Epidemiological Link Research Articles

The mobilome of Staphylococcus aureus from wild ungulates reveals epidemiological links at the animal-human interface

Staphylococcus aureus thrives at animal-human-environment interfaces. A large-scale work from our group indicated that antimicrobial resistance (AMR) in commensal S. aureus strains from wild ungulates is associated with agricultural land cover and livestock farming, raising the hypothesis that AMR genes in wildlife strains may originate from different hosts, namely via exchange of mobile genetic elements (MGE). In this work, we generate the largest available dataset of S. aureus draft genomes from wild ungulates in Portugal and explore their mobilome, which can determine important traits such as AMR, virulence, and host specificity, to understand MGE exchange. Core genome multi-locus sequence typing based on 98 newly generated draft genomes and 101 publicly available genomes from Portugal demonstrated that the genomic relatedness of S. aureus from wild ungulates assigned to livestock-associated sequence types (ST) is greater compared to wild ungulate isolates assigned to human-associated STs. Screening of host specificity determinants disclosed the unexpected presence in wildlife of the immune evasion cluster encoded in φSa3 prophage, described as a human-specific virulence determinant. Additionally, two plasmids, pAVX and pETB, previously associated with avian species and humans, respectively, and the Tn553 transposon were detected. Both pETB and Tn553 encode penicillin resistance through blaZ. Pangenome analysis of wild ungulate isolates shows a core genome fraction of 2133 genes, with isolates assigned to ST72 and ST3224 being distinguished from the remaining by MGEs, although there is no reported role of these in adaptation to wildlife. AMR related gene clusters found in the shell genome are directly linked to resistance against penicillin, macrolides, fosfomycin, and aminoglycosides, and they represent mobile ARGs. Altogether, our findings support epidemiological interactions of human and non-human hosts at interfaces, with MGE exchange, including AMR determinants, associated with putative indirect movements of S. aureus among human and wildlife hosts that might be bridged by livestock.

Comparison of CTX-M encoding plasmids present during the early phase of the ESBL pandemic in western Sweden

Plasmids encoding blaCTX-M genes have greatly shaped the evolution of E. coli producing extended-spectrum beta-lactamases (ESBL-E. coli) and adds to the global threat of multiresistant bacteria by promoting horizontal gene transfer (HGT). Here we screened the similarity of 47 blaCTX-M -encoding plasmids, from 45 epidemiologically unrelated and disperse ESBL-E. coli strains, isolated during the early phase (2009–2014) of the ESBL pandemic in western Sweden. Using optical DNA mapping (ODM), both similar and rare plasmids were identified. As many as 57% of the plasmids formed five ODM-plasmid groups of at least three similar plasmids per group. The most prevalent type (28%, IncIl, pMLST37) encoded blaCTX-M-15 (n = 10), blaCTX-M-3 (n = 2) or blaCTX-M-55 (n = 1). It was found in isolates of various sequence types (STs), including ST131. This could indicate ongoing local HGT as whole-genome sequencing only revealed similarities with a rarely reported, IncIl plasmid. The second most prevalent type (IncFII/FIA/FIB, F1:A2:B20) harboring blaCTX-M-27, was detected in ST131-C1-M27 isolates, and was similar to plasmids previously reported for this subclade. The results also highlight the need for local surveillance of plasmids and the importance of temporospatial epidemiological links so that detection of a prevalent plasmid is not overestimated as a potential plasmid transmission event in outbreak investigations.

