Impact of the COVID-19 Pandemic on the Reported Incidence of Select Bacterial Enteric Diseases in Canada, 2020.

The aim of this study was to describe the impact of the COVID-19 pandemic on reported cases and clusters of select enteric diseases in Canada, for the period of March 2020 to December 2020. Weekly counts of laboratory confirmed cases of Salmonella, Shigella, Shiga toxin-producing Escherichia coli (STEC), and Listeria monocytogenes were obtained from laboratory surveillance data. These data were supplemented with epidemiological information on the suspected source of illness, collected for cases identified within whole genome sequencing clusters. Incidence rate ratios were calculated for each pathogen. All data were compared with a prepandemic reference period. Decreases in the number of reported cases in 2020 compared with the previous 5-year period were noted for Salmonella, Shigella, Escherichia coli O157, and non-O157 STEC. Reported number of cases for L. monocytogenes in 2020 remained similar to those of the previous 5-year period. There was a considerable decline (59.9%) in the number of cases associated with international travel compared with a 10% decline in the number of domestic cases. Comparison of reported incidence rates of clustered versus sporadic cases for each pathogen showed little variation. This study represents the first formal assessment of the impact of COVID-19 on reported enteric diseases in Canada. Reported case counts across several pathogens saw notable declines in 2020 compared with prepandemic levels, with restrictions on international travel playing a key role. Additional research is needed to understand how limitations on social gatherings, lock downs, and other public health measures have impacted enteric diseases.

Trends in the Rates of Extended-Spectrum-ß-Lactamase-Producing Enterobacterales Isolated from Urine Cultures during the COVID-19 Pandemic in Ontario, Canada.

Worldwide, extended-spectrum ß-lactamase (ESBL) rates are increasing at an alarming level with increasing rates of health care exposures, international travel, and antibiotic usage. In this study, we investigated whether enhanced social isolation, travel restrictions, and the reduced use of antibiotics in Ontario, Canada during coronavirus disease 2019 (COVID-19) pandemic had an impact on ESBL rates in urine cultures collected from the community and long-term-care (LTC) facilities across the province. Data from a total of 8.6 million urine cultures performed at LifeLabs Ontario from 2016 to 2021 were utilized for analysis. ESBL-producing Escherichia coli (ESBL Escherichia coli) and ESBL Klebsiella pneumoniae were identified using standard operating procedures. Data trends were estimated by interrupted time series (ITS) regression analysis. Among 2.3 million positive urine cultures, 48.9% and 7.2% grew E. coli and K. pneumoniae, of which 5.8% and 3.3% produced ESBLs, respectively. While the overall rate of ESBL isolation was higher in the pandemic period than in the prepandemic period, by ITS regression analysis of the monthly rates of ESBL isolation, decreasing trends were noted for ESBL E. coli in both the community and LTC facilities and for ESBL K. pneumoniae in the community. The ESBL K. pneumoniae rates in LTC facilities continued to increase throughout the COVID-19 period. By subgroup analysis for different genders, age groups, and local health integration network (LHIN) units, similar trends were seen in most cases (P < 0.05), except for a few densely populated LHINs where rate changes were not statistically significant. IMPORTANCE Community-onset urinary tract infections (UTIs) caused by ESBL-producing Enterobacterales, particularly E. coli and K. pneumoniae, are a major public health concern. In this study, we assessed the impact of COVID-19 on ESBL rates in urine cultures in Ontario, Canada. Our results show the recent epidemiology of ESBL-producing Enterobacterales in urine cultures from both the community and LTC facilities in Ontario, Canada, and the impact of COVID-19 restrictions on ESBL trends for the entire province as well as different subgroups of the population based on demographic and geographic characteristics. Our results may have important public health implications in the context of the gradual easing of COVID-19 restrictions.

Has the COVID-19 Pandemic Affected Community-Acquired Urinary Tract Infections in Children?

PURPOSE: To evaluate whether there were any changes in the rates of urinary tract infection (UTI) and antibiotic resistance in pediatric patients during the pandemic period. MATERIALS AND METHODS: Urine culture samples collected due to suspected UTI were searched retrospectively from our hospital database, and the patients with growth in urine culture were identified. They were divided into 2 groups as Group A (before COVID-19, March 11, 2019- March 11, 2020) and Group B (COVID-19 period, March 11, 2020- March 11, 2021). Also, COVID-19 period was divided into 3 subgroups (March 2020- June 2020: first epidemic peak, July 2020 - November 2020: normalization process, December 2020- March 2021: second epidemic peak). We adjusted the patient age as <1, 1-6 and 7-18 years. Age, gender, microorganism strain types, and their antibiotic resistance patterns were compared between the 2 groups Results: This cross-sectional study included 250 eligible patients (Group A, n=182 and Group B, n=68) with a mean age of 10.91 ± 5.58 years. The male/female ratio was higher in Group B than in Group A (p = .004). Incidence of UTIs was lower in the curfew and restriction periods due to epidemic peaks than normalization process (p = .001). The proportion of E.coli decreased from 80.2% to 61.8% during the pandemic period when compared to pre-pandemic period (p = .001). Group B had lower rates of resistance to ampicillin, fosfomycin and nitrofurantoin for E.coli than Group A (p = .001, p = .012 and p = .001, respectively). Also, Group B had higher rate of uncommon microorganisms and lower rate of resistance to nitrofurantoin for E.coli than Group A in patients aged 7-18 years (p = .003 and p = .023, respectively). CONCLUSION: Our study demonstrates that the ongoing COVID-19 pandemic process has caused alterations in community-acquired UTIs in children. More hygienic lifestyle may be considered as the main factor in this change.

