Alert for pharynx-centered gastrointestinal and respiratory cross-infection and cryptic cross-transmission routes of 2019-nCoV.

We proposed that the pharynx, as a common organ of the respiratory and digestive tracts, may be a respiratory and digestive tract cross cryptic transmission pathway for 2019-nCoV infection from the nasal cavities to the pharynx and lung, then to nasal cavities by aerosol (respiratory route) to the pharynx and the gastrointestinal tract, then to the oral cavity by feces (fecal-oral route) and to pharynx, lungs, or gastrointestinal tract.

Impact of interventions to reduce nosocomial transmission of SARS-CoV-2 in English NHS Trusts: a computational modelling study.

BACKGROUND: Prior to September 2021, 55,000-90,000 hospital inpatients in England were identified as having a potentially nosocomial SARS-CoV-2 infection. This includes cases that were likely missed due to pauci- or asymptomatic infection. Further, high numbers of healthcare workers (HCWs) are thought to have been infected, and there is evidence that some of these cases may also have been nosocomially linked, with both HCW to HCW and patient to HCW transmission being reported. From the start of the SARS-CoV-2 pandemic interventions in hospitals such as testing patients on admission and universal mask wearing were introduced to stop spread within and between patient and HCW populations, the effectiveness of which are largely unknown. MATERIALS/METHODS: Using an individual-based model of within-hospital transmission, we estimated the contribution of individual interventions (together and in combination) to the effectiveness of the overall package of interventions implemented in English hospitals during the COVID-19 pandemic. A panel of experts in infection prevention and control informed intervention choice and helped ensure the model reflected implementation in practice. Model parameters and associated uncertainty were derived using national and local data, literature review and formal elicitation of expert opinion. We simulated scenarios to explore how many nosocomial infections might have been seen in patients and HCWs if interventions had not been implemented. We simulated the time period from March-2020 to July-2022 encompassing different strains and multiple doses of vaccination. RESULTS: Modelling results suggest that in a scenario without inpatient testing, infection prevention and control measures, and reductions in occupancy and visitors, the number of patients developing a nosocomial SARS-CoV-2 infection could have been twice as high over the course of the pandemic, and over 600,000 HCWs could have been infected in the first wave alone. Isolation of symptomatic HCWs and universal masking by HCWs were the most effective interventions for preventing infections in both patient and HCW populations. Model findings suggest that collectively the interventions introduced over the SARS-CoV-2 pandemic in England averted 400,000 (240,000 - 500,000) infections in inpatients and 410,000 (370,000 - 450,000) HCW infections. CONCLUSIONS: Interventions to reduce the spread of nosocomial infections have varying impact, but the package of interventions implemented in England significantly reduced nosocomial transmission to both patients and HCWs over the SARS-CoV-2 pandemic.

Identifying Contact Time Required for Secondary Transmission of Clostridioides difficile Infections by Using Real-Time Locating System.

Considering patient room shortages and prevalence of other communicable diseases, reassessing the isolation of patients with Clostridioides difficile infection (CDI) is imperative. We conducted a retrospective study to investigate the secondary CDI transmission rate in a hospital in South Korea, where patients with CDI were not isolated. Using data from a real-time locating system and electronic medical records, we investigated patients who had both direct and indirect contact with CDI index patients. The primary outcome was secondary CDI transmission, identified by whole-genome sequencing. Among 909 direct and 2,711 indirect contact cases, 2 instances of secondary transmission were observed (2 [0.05%] of 3,620 cases), 1 transmission via direct contact and 1 via environmental sources. A low level of direct contact (113 minutes) was required for secondary CDI transmission. Our findings support the adoption of exhaustive standard preventive measures, including environmental decontamination, rather than contact isolation of CDI patients in nonoutbreak settings.