Sudan virus disease super-spreading, Uganda, 2022

BackgroundOn 20 September 2022, Uganda declared its fifth Sudan virus disease (SVD) outbreak, culminating in 142 confirmed and 22 probable cases. The reproductive rate (R) of this outbreak was 1.25. We described persons who were exposed to the virus, became infected, and they led to the infection of an unusually high number of cases during the outbreak.MethodsIn this descriptive cross-sectional study, we defined a super-spreader person (SSP) as any person with real-time polymerase chain reaction (RT-PCR) confirmed SVD linked to the infection of ≥ 13 other persons (10-fold the outbreak R). We reviewed illness narratives for SSPs collected through interviews. Whole-genome sequencing was used to support epidemiologic linkages between cases.ResultsTwo SSPs (Patient A, a 33-year-old male, and Patient B, a 26-year-old male) were identified, and linked to the infection of one probable and 50 confirmed secondary cases. Both SSPs lived in the same parish and were likely infected by a single ill healthcare worker in early October while receiving healthcare. Both sought treatment at multiple health facilities, but neither was ever isolated at an Ebola Treatment Unit (ETU). In total, 18 secondary cases (17 confirmed, one probable), including three deaths (17%), were linked to Patient A; 33 secondary cases (all confirmed), including 14 (42%) deaths, were linked to Patient B. Secondary cases linked to Patient A included family members, neighbours, and contacts at health facilities, including healthcare workers. Those linked to Patient B included healthcare workers, friends, and family members who interacted with him throughout his illness, prayed over him while he was nearing death, or exhumed his body. Intensive community engagement and awareness-building were initiated based on narratives collected about patients A and B; 49 (96%) of the secondary cases were isolated in an ETU, a median of three days after onset. Only nine tertiary cases were linked to the 51 secondary cases. Sequencing suggested plausible direct transmission from the SSPs to 37 of 39 secondary cases with sequence data.ConclusionExtended time in the community while ill, social interactions, cross-district travel for treatment, and religious practices contributed to SVD super-spreading. Intensive community engagement and awareness may have reduced the number of tertiary infections. Intensive follow-up of contacts of case-patients may help reduce the impact of super-spreading events.

Epidemiology, linkage to care and natural history of women of childbearing age with chronic hepatitis B: A population-based study.

Pregnant women with chronic hepatitis B (CHB) are a priority population for hepatitis B care. Identification of HBV status prior to pregnancy would facilitate timely maternal interventions and perinatal care. In our study, we aimed to study the epidemiology of CHB among women of childbearing age (WoCBA, 18-49 years) in Alberta, Canada. We retrospectively analysed Alberta Analytics databases to study CHB epidemiology, natural history and care linkage among WoCBA in Alberta, between April 2012 and March 2021. A Poisson regression was conducted to estimate incidence of newly identified CHB cases and prevalence trends, whereas predictors of care linkage were determined using logistic regression. Age/sex-adjusted incidence of newly identified CHB among WoCBA between 2015 and 2020 was 36.2/100,000 person/years, highest among individuals aged 30-39 years. Incidence of newly identified CHB decreased from 52.6 to 18.2/100,000 between 2015 and 2020, but prevalence increased from 131.7 to 248.6/100,000 in the same period. Newly identified CHB incident cases (n = 2124) had lower survival rates than age/sex-matched Canadians, with a standardized mortality ratio of 5.7 (95% CI 2.6-11.0). Increasing age (years) at diagnosis (HR, 1.2; 95% CI 1.1-1.3) was independently associated with mortality. Comorbid hepatocellular carcinoma, anti-HBV treatment and year of diagnosis were not significantly associated with mortality. Of the 1927 women with 2436 hepatitis B surface antigen-positive pregnancies from 2012 to 2020, only 27.6% had recommended HBV assessment during pregnancy. Of those women meeting criteria for antiviral therapy to prevent mother-to-child transmission (MTCT), only 66.4% received treatment. Suboptimal management during pregnancy and overall lower survival rates highlight the need to address care linkage barriers in women of childbearing age living with CHB.

Anti-monkeypox virus-neutralizing activities of human immunoglobulin manufactured between 1999 and 2021 and derived from donors in the United States and Japan.

In May 2022, the United Kingdom reported the first case of chained transmission of the monkeypox (mpox) virus without any known epidemiological links to west or central Africa. The monthly number of mpox patients currently has passed a peak and is declining globally, and infected patients include both non-vaccinated and vaccinated individuals. Herein, the virus-neutralizing (VN) activity against vaccinia viruses, which are considered to cross-react with the mpox virus, in the intravenous immunoglobulin (IVIG) lots derived from donors, including vaccinated Japanese populations, was evaluated to clarify the status of the Japanese blood donor population. VN titres against vaccinia and human mpox viruses in IVIG lots derived from donors in Japan and the United States manufactured between 1999 and 2021 and 1995 and 2001, respectively, were evaluated by neutralization testing. VN titres of IVIG derived from donors in Japan and the United States against vaccinia and mpox viruses showed a slowly decreasing trend between 1999 and 2021. VN titres are expected to decrease in the future since the percentage of vaccinated donors in the donor population seems to have decreased. Therefore, continuous monitoring of VN titres is required.

Modeled estimates of HIV-serodifferent couples in tuberculosis-affected households in four sub-Saharan African countries.