The Challenge to Control Emergence of Antibiotic Resistance in Virulent Escherichia coli Isolates in Latin America.

The Latin American Coalition for Escherichia coli Research (LACER) was created as a network of investigators using One Health approaches trying to understand infections caused by regional E. coli isolates and to sound the alarm due to the evolution of strains that are multiresistant to antibiotics (resistome) that also display different virulence profiles (virulome). After the COVID19 pandemic, a major concern by investigators has been the appearance of more virulent and resistant strains. Recently, a paper published in Microbiology Spectrum by Brazilian investigators (Fuga B., et al. Microbiol Spectr 10:e0125621, 2022, https://doi.org/10.1128/spectrum.01256-21) has used a genomic approach to demonstrate that during a period of 45 years, a wide resistome and virulome has converged, resulting in the appearance and persistence of high-risk clones affecting humans, animals and the environment, and its rapid dissemination is becoming an unattended international threat.

Multidrug-resistant enteroaggregative Escherichia coli (EAEC) enters dormant state during heat treatment: A potential hazard in municipal sludge.

Reuse of sewage sludge is a general trend and land application is an essential way to reuse sludge. The outbreak of coronavirus disease has raised concerns about human pathogens and their serious threat to public health. The risk of pathogenic bacterial contamination from land application of municipal sludge has not been well assessed. The purpose of this study was to investigate the presence of pathogenic bacteria in municipal sewage sludge and to examine the survival potential of certain multidrug-resistant enteroaggregative Escherichia coli (EAEC) strain isolated from sewage sludge during heat treatment. The sewage sludge produced in the two wastewater treatment plants contained pathogenic bacteria such as pathogenic E. coli, Shigella flexneri, and Citrobacter freundii. The environmental strain of EAEC isolated from the sludge was resistant to eight types of antibiotics. It could also enter the dormant state after 4.5 h of treatment at 55 °C and regrow at 37 °C, while maintaining its antibiotic resistance. Our results indicate that the dormancy of EAEC might be why it is heat-resistant and could not be killed completely during the sludge heat treatment process. Owing to the regrowth of the dormant pathogenic bacteria, it is risky to apply the sludge to land even if the sludge is heat-treated, and there is also a risk of spreading antibiotic resistance.

Co-infection of Uropathogenic Escherichia coli among COVID-19 Patients Admitted to a Tertiary Care Centre: A Descriptive Cross-sectional Study.

Introduction: Simultaneous infection of antibiotic-resistant uropathogens in patients with COVID-19 has necessitated the revision of the prescription of broad-spectrum antibiotics on the grounds of evidence-based studies and antimicrobial stewardship principles. The objective of this study was to find out the prevalence of uropathogenic Escherichia coli co-infection among hospital-admitted COVID-19 patients of a tertiary care centre. Methods: This descriptive cross-sectional study was conducted in urinary tract infection suspected COVID-19 patients admitted to a tertiary care hospital, from 25th June to 24th December 2021 after ethical clearance from the Institutional Review Committee with registration number 207707860. Convenience sampling was used. Serum procalcitonin levels were also measured. Data analysis was performed using the Statistical Package for the Social Sciences software version 17.0. Point estimate at 95% Confidence Interval was calculated along with frequency and proportion for binary data, and mean and standard deviation for continuous data. Results: Among the 49 hospital-admitted COVID-19 patients, 3 (6.12%) (0.59-12.83 at 95% Confidence Interval) were co-infected with uropathogenic Escherichia coli. Absolute non-susceptibility of Escherichia coli to antibiotics such as ceftriaxone, cotrimoxazole, nalidixic acid, gentamicin, and ampicillin was observed. All isolates were multidrug-resistant. All co-infected patients were female and had a median age of 35 years. Mean±SD value for procalcitonin in patients with co-infection (6.13±7.88 ng/ml) was six times higher than for the patients without co-infection (0.95±1.11 ng/ml). Conclusions: Escherichia coli co-infection in hospitalised COVID-19 patients was less frequent as compared to published literature. The serum procalcitonin value in patients with co-infection was substantially higher than that of patients without co-infection. Keywords: antimicrobial drug resistance; co-infection; COVID-19; Escherichia coli; procalcitonin.