Proporção de casos nosocomiais de COVID-19 no Brasil: análise de seus fatores associados em 1.631.47 registros de 2020 a 2022 / Proporción de casos nosocomiales de COVID-19 en Brasil: análisis de sus factores asociados en 1.631.47 registros de 2020 a 2022 / Proportionof nosocomial cases of COVID-19 in Brazil: analysisof1.631.47 case records from 2020 to 2022

Introdução: Infecções nosocomiais, adquiridas após a internação hospitalar, são o evento adverso mais comum que ameaça a saúde dos pacientes hospitalizados, sendo a pneumonia, incluindo a causada pelo SARS-Cov-2, responsável por mais de 80% das infecções nosocomiais. A pandemia declarada pela OMS em março de 2020 reflete o rápido aumento de casos, impulsionado pela disseminação do vírus através de gotículas e aerossóis. A transmissão nosocomial do SARS-Cov-2 foi observada desde o início do surto em Wuhan, representando um desafio adicional na qualidade de vida dos pacientes. Estudos internacionais em hospitais reportam incidências de infecção nosocomial por COVID-19 entre 11% e 44%.Objetivo: Identificar a proporção de infecção nosocomial por SARS-COV-2 no Brasil entre março de 2020 até dezembro de 2022.Metodologia:Trata-se de um estudo analítico, retrospectivo, de corte transversal, sobre a proporção de infecção nosocomial por Sars-Cov-2 no Brasil, através de dados secundários oriundos do Sistema de Informação da Vigilância Epidemiológica da Gripe. No presente estudo a variável dependente analisada foi a proporção de infecção nosocomial por Sars-cov-2. Como variáveis independentes exploratórias foram utilizadas: faixa etária, sexo, comorbidades e macrorregião de residência. Resultados: O estudo identificou uma proporção de casos nosocomiais de 2,58%, sendo maior no terceiro ano da pandemia 2022 (5,5%) na região Norte (7,57%), entre os indivíduos de 18-59 anos de idade (6,93%)Conclusões: Este estudo sobre casos nosocomiais de COVID-19 no Brasil revela uma proporção de 2,58% entre 2020 e 2022, com associações identificadas em relação à região, idade e comorbidades. Diferenças em relação a estudos internacionais sugerem questões metodológicas específicas. Essa pesquisa é de importância crítica, visto ser de abrangência nacional com grande amplitude, e estabelece uma base sólida para futuros estudos epidemiológicos (AU).

Introduction: Nosocomial infections, acquired after hospital admission, are the most common adverse events threatening patient health, with pneumonia, including that caused by SARS-CoV-2, responsible for over 80% of nosocomial infections. The pandemic declared by the WHO in March 2020 reflects the rapid rise in cases driven by the virus's spread through droplets and aerosols. Nosocomial transmission of SARS-CoV-2 has been observed since the outbreak's onset in Wuhan, posing an additional challenge to patient quality of life. International hospital studies report nosocomial COVID-19 infection rates between 11% and 44%. Objective: Identifying the proportion of nosocomial SARS-CoV-2 infection in Brazil between March 2020 and December 2022.Methodology:This is an analytical, retrospective, cross-sectional study on the proportion of nosocomial SARS-CoV-2 infection in Brazil, using secondary data from the Influenza Epidemiological Surveillance Information System. In this study, the analyzed dependent variable was the proportionof nosocomial SARS-CoV-2 infection. The exploratory independent variables included: age group, gender, comorbidities, and macro-region of residence.Results:The study identified a proportion of nosocomial cases of 2.58%, with a higher proportion in the third year of the pandemic, 2022 (5.5%) in the North region (7.57%), among individuals aged 18-59 years (6.93%). Conclusions: This study on nosocomial cases of COVID-19 in Brazil reveals a proportion of 2.58% between 2020 and 2022, with associations identified regarding region, age, and comorbidities. Differences compared to international studies suggest specific methodological issues. This research is of critical importance, given its national scope and broad coverage, and establishes a solid foundation for future epidemiological studies (AU).