Household-based tuberculosis (TB) contact evaluation may be an efficient strategy to reach people who could benefit from oral pre-exposure prophylaxis (PrEP) because of the epidemiological links between HIV and TB. This study estimated the number of HIV serodifferent couples in TB-affected households and potential HIV acquisitions averted through their PrEP use in 4 TB-HIV high-burden countries. We conducted a model-based analysis set in Ethiopia, Kenya, South Africa, and Uganda using parameters from population-based household surveys, systematic literature review and meta-analyses, and estimates from the Global Burden of Diseases, Injuries, and Risk Factors Study 2019. We parameterized the nonlinear relationship between the proportion of serodifferent couples among people living with HIV and population-level HIV prevalence using Markov chain Monte Carlo methods. We integrated all parameters in a mathematical model and propagated uncertainty using a Monte Carlo approach. We estimated the HIV prevalence among adults aged 15-49 living in TB-affected households to be higher than in the general population in all 4 countries. The proportion of serodifferent couples among all couples in TB-affected households was also higher than in the general population (South Africa: 20.7% vs. 15.7%, Kenya: 15.7% vs. 5.7%, Uganda: 14.5% vs. 6.0%, Ethiopia: 4.1% vs. 0.8%). We estimated that up to 1,799 (95% UI: 1,256-2,341) HIV acquisitions in South Africa could be prevented annually by PrEP use in serodifferent couples in TB-affected households, 918 (95% UI: 409-1,450) in Kenya, 686 (95% UI: 505-871) in Uganda, and 408 (95% UI: 298-522) in Ethiopia. As couples in TB-affected households are more likely to be serodifferent than couples in the general population, offering PrEP during household TB contact evaluation may prevent a substantial number of HIV acquisitions.

Shedding of measles vaccine RNA in children after receiving measles, mumps and rubella vaccination

BackgroundMeasles, mumps, and rubella(MMR) vaccination is critical to measles outbreak responses. However, vaccine reactions and detection of measles vaccine RNA in recently immunized persons may complicate case classification especially in those presenting with another respiratory viral illness. We aim to characterize cases of measles vaccine shedding in recently vaccinated children presenting with respiratory viral symptoms. MethodsChildren who were tested with a multiplex respiratory panel <30 days after receiving MMR were identified. Remnant nasopharyngeal(NP) samples were tested for measles vaccine by PCR. Medical records were reviewed for demographics, presenting symptoms, and test results. ResultsFrom January 2022 to March 2023, 127 NP from children who received MMR were tested. Ninety-six NP were collected after the first dose, of which 33(34.4 %) were positive for vaccine RNA. The median interval between MMR and detection was 11.0 days. Thirty-one NP were collected after the second MMR and 1(3.2 %) was positive; time between the vaccination and detection was 18.9 days. Median cycle threshold(Ct) value of the measles PCR for vaccine shedding was significantly higher than median Ct in children with wild-type infection. ConclusionShedding of measles vaccine RNA is not uncommon and vaccine RNA can be detected up to 29 days post MMR; the amount of vaccine RNA shedding is low indicated by high Ct values. Clinicians and public health officials should consider performing measles vaccine testing on those testing positive for measles within one month of MMR vaccination, especially if the Ct value is high and definitive epidemiological links are absent.

Commentary on the adoption of a test-based versus syndromic-based approach to outbreak declaration and management in hospital and institutional settings.

At present, Ontario, like most other jurisdictions in Canada, uses a syndromic-based surveillance definition for acute respiratory infection (ARI) outbreaks in institutions and public hospitals. Confirmed outbreaks are defined as either two or more ARIs in 48 hours with any common epidemiological link and at least one that is laboratory-confirmed; or three cases of ARIs occurring within 48 hours with any common epidemiological link, and not necessarily with lab confirmation. However, with the adoption of broader test-based approaches for sick patients/residents throughout the pandemic, new challenges have surfaced regarding the declaration and management of ARI outbreaks with a variety of scenarios in respiratory testing results. Decisions, including the determination of epidemiological linkage when there are discordant/negative test results, have become more complicated with the addition of virus-specific test results for every sick individual. The ARI outbreak case definition and management guidance was updated in 2018. The purpose of this commentary is to highlight epidemiological trends in ARI outbreaks in Ontario over the 2022-2023 season compared to the 2018-2019 and 2019-2020 pre-pandemic seasons. This is followed by a discussion around some of the benefits and challenges of implementing a test-based versus syndromic-based approach to ARI outbreaks.