Outbreak of NDM-1-Producing Escherichia coli in a Coronavirus Disease 2019 Intensive Care Unit in a Mexican Tertiary Care Center.

Emergency department areas were repurposed as intensive care units (ICUs) for patients with acute respiratory distress syndrome during the initial months of the coronavirus disease 2019 (COVID-19) pandemic. We describe an outbreak of New Delhi metallo-ß-lactamase 1 (NDM-1)-producing Escherichia coli infections in critically ill COVID-19 patients admitted to one of the repurposed units. Seven patients developed infections (6 ventilator-associated pneumonia [VAP] and 1 urinary tract infection [UTI]) due to carbapenem-resistant E. coli, and only two survived. Five of the affected patients and four additional patients had rectal carriage of carbapenem-resistant E. coli. The E. coli strain from the affected patients corresponded to a single sequence type. Rectal screening identified isolates of two other sequence types bearing blaNDM-1. Isolates of all three sequence types harbored an IncFII plasmid. The plasmid was confirmed to carry blaNDM-1 through conjugation. An outbreak of clonal NDM-1-producing E. coli isolates and subsequent dissemination of NDM-1 through mobile elements to other E. coli strains occurred after hospital conversion during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. This emphasizes the need for infection control practices in surge scenarios. IMPORTANCE The SARS-CoV-2 pandemic has resulted in a surge of critically ill patients. Hospitals have had to adapt to the demand by repurposing areas as intensive care units. This has resulted in high workload and disruption of usual hospital workflows. Surge capacity guidelines and pandemic response plans do not contemplate how to limit collateral damage from issues like hospital-acquired infections. It is vital to ensure quality of care in surge scenarios.

High levels of gut carriage of antimicrobial-resistant Escherichia coli in community settings in Rio de Janeiro, Brazil.

The prevalence and risk factors for gut carriage of antimicrobial-resistant Escherichia coli among individuals living in the community in Rio de Janeiro, Brazil, are unknown. The aim of this study was to determine the prevalence of colonization with antimicrobial-resistant E. coli, including isolates producing ESBL and harboring plasmid-mediated quinolone resistant (PMQR) genes in this community. We performed a cross-sectional study and analyzed fecal specimens of individuals attending outpatient clinics in the city from January 2015 to July 2019. We investigated susceptibility to antimicrobial agents by disc diffusion tests and used PCR to determine ESBL types, PMQR, and the virulence genes that characterize an isolate as extraintestinal pathogenic E. coli (ExPEC). Among the 623 subjects, 212 (34%) carried an isolate resistant to at least one of the tested antimicrobial agents, with the highest frequencies of resistance to ampicillin (26%), trimethoprim-sulfamethoxazole (19%), cefazolin (14%), and ciprofloxacin (CIP, 9%). In addition, 13% (81) of subjects carried a multidrug-resistant-E. coli (MDR-E), including 47 (8% of all isolates) ESBL-producing E. coli (ESBL-E), mainly of CTX-M-8 (15, 32%) and CTX-M-15 (9, 20%) types. PMQR genes were present in 7% (42) of all isolates, including 60% (32) of the 53 resistant to CIP. Previous use of antimicrobial agents, particularly fluoroquinolones, was a risk factor for colonization with MDR-E (25%, 20/81 vs 13%, 70/542, p = 0.01), ESBL-E (28%, 13/47, vs 13%, 77/576, p = 0.01), and resistance to CIP (26%, 14/53, vs 12%, 70/570, p = 0.01). The most pathogenic phylogroups B2, C, and D were 37% of the MDR-E, 30% of the ESBL-E, 38% of the CIP-resistant, and 31% of PMQR gene carrying E. coli isolates. We show that carriage of MDR-E (mostly ESBL-E) reached high levels in the community in Rio de Janeiro, increased by the selection of antimicrobial agents. Much of the resistant E. coli isolates are potential pathogenic strains. The widespread use of antimicrobial agents during the COVID-19 pandemic in Brazil may have worsened this picture.

Protective effect of SARS-CoV-2 preventive measures against ESKAPE and Escherichia coli infections.