Introducción: Las infecciones nosocomiales, adquiridas tras la hospitalización, son el evento adverso más común que amenaza la salud de los pacientes hospitalizados, siendo la neumonía, incluida la causada por el SARS-Cov-2, la responsable de más del 80% de las infecciones. La pandemia declarada por la OMS en marzo de 2020 refleja el rápido aumento de casos, impulsado por la propagación del virus a través de gotitas y aerosoles. La transmisión nosocomial del SRAS-Cov-2 se ha observado desde el inicio del brote en Wuhan, lo que supone un reto adicional para la calidad de vida de los pacientes. Estudios internacionales realizados en hospitales informan de incidencias de infecciones nosocomiales por COVID-19 de entre el 11% y el 44%. Objetivo: Identificar la proporción de infección nosocomial por SARS-CoV-2 en Brasil entre marzo de 2020 y diciembre de 2022. Metodología: Se trata de un estudio analítico, retrospectivo y transversal sobre la proporción de infección nosocomial por SARS-CoV -2 en Brasil, utilizando datos secundarios del Sistema de Información de Vigilancia Epidemiológica de Influenza. La variable dependiente analizada fue la proporción de infección nosocomial por SARS-CoV-2. Como variables independientes exploratorias se utilizaron: grupo de edad, sexo, comorbilidades y macrorregión de residencia. Resultados:El estudio identificó una proporción de casos nosocomiales del 2,58%, siendo mayor en el tercer año de la pandemia de 2022 (5,5%) en la región Norte (7,57%), entre individuos de 18 a 59 años (6,93%). Conclusiones:Este estudio de casos de COVID-19 hospitalizados en Brasil revela una proporción de 2,58% entre 2020 y 2022, con asociaciones identificadas en relación a la región, edad y comorbilidades. Las disparidades en relación a estudios internacionales sugieren la presencia de cuestiones metodológicas específicas. Esta investigación es de extrema importancia para orientar estrategias preventivas y mejorar el control de las infecciones hospitalarias (AU).

Genomic analysis of inter-hospital transmission of vancomycin-resistant Enterococcus faecium sequence type 80 isolated during an outbreak in Hiroshima, Japan.

Outbreaks caused by vancomycin-resistant enterococci that transcend jurisdictional boundaries are occurring worldwide. This study focused on a vancomycin-resistant enterococcus outbreak that occurred between 2018 and 2021 across two cities in Hiroshima, Japan. The study involved genetic and phylogenetic analyses using whole-genome sequencing of 103 isolates of vancomycin-resistant enterococci to identify the source and transmission routes of the outbreak. Phylogenetic analysis was performed using core genome multilocus sequence typing and core single-nucleotide polymorphisms; infection routes between hospitals were inferred using BadTrIP. The outbreak was caused by Enterococcus faecium sequence type (ST) 80 carrying the vanA plasmid, which was derived from strain A10290 isolated in India. Of the 103 isolates, 93 were E. faecium ST80 transmitted across hospitals. The circular vanA plasmid of the Hiroshima isolates was similar to the vanA plasmid of strain A10290 and transferred from E. faecium ST80 to other STs of E. faecium and other Enterococcus species by conjugation. The inferred transmission routes across hospitals suggest the existence of a central hospital serving as a hub, propagating vancomycin-resistant enterococci to multiple hospitals. Our study highlights the importance of early intervention at the key central hospital to prevent the spread of the infection to small medical facilities, such as nursing homes, with limited medical resources and a high number of vulnerable individuals.

Hospital outbreak of Carbapenem-resistant acinetobacter baumannii in the context of local facility transmission.

Carbapenem-resistant Acinetobacter baumannii are of increasing concern in the health care setting. We describe a cluster of 9 cases in hospitalized patients over a 3-month period that reflected ongoing community transmission from high-risk facilities. Robust surveillance and knowledge of local epidemiology are critical to mitigating onward transmission in the health care setting.

Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting.

BACKGROUND: Infection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network analyses, we determined if IP measures used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic were adequate in protecting healthcare workers (HCWs) and patients from acquiring SARS-CoV-2. METHODS: We performed retrospective cross-sectional analyses of viral genomics from all available SARS-CoV-2 viral samples collected at UC San Diego Health and social network analysis using the electronic medical record to derive temporospatial overlap of infections among related viromes and supplemented with contact tracing data. The outcome measure was any instance of healthcare transmission, defined as cases with closely related viral genomes and epidemiological connection within the healthcare setting during the infection window. Between November 2020 through January 2022, 12 933 viral genomes were obtained from 35 666 patients and HCWs. RESULTS: Among 5112 SARS-CoV-2 viral samples sequenced from the second and third waves of SARS-CoV-2 (pre-Omicron), 291 pairs were derived from persons with a plausible healthcare overlap. Of these, 34 pairs (12%) were phylogenetically linked: 19 attributable to household and 14 to healthcare transmission. During the Omicron wave, 2106 contact pairs among 7821 sequences resulted in 120 (6%) related pairs among 32 clusters, of which 10 were consistent with healthcare transmission. Transmission was more likely to occur in shared spaces in the older hospital compared with the newer hospital (2.54 vs 0.63 transmission events per 1000 admissions, P < .001). CONCLUSIONS: IP strategies were effective at identifying and preventing healthcare SARS-CoV-2 transmission.

The burden and dynamics of hospital-acquired SARS-CoV-2 in England.

Hospital-based transmission had a dominant role in Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV) epidemics1,2, but large-scale studies of its role in the SARS-CoV-2 pandemic are lacking. Such transmission risks spreading the virus to the most vulnerable individuals and can have wider-scale impacts through hospital-community interactions. Using data from acute hospitals in England, we quantify within-hospital transmission, evaluate likely pathways of spread and factors associated with heightened transmission risk, and explore the wider dynamical consequences. We estimate that between June 2020 and March 2021 between 95,000 and 167,000 inpatients acquired SARS-CoV-2 in hospitals (1% to 2% of all hospital admissions in this period). Analysis of time series data provided evidence that patients who themselves acquired SARS-CoV-2 infection in hospital were the main sources of transmission to other patients. Increased transmission to inpatients was associated with hospitals having fewer single rooms and lower heated volume per bed. Moreover, we show that reducing hospital transmission could substantially enhance the efficiency of punctuated lockdown measures in suppressing community transmission. These findings reveal the previously unrecognized scale of hospital transmission, have direct implications for targeting of hospital control measures and highlight the need to design hospitals better equipped to limit the transmission of future high-consequence pathogens.

Mpox exposure and transmission in healthcare settings during the 2022 global outbreak.

PURPOSE OF REVIEW: The risk of nosocomial transmission of mpox during the 2022 global outbreak is not well described. We evaluated reports of exposures to healthcare personnel (HCP) and patients in healthcare settings and risk of transmission. RECENT FINDINGS: Reported nosocomial transmission of mpox has been rare and associated primarily with sharps injuries and breaches in transmission-based precautions. SUMMARY: Currently recommended infection control practices, including the use of standard and transmission-based precautions in the care of patients with known or suspected mpox are highly effective. Diagnostic sampling should not involve the use of needles or other sharp instruments.

Detailed analysis of in-hospital transmission of SARS-CoV-2 using whole genome sequencing.