First time whole genome sequencing of Mycobacterium bovis from the environment supports transmission at the animal-environment interface

Spreading of Mycobacterium bovis causing animal tuberculosis (TB) at livestock-wildlife-environment interfaces remains a significant problem. Recently, we provided evidence of widespread environmental contamination of an endemic animal TB setting with viable and dormant M. bovis cells able to recover metabolic activity, making indirect transmission via environmental contamination plausible. We now report the first whole genome sequences of M. bovis recovered from the environment. We establish epidemiological links at the environment-animal interface by phylogenomic comparison of these M. bovis genomes with those isolated from livestock and wild ungulates from the same area. Environmental and animal genomes are highly intertwined and distribute similarly into the same M. bovis lineages, supporting several instances of environmental contamination. This study provides compelling evidence of M. bovis excretion into the environment and viability maintenance, supporting the environment as a potential source of new infection. These insights have clear implications for policy formulation, advocating environmental surveillance and an ecosystem perspective in TB control programs. Environmental ImplicationWe report the first whole genome sequences of M. bovis from the environment and establish epidemiological links at the environment-animal interface, demonstrating close phylogenomic relatedness of animal and environmental M. bovis. Definitive evidence of M. bovis excretion into the environment with viability maintenance is provided, supporting the environment as a potential source of new infection. Implications of this work include methodological innovations offering a tool to resolve indirect transmission chains and support customized biosecurity measures. Policy formulation aiming at the control of animal tuberculosis and cost mitigation should consider these findings, encouraging environmental surveillance in official eradication programmes.

Nonpharmacological Treatment for Nontuberculous Mycobacterial Pulmonary Disease.

Nontuberculous mycobacterial pulmonary disease (NTM-PD) results from the exposure of susceptible hosts to a diverse group of environmental mycobacteria. The emphasis on nonpharmacological strategies is motivated by the widespread presence of NTM in various environments, and the inconsistent success rates of pharmacological treatments. Modifiable factors contributing to NTM-PD development include impaired airway clearance, low body mass index, gastroesophageal reflux disease, and exposure to NTM habitats. This suggests that lifestyle and environmental modifications could affect disease development and progression. The review highlights several modalities that can modify the risk factors. Airway clearance techniques, informed by the "gel-on-brush" model of the bronchial epithelium, aim to enhance mucociliary clearance, and have the potential to alleviate symptoms and improve lung function. The impact of nutritional status is also examined, with a lower body mass index linked to an increased risk and progression of NTM-PD, indicating the importance of targeted nutritional support. Additionally, the theoretical and epidemiological links between gastroesophageal reflux disease and NTM-PD advocate careful management of reflux episodes. Understanding the risk of NTM transmission through environmental exposure to contaminated water and soil is also crucial. Strategies to mitigate this risk, including effective water management and minimizing soil contact, are presented as vital preventive measures. The review supports the inclusion of nonpharmacological treatments within a comprehensive NTM-PD management strategy, alongside conventional pharmacological therapies. This integrated approach seeks to improve the overall understanding and handling of NTM-PD.

Understanding the potential role of whole genome sequencing (WGS) in managing patients with gonorrhoea: A systematic review of WGS use on human pathogens in individual patient care

The utility of whole genome sequencing (WGS) to inform sexually transmitted infection (STI) patient management is unclear. Timely WGS data might support clinical management of STIs by characterising epidemiological links and antimicrobial resistance profiles. We conducted a systematic review of clinical application of WGS to any human pathogen that may be transposable to gonorrhoea. We searched six databases for articles published between 01/01/2010-06/02/2023 that reported on real/near real-time human pathogen WGS to inform clinical intervention. All article types from all settings were included. Findings were analysed using narrative synthesis. We identified 12,179 articles, of which eight reported applications to inform tuberculosis (n=7) and gonorrhoea (n=1) clinical patient management. WGS data were successfully used as an adjunct to clinical and epidemiological data to enhance contact-tracing (n=2), inform antimicrobial therapy (n=5) and identify cross-contamination (n=1). WGS identified gonorrhoea transmission chains that were not established via partner notification. Future applications could include insights into pathogen exposure detected within sexual networks for targeted patient management. While there was some evidence of WGS use to provide individualised tuberculosis and gonorrhoea treatment, the eight identified studies contained few participants. Future research should focus on testing WGS intervention effectiveness and examining ethical considerations of STI WGS use.

