood-stream infections, ventilator-associated pneumonia, and catheter-associated urinary tract infections were monitored. HH and CP compliance were monitored weekly by infection prevention staff outside of the unit. Poisson regression and multiple linear regression were used to compare rates between pre- and post-implementation periods. Results: Healthcare acquisition of CRE colonization remainedstable between pre- and post-implementation (incidence rate ratio: 0.88 (95%CI, 0.73-1.05; P=0.16) despite an increase in CRE colonization pressure of 8.6% over baseline (from 7.84% pre- to 16.39% post-implementation (95% confidence interval [CI], 4.13-12.96%; P=.001)). The latter was driven by reduced turnover of CRE-colonized patients in the post-implementation period (mean patient-day reduced by 10.33; 95%CI, 3.06-17.61; P=0.006). Incidence of HAIs also remained stable (global incidence 3.12 vs 3.30, pre- and post-intervention, respectively; P=0.2). HH compliance was high prior to the transition (95.7%) and increased slightly but not significantly post-intervention (97.5%; P=0.3). CP compliance improved by 9.83%, especially in gown and glove changes after each patient interaction, from 90.62% pre- to 100% post-implementation (95%CI, 1.52-17.22; P=.02). Conclusion The move to an ICU with exclusively single-patient rooms was associated with increase in CP compliance. This could help explain why HAI incidence and healthcare acquisition of CRE colonization remained stable despite a significant increase in CRE colonization pressure.Disclosure: Matias Salomao: Speaker - Cepheid