BACKGROUND: Hospital transmission of SARS-CoV-2 has proved difficult to control, with healthcare-associated infections troublesome throughout. AIM: To understand factors contributing to hospital transmission of infections, which is necessary for containing spread. METHODS: An outbreak of 56 staff and patient cases of COVID-19 over a 31-day period in a tertiary referral unit is presented, with at least a further 29 cases identified outside of the unit and the hospital by whole genome sequencing (WGS). FINDINGS: Transmission is documented from staff to staff, staff to patients, and patients to staff, showing disruption of a tertiary referral service, despite implementation of nationally recommended control measures, superior ventilation, and use of personal protective equipment. There was extensive spread from the index case, despite this patient spending only 10 h bed bound on the ward in strict cubicle isolation and with an initial single target low level (CT = 32) polymerase chain reaction test. CONCLUSION: This investigation highlights how effectively and rapidly SARS-CoV-2 can spread in certain circumstances. It raises questions about infection control measures in place at the time and calls into question the premise that transmissibility can be reliably detected by using lower sensitivity rapid antigen lateral flow tests. We also highlight the value of early intervention in reducing impact as well as the value of WGS in understanding outbreaks.

Role of hospital environmental surfaces in the transmission of the severe acute respiratory syndrome - Coronavirus-2.

INTRODUCTION: Severe acute respiratory syndrome - Coronavirus-2 (SARS-CoV-2) is mainly transmitted via respiratory secretions through coughing, sneezing, or contact with contaminated surfaces. This virus can be present in feces and many body fluids. The study aimed to screen the hospital environment as a potential source for SARS-CoV-2 transmission and identify the hospital zones with the highest contamination levels. METHODOLOGY: Swabs were collected from different sites in the hospital before and after routine cleaning/disinfection, transported in vials containing 1-3 mL of viral transport medium, and stored at -80 ℃ as soon as possible until the time of testing. The real-time reverse-transcription PCR (rRT-PCR) system targeting RNA-dependent RNA polymerase and E genes was used to detect the SARS-CoV-2 RNA. RESULTS: Moderate environmental contamination by SARS-CoV-2 RNA was detected by rRT-PCR before routine cleaning/disinfection (52% of the swabs were positive). The hospital surfaces with the highest contamination levels were elevators' buttons, sinks and faucets' handles at the waiting rooms, patient's room and bathroom, call buttons and telephones in the patient's room, toilet bowl surface, the doorknob and light switches at the X-ray room, and the computer keyboard at the staffroom. All the swabs collected after routine cleaning/disinfection were negative for SARS-CoV-2 RNA by rRT-PCR. CONCLUSIONS: The hospital environment is a high-risk area that can be contaminated by SARS-CoV-2 through contact, respiratory, and maybe fecal shedding of the virus. To limit this fatal virus transmission, strict adherence to proper hand hygiene with frequent optimal decontamination of hospital environmental surfaces is essential.

Resistência antimicrobiana na infecção urinária em unidade de terapia intensiva / Antimicrobial resistance in urinary tract infection in the intensive care unit / Resistencia a los antimicrobianos en la infección del tracto urinario en la unidad de cuidados intensivos

A infecção do trato urinário (ITU) nada mais é do que o acometimento das vias urinárias por microrganismo. Entre as infecções hospitalares de maior incidência está a infecção do trato urinário, acometendo mais mulheres do que homens. Uma das possíveis causas dessa infecção, em pacientes na unidade de terapia intensiva (UTI), é o uso de cateter vesical. Seu tratamento inadequado pode ocasionar uma pielonefrite, podendo adentrar à circulação sanguínea, gerando uma infecção sistêmica e levar o paciente a óbito. A resistência antimicrobiana é uma das principais dificuldades encontrada em UTI sendo considerado um problema de saúde pública. O objetivo deste trabalho foi realizar um breve relato, baseado na literatura, sobre a resistência antimicrobiana na infecção urinária em unidade de terapia intensiva adulta. Em ambientes hospitalares o principal microrganismo causador de ITU é Escherichia coli, sendo 55,5% das culturas positivas estão associadas a procedimentos invasivos, como as sondas vesicais de demora, como consequência este é o microrganismo que mais apresenta resistência aos antimicrobianos utilizados como a ampicilina, trimetoprima e ciprofloxacino. O uso indiscriminado de antibióticos deixa em evidência a necessidade de análise criteriosa da real necessidade de qual antimicrobianos usar, tempo de uso e forma correta de administração. Portanto é necessária a ação dos profissionais de saúde frente a atenção ao paciente, desde a higiene das mãos, uso do cateter, quando necessário observar a real necessidade do uso do antimicrobianos e que esse seja feito após cultura e antibiograma.