Kawasaki disease versus Multisystem Inflammatory Syndrome COVID-19 with Kawasaki disease phenotype. Single-center experience

to compare the clinical presentation, laboratory testing, and evolution of KD with PIMS Kawasaki phenotype (PIMS-KD) in patients hospitalized before the pandemic, compared with the pandemic period. Cross-sectional study in two groups of patients at the Hospital Exequiel González Cortés: typical KD (group 1) and PIMS-KD (group 2). Data on demographic, clinical, and biochemical details were collected, as well as echocardiogram, treatment, and evolution records. IgG and IgM serology for SARS-CoV-2 was performed in both groups. In the KD group and the PIMS-KD group, 20 and 33 patients were analyzed, respectively. There were differences in age, days of fever, count of leukocytes, lymphocytes, and platelets, erythrocyte sedimentation rate (ESR), and hospital stay. In 25% of the KD group, there were alterations in the echocardiogram and, in the PIMS-K group, all patients received corticosteroids and 25 patients received intravenous immunoglobulin (IVIG). In both groups, a favorable clinical evolution was observed, characterized by the absence of complications and mortality. Based on the data obtained in our study, the importance of the epidemiological link is emphasized as an essential factor in differentiating between both pathologies, highlighting the need to consider factors such as age, duration of fever, count of leukocytes, lymphocytes, and platelets, and degree of cardiac involvement, for a differential evaluation between patients with PIMS-KD versus KD.

Association between per- and poly-fluoroalkyl substances and nonalcoholic fatty liver disease: A nested case-control study in northwest China

Per- and poly-fluoroalkyl substances (PFAS) have been reported to have hepatotoxic effects. However, it is unclear whether they are linked to non-alcoholic fatty liver disease (NAFLD). This nested case-control study focused on the epidemiological links between PFAS and the prevalence of NAFLD. We selected 476 new cases of NAFLD and 952 age- and sex-matched controls from the Jinchang cohort population between 2014 and 2019. Serum concentrations of PFAS were measured using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Only PFAS with a detection rate of ≥90 % were included for analysis, which included PFPeA, PFOA, PFNA, PFHxS, PFOS, and 9Cl-PF3ONS. The relationship between single and co-exposure to PFAS and the occurrence of NAFLD was evaluated using conditional logistic regression, Quantile g-computation (QgC), and Bayesian kernel machine regression (BKMR) model. Logistic regression indicated that PFPeA, PFOA, and 9Cl-PF3ONS were positive correlation with the incidence of NAFLD after adjusting for confounders, with odds ratios (OR) and 95 % confidence interval (CI) of 3.13 (95 % CI: 2.53, 3.86), 1.39 (95 % CI: 1.12, 1.73), and 1.41 (95 % CI: 1.20, 1.66), respectively. PFNA, PFHxS, and PFOS were nonlinearly and negatively associated with the incidence of NAFLD, with OR (95 % CI) of 0.53 (0.46, 0.62), 0.83 (0.73, 0.95), and 0.52 (0.44, 0.61), respectively. QgC showed a significant joint effect of PFAS mixture on NAFLD onset (OR: 1.52, 95 % CI: 1.24, 1.88). BKMR showed a weak positive trend between PFAS mixtures and NAFLD incidence. Positive correlations were primarily driven by PFPeA and 9Cl-PF3ONS, while negative correlations were mainly influenced by PFNA and PFOS. The BKMR model also suggested that there was an interaction between PFOS and PFNA and other four PFAS compounds. In conclusion, our findings suggest that individual and co-exposure to PFAS is associated with a risk of NAFLD onset.

Phylogenetic and Molecular Characteristics of Wild Bird-Origin Avian Influenza Viruses Circulating in Poland in 2018−2022: Reassortment, Multiple Introductions, and Wild Bird–Poultry Epidemiological Links

Since 2020, a significant increase in the severity of H5Nx highly pathogenic avian influenza (HPAI) epidemics in poultry and wild birds has been observed in Poland. To further investigate the genetic diversity of HPAI H5Nx viruses of clade 2.3.4.4b, HPAIV-positive samples collected from dead wild birds in 2020–2022 were phylogenetically characterized. In addition, zoonotic potential and possible reassortment between HPAIVs and LPAIVs circulating in the wild avifauna in Poland have been examined. The genome-wide phylogenetic analysis revealed the presence of three different avian influenza virus (AIV) subtypes (H5N8, H5N5, and H5N1) during the HPAI 2020/2021 season, while in the next HPAI 2021/2022 epidemic only one H5N1 subtype encompassing seven various genotypes (G1–G7) was confirmed. No reassortment events between LPAIVs (detected in the framework of active surveillance) and HPAIVs circulating in Poland have been captured, but instead, epidemiological links between wild birds and poultry due to bidirectional, i.e., wild bird-to-poultry and poultry-to-wild bird HPAIV transmission were evident. Furthermore, at least five independent H5N8 HPAIV introductions into the Baltic Sea region related to unprecedented mass mortality among swans in February–March 2021 in Poland, as well as a general tendency of current H5Nx viruses to accumulate specific mutations associated with the ability to break the interspecies barrier were identified. These results highlight the importance of continuous active and passive surveillance for AI to allow a rapid response to emerging viruses.

Candida auris Outbreak in a Multidisciplinary Hospital in Romania during the Post-Pandemic Era: Potential Solutions and Challenges in Surveillance and Epidemiological Control.

Candida auris is a newly emerging yeast, which is raising public health concerns due to its outbreak potential, lack of protocols for decontamination and isolation of patients or contacts, increased resistance to common antifungals, and associated high mortality. This research aimed to describe the challenges related to identifying the outbreak, limiting further contamination, and treating affected individuals. We retrospectively analyzed all cases of C. auris detected between October 2022 and August 2023, but our investigation focused on a three-month-long outbreak in the department of cardio-vascular surgery and the related intensive care unit. Along with isolated cases in different wards, we identified 13 patients who became infected or colonized in the same area and time, even though the epidemiological link could only be traced in 10 patients, according to the epidemiologic investigation. In conclusion, our study emphasizes the substantial challenge encountered in clinical practice when attempting to diagnose and limit the spread of an outbreak. Therefore, it is crucial to promptly apply contact precaution measures and appropriate environmental cleaning, from the first positive case detected.

Evidence of transmission of New Delhi metallo-β-lactamase-producing Klebsiella pneumoniae through a gastrointestinal endoscope without an elevator channel.

To investigate the source and transmission dynamics of an endoscope-associated New Delhi metallo-β-lactamase-producing Klebsiella pneumonia (NDM-KP) outbreak. Epidemiological and genomic investigation. Academic acute care hospital in New Jersey. Five patients with active NDM-KP infection identified on clinical isolates, and four NDM-KP colonized patients identified via rectal swab screening. Over a twelve-month period, nine patients were identified with NDM-KP infection or colonization. Whole-genome sequencing (WGS) revealed that all of the identified cases were related by 25 mutational events or less. Seven of the cases were linked to gastrointestinal endoscopic procedures (four clinical cases and three positive screens among patients exposed to endoscopes suspected of transmission). Two cases demonstrated delayed transmission that occurred five months after the initial outbreak, likely through shared usage of a non-therapeutic gastroscope without an elevator channel. Although all endoscope cultures in our investigation were negative, the epidemiological link to gastrointestinal endoscopes, the high degree of relatedness via WGS, and the identification of asymptomatic NDM-KP colonization among patients exposed to shared endoscopes make the endoscopic mode of transmission most likely. This investigation highlights the probable transmission of NDM-KP via a gastroscope without an elevator channel, observed several months after an initial outbreak. We hypothesize that persistent mechanical defects may have contributed to the delayed device-related transmission of NDM-KP.

Persistent Colonization of Ciprofloxacin-Resistant and Extended-Spectrum β-Lactamase (ESBL)-Producing Salmonella enterica Serovar Kentucky ST198 in a Patient with Inflammatory Bowel Disease.