Urinary tract infection (UTI) is nothing more than the involvement of the urinary tract by a microorganism. Among the hospital infections with the highest incidence is urinary tract infections, affecting more women than men. One of the possible causes of this infection in patients in the intensive care unit (ICU) is the use of a bladder catheter. Its inadequate treatment can cause pyelonephritis, which can enter the bloodstream, generating a systemic infection and leading the patient to death. Antimicrobial resistance is one of the main difficulties encountered in ICUs and is considered a public health problem. The objective of this study was to present a brief report, based on the literature, on antimicrobial resistance in urinary tract infections in an adult intensive care unit. In hospital environments, the main microorganism that causes UTI is Escherichia coli, and 55.5% of positive cultures are associated with invasive procedures, such as indwelling urinary catheters, as a consequence, this is the microorganism that is most resistant to antimicrobials used, such as ampicillin, trimethoprim and ciprofloxacin. The indiscriminate use of antibiotics highlights the need for a careful analysis of the real need for which antimicrobials to use, time of use, and correct form of administration. Therefore, it is necessary for the action of health professionals in the care of the patient, from the hygiene of the professional to, the use of the catheter, when necessary to observe the real need for the use of antimicrobials and that this is done after culture and antibiogram.

La infección del tracto urinario (ITU) no es más que la afectación de las vías urinarias por un microorganismo. Entre las infecciones hospitalarias con mayor incidencia se encuentra la infección del tracto urinario, que afecta más a mujeres que a hombres. Una de las posibles causas de esta infección en pacientes en la unidad de cuidados intensivos (UCI) es el uso de una sonda vesical. Su tratamiento inadecuado puede causar pielonefritis, la cual puede ingresar al torrente sanguíneo, generando una infección sistémica y llevando al paciente a la muerte. La resistencia a los antimicrobianos es una de las principales dificultades encontradas en las UCI y se considera un problema de salud pública. El objetivo de este estudio fue presentar un breve informe, basado en la literatura, sobre la resistencia antimicrobiana en infecciones del tracto urinario en una unidad de cuidados intensivos de adultos. En ambientes hospitalarios, el principal microorganismo causante de ITU es Escherichia coli, y el 55,5% de los cultivos positivos están asociados a procedimientos invasivos, como sondas vesicales permanentes, por lo que este es el microorganismo más resistente a los antimicrobianos utilizados, como la ampicilina. ., trimetoprima y ciprofloxacino. El uso indiscriminado de antibióticos pone de relieve la necesidad de un análisis cuidadoso de la necesidad real de qué antimicrobianos utilizar, el momento de uso y la forma correcta de administración. Por lo tanto, es necesaria la actuación de los profesionales de la salud en el cuidado del paciente, desde la higiene del profesional, uso del catéter, cuando sea necesario observar la necesidad real del uso de antimicrobianos y que este se realice previo cultivo y antibiograma.

Chapare Hemorrhagic Fever and Virus Detection in Rodents in Bolivia in 2019.