Salmonella enterica serovar Kentucky ST198 has emerged as a global threat to humans. In this study, we aimed to characterize the prolonged carriage of ciprofloxacin-resistant and extended-spectrum β-lactamase (ESBL)-producing S. Kentucky ST198 in a single patient with inflammatory bowel disease (IBD). Three S. Kentucky strains were collected from a single patient with IBD on 11th January, 23rd January, and 8th February, 2022, respectively. Antimicrobial susceptibility testing, whole-genome sequencing, and phylogenetic analysis with 38 previously described Chinese S. Kentucky ST198 strains from patients and food were performed. All three S. Kentucky isolates belonged to ST198. They carried identical 16 resistance genes, such as blaCTX-M-55, tet(A), and qnrS1, and had identical mutations within gyrA (S83F and D87N) and parC (S80I). Therefore, they exhibited identical multidrug-resistant profiles, including the clinically important antibiotics cephalosporins (ceftazidime and cefepime), fluoroquinolones (ciprofloxacin and levofloxacin), and third-generation tetracycline (tigecycline). Our three S. Kentucky strains were classified into the subclade ST198.2-2, and were genetically identical (2-6 SNPs) to each other. They exhibited a close genetic similarity (15-20 SNPs) to the isolate NT-h3189 from a patient and AH19MCS1 from chicken meat in China, indicating a possible epidemiological link between these S. Kentucky ST198 isolates from the patients and chicken meat. Long-term colonization of ciprofloxacin-resistant and ESBL-producing S. Kentucky ST198 in a single patient is a matter of concern. Due to the potential transfer of S. Kentucky ST198 from food sources to humans, ongoing surveillance of this particular clone in animals, animal-derived food products, and humans should be strengthened.

Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions.

Genomic epidemiology enhances the ability to detect and refute methicillin-resistant Staphylococcus aureus (MRSA) outbreaks in healthcare settings, but its routine introduction requires further evidence of benefits for patients and resource utilization. We performed a 12 month prospective study at Cambridge University Hospitals NHS Foundation Trust in the UK to capture its impact on hospital infection prevention and control (IPC) decisions. MRSA-positive samples were identified via the hospital microbiology laboratory between November 2018 and November 2019. We included samples from in-patients, clinic out-patients, people reviewed in the Emergency Department and healthcare workers screened by Occupational Health. We sequenced the first MRSA isolate from 823 consecutive individuals, defined their pairwise genetic relatedness, and sought epidemiological links in the hospital and community. Genomic analysis of 823 MRSA isolates identified 72 genetic clusters of two or more isolates containing 339/823 (41 %) of the cases. Epidemiological links were identified between two or more cases for 190 (23 %) individuals in 34/72 clusters. Weekly genomic epidemiology updates were shared with the IPC team, culminating in 49 face-to-face meetings and 21 written communications. Seventeen clusters were identified that were consistent with hospital MRSA transmission, discussion of which led to additional IPC actions in 14 of these. Two outbreaks were also identified where transmission had occurred in the community prior to hospital presentation; these were escalated to relevant IPC teams. We identified 38 instances where two or more in-patients shared a ward location on overlapping dates but carried unrelated MRSA isolates (pseudo-outbreaks); research data led to de-escalation of investigations in six of these. Our findings provide further support for the routine use of genomic epidemiology to enhance and target IPC resources.

Cancer epidemiological database linkage study of China: Design, methods, and quality evaluation.

Cancer epidemiological database linkage study of China: Design, methods, and quality evaluation.

Use of whole genomic sequencing to detect New Delhi metallo-B-lactamase (NDM)-producing Escherichia coli outbreak associated with endoscopic procedures.

Whole-genome sequencing (WGS) has emerged as an alternative genotyping tool for outbreak investigations in the healthcare setting. We describe the investigation and control of a New Delhi metallo-B-lactamase (NDM)-producing Escherichia coli cluster in Southeast Michigan. Michigan Bureau of Laboratories identified several closely related NDM-producing E. coli isolates with WGS. An epidemiologic investigation, including case-control study, assessment of infection control practices, and endoscope culturing, was performed to identify source of transmission. Targeted screening of potentially exposed patients was performed following identification of probable source. Between July 2021 and February 2023, nine patients were identified. Phylogenetic analysis confirmed the isolates were closely related with less than 26 single nucleotide polymorphism (SNP) differences between isolates, suggesting an epidemiological link. Eight (89%) patients had a duodenoscope and/or gastroscope exposure. Cases were compared with 23 controls. Cases had significantly higher odds of exposure to duodenoscopes (odds ratio 15.0; 95% CI, 1.8-142.2; P=.015). The mean incubation period, estimated as date of procedure to positive index culture, was 86 days (range, 1-320 days). No lapses in endoscope reprocessing were identified; NDM-producing E. coli was not recovered from reprocessed endoscopes or during targeted screening. No additional cases were identified after removal of implicated gastroscopes and replacement of duodenoscope with disposable end caps. In this investigation, WGS was utilized to identify transmission of an NDM-producing E. coli outbreak associated with endoscope exposure. Coupled with epidemiologic data, WGS can facilitate outbreak investigations by rapidly identifying linked cases and potential sources to prevent further transmission.