BACKGROUND: In June 2019, the Bolivian Ministry of Health reported a cluster of cases of hemorrhagic fever that started in the municipality of Caranavi and expanded to La Paz. The cause of these cases was unknown. METHODS: We obtained samples for next-generation sequencing and virus isolation. Human and rodent specimens were tested by means of virus-specific real-time quantitative reverse-transcriptase-polymerase-chain-reaction assays, next-generation sequencing, and virus isolation. RESULTS: Nine cases of hemorrhagic fever were identified; four of the patients with this illness died. The etiologic agent was identified as Mammarenavirus Chapare mammarenavirus, or Chapare virus (CHAPV), which causes Chapare hemorrhagic fever (CHHF). Probable nosocomial transmission among health care workers was identified. Some patients with CHHF had neurologic manifestations, and those who survived had a prolonged recovery period. CHAPV RNA was detected in a variety of human body fluids (including blood; urine; nasopharyngeal, oropharyngeal, and bronchoalveolar-lavage fluid; conjunctiva; and semen) and in specimens obtained from captured small-eared pygmy rice rats (Oligoryzomys microtis). In survivors of CHHF, viral RNA was detected up to 170 days after symptom onset; CHAPV was isolated from a semen sample obtained 86 days after symptom onset. CONCLUSIONS: M. Chapare mammarenavirus was identified as the etiologic agent of CHHF. Both spillover from a zoonotic reservoir and possible person-to-person transmission were identified. This virus was detected in a rodent species, O. microtis. (Funded by the Bolivian Ministry of Health and others.).

Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults.

Bacterial bloodstream infections are a major cause of morbidity and mortality among patients undergoing hematopoietic cell transplantation (HCT). Although previous research has demonstrated that pathogens may translocate from the gut microbiome into the bloodstream to cause infections, the mechanisms by which HCT patients acquire pathogens in their microbiome have not yet been described. Here, we use linked-read and short-read metagenomic sequencing to analyze 401 stool samples collected from 149 adults undergoing HCT and hospitalized in the same unit over three years, many of whom were roommates. We use metagenomic assembly and strain-specific comparison methods to search for high-identity bacterial strains, which may indicate transmission between the gut microbiomes of patients. Overall, the microbiomes of patients who share time and space in the hospital do not converge in taxonomic composition. However, we do observe six pairs of patients who harbor identical or nearly identical strains of the pathogen Enterococcus faecium, or the gut commensals Akkermansia muciniphila and Hungatella hathewayi. These shared strains may result from direct transmission between patients who shared a room and bathroom, acquisition from a common hospital source, or transmission from an unsampled intermediate. We also identify multiple patients with identical strains of species commonly found in commercial probiotics, including Lactobacillus rhamnosus and Streptococcus thermophilus. In summary, our findings indicate that sharing of identical pathogens between the gut microbiomes of multiple patients is a rare phenomenon. Furthermore, the observed potential transmission of commensal, immunomodulatory microbes suggests that exposure to other humans may contribute to microbiome reassembly post-HCT.

Outbreak of COVID-19 among children and young adults in a cancer centre daycare unit.

Nosocomial transmission of COVID-19 among immunocompromised hosts can have a serious impact on COVID-19 severity, underlying disease progression and SARS-CoV-2 transmission to other patients and healthcare workers within hospitals. We experienced a nosocomial outbreak of COVID-19 in the setting of a daycare unit for paediatric and young adult cancer patients. Between 9 and 18 November 2020, 473 individuals (181 patients, 247 caregivers/siblings and 45 staff members) were exposed to the index case, who was a nursing staff. Among them, three patients and four caregivers were infected. Two 5-year-old cancer patients with COVID-19 were not severely ill, but a 25-year-old cancer patient showed prolonged shedding of SARS-CoV-2 RNA for at least 12 weeks, which probably infected his mother at home approximately 7-8 weeks after the initial diagnosis. Except for this case, no secondary transmission was observed from the confirmed cases in either the hospital or the community. To conclude, in the day care setting of immunocompromised children and young adults, the rate of in-hospital transmission of SARS-CoV-2 was 1.6% when applying the stringent policy of infection prevention and control, including universal mask application and rapid and extensive contact investigation. Severely immunocompromised children/young adults with COVID-19 would have to be carefully managed after the mandatory isolation period while keeping the possibility of prolonged shedding of live virus in mind.

Transient dynamics of infection transmission in a simulated intensive care unit.

Healthcare-associated infections (HAIs) remain a serious public health problem. In previous work, two models of an intensive care unit (ICU) showed that differing population structures had markedly different rates of Staphylococcus aureus (MRSA) transmission. One explanation for this difference is the models having differing long-term equilbrium dynamics, resulting from different basic reproductive numbers, R0. We find in this system however that this is not the case, and that both models had the same value for R0. Instead, short-term, transient dynamics, characterizing a series of small, self-limiting outbreaks caused by pathogen reintroduction were responsible for the differences. These results show the importance of these short-term factors for disease systems where reintroduction events are frequent, even if they are below the epidemic threshold. Further, we examine how subtle changes in how a hospital is organized-or how a model assumes a hospital is organized-in terms of the admission of new patients may impact transmission rates. This has implications for both novel pathogens introduced into ICUs, such as Ebola, MERS or COVID-19, as well as existing healthcare-associated infections such as carbapenem-resistant Enterobacteriaceae.

Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves.

Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services and yet little is known about transmission within this setting. We characterise within hospital transmission by combining viral genomic and epidemiological data using Bayesian modelling amongst 2181 patients and healthcare workers from a large UK NHS Trust. Transmission events were compared between Wave 1 (1st March to 25th J'uly 2020) and Wave 2 (30th November 2020 to 24th January 2021). We show that staff-to-staff transmissions reduced from 31.6% to 12.9% of all infections. Patient-to-patient transmissions increased from 27.1% to 52.1%. 40%-50% of hospital-onset patient cases resulted in onward transmission compared to 4% of community-acquired cases. Control measures introduced during the pandemic likely reduced transmissions between healthcare workers but were insufficient to prevent increasing numbers of patient-to-patient transmissions. As hospital-acquired cases drive most onward transmission, earlier identification of nosocomial cases will be required to break hospital transmission chains.

Improving mathematical modeling of interventions to prevent healthcare-associated infections by interrupting transmission or pathogens: How common modeling assumptions about colonized individuals impact intervention effectiveness estimates.

Mathematical models are used to gauge the impact of interventions for healthcare-associated infections. As with any analytic method, such models require many assumptions. Two common assumptions are that asymptomatically colonized individuals are more likely to be hospitalized and that they spend longer in the hospital per admission because of their colonization status. These assumptions have no biological basis and could impact the estimated effects of interventions in unintended ways. Therefore, we developed a model of methicillin-resistant Staphylococcus aureus transmission to explicitly evaluate the impact of these assumptions. We found that assuming that asymptomatically colonized individuals were more likely to be admitted to the hospital or spend longer in the hospital than uncolonized individuals biased results compared to a more realistic model that did not make either assumption. Results were heavily biased when estimating the impact of an intervention that directly reduced transmission in a hospital. In contrast, results were moderately biased when estimating the impact of an intervention that decolonized hospital patients. Our findings can inform choices modelers face when constructing models of healthcare-associated infection interventions and thereby improve their validity.

regentrans: a framework and R package for using genomics to study regional pathogen transmission.

Increasing evidence of regional pathogen transmission networks highlights the importance of investigating the dissemination of multidrug-resistant organisms (MDROs) across a region to identify where transmission is occurring and how pathogens move across regions. We developed a framework for investigating MDRO regional transmission dynamics using whole-genome sequencing data and created regentrans, an easy-to-use, open source R package that implements these methods (https://github.com/Snitkin-Lab-Umich/regentrans). Using a dataset of over 400 carbapenem-resistant isolates of Klebsiella pneumoniae collected from patients in 21 long-term acute care hospitals over a one-year period, we demonstrate how to use our framework to gain insights into differences in inter- and intra-facility transmission across different facilities and over time. This framework and corresponding R package will allow investigators to better understand the origins and transmission patterns of MDROs, which is the first step in understanding how to stop transmission at the regional level.