BACKGROUND/OBJECTIVES: We investigated whether behavioral precautions adopted during Coronavirus disease (COVID-19) pandemic also influenced the spreading and multidrug resistance (MDR) of ESKAPEEc (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii [AB], Pseudomonas aeruginosa, Enterobacter spp and Escherichia Coli, [EC]) among Intensive Care Unit (ICU) patients. SUBJECTS/METHODS: We performed a single-center retrospective study in adult patients admitted to our COVID-19-free surgical ICU. Only patients staying in ICU for more than 48 hours were included. The ESKAPEEc infections recorded during the COVID-19 period (June 1, 2020 - February 28, 2021) and in the corresponding pre-pandemic period (June 1, 2019 - February 28, 2020) were compared. An interrupted time series analysis was performed to rule out possible confounders. RESULTS: Overall, 173 patients in the COVID-19 period and 132 in the pre-COVID-19 period were investigated. The ESKAPEEc infections were documented in 23 (13.3%) and 35 (26.5%) patients in the pandemic and the pre-pandemic periods, respectively (p = 0.005). Demographics, diagnosis, comorbidities, type of surgery, Simplified Acute Physiology Score II, length of mechanical ventilation, hospital and ICU length of stay, ICU death rate, and 28-day hospital mortality were similar in the two groups. In comparison with the pre-pandemic period, no AB was recorded during COVID-19 period, (p = 0.017), while extended-spectrum beta-lactamase-producing EC infections significantly decreased (p = 0.017). Overall, the ESKAPEEc isolates during pandemic less frequently exhibited multidrug-resistant (p = 0.014). CONCLUSIONS: These findings suggest that a robust adherence to hygiene measures together with human contact restrictions in a COVID-19 free ICU might also restrain the transmission of ESKAPEEc pathogens.

Decreasing proportion of extended-spectrum beta-lactamase among E. coli infections during the COVID-19 pandemic in France.

OBJECTIVES: We investigated the impact of the COVID-19 and national pandemic response on the epidemiology of Extended Spectrum Beta-Lactamase producing E. coli (ESBL-E.coli) in France. METHODS: Individual microbiology records from clinical laboratories were analyzed between 1 January 2019 to 31 December 2020. The ESBL-E.coli rates from clinical samples of patients in primary care and nursing home residents were compared before and after the general lockdown in March 2020, according to demographic and geographical characteristics. Interrupted time series analyses were performed to detect measurable changes in the trend of ESBL-E.coli rates. RESULTS: Records covering 793,954 E. coli isolates from 1022 clinical laboratories were analyzed. In primary care, 3.1% of E. coli isolates from clinical samples were producing ESBL before March 2020 and 2.9% since May 2020 (p < 0.001). The proportion of ESBL-E.coli decreased significantly among urine cultures, females, age categories 5-19, 40-64, > 65 year-old, and in the North, West, East and South-East regions. In nursing home, the ESBL-E.coli rate was 9.3% (monthly rate min-max: 6.5-10.5%) before March 2020 and 8.3% (7.2-9.1%) since May 2020 (p < 0.001). The reduction rate accelerated from -0.04%/month to -0.22%/month from May 2020 (p < 0.001). CONCLUSION: Investigation of factors that led to the decreased proportion of ESBL-E.coli during the COVID-19 pandemic is urgently needed.

Daily inpatient ertapenem therapy can be an alternative to hospitalization for the treatment of complicated urinary tract infections during the COVID-19 pandemic.

BACKGROUND: Physicians hospitalize the patients with complicated urinary tract infections (cUTIs) when they need intravenous antibiotics and outpatient parenteral antimicrobial therapy (OPAT) is unavailable. Daily inpatient antimicrobial therapy is an alternative to hospitalization, which is similar to OPAT; patients go home after they are administered antibiotics in a separate room in the hospital setting. OBJECTIVES: We assessed our previous daily inpatient practice to revitalize the model in the COVID-19 era. MATERIALS AND METHODS: We retrospectively evaluated the clinical and microbiological responses and the cost effectiveness of the patients with cUTIs who received daily inpatient ertapenem therapy. RESULTS: Our study population was 136 patients in 156 episodes. It was a difficult-to-treat group with older age (mean 63.0 ± 14.8 years) and a high burden of underlying conditions (86.5%). The most common causative organisms were Escherichia coli (74.4%) and Klebsiella pneumoniae (19.2%); 89.7% of the isolates were producing extended-spectrum beta lactamase (ESBL). The microbiologic and clinical success rates were 82.1% and 95.5%, respectively. The patients required hospitalization in 16 episodes (10.2%) because of clinical failures (3.8%), superinfections (2%), planned invasive interventions (3.2%), and side effects (1.2%). Our university hospital saved 1608 bed-days and 2596 € (9702 TL) bed costs. CONCLUSIONS: In the COVID-19 pandemic period, this seems to be an effective, safe, and cost-effective way to decrease hospitalizations for cUTIs in settings where OPAT is unavailable.

Infectious disease surveillance of apparently healthy horses at a multi-day show using a novel nanoscale real-time PCR panel.

In the United States, horses are used for a variety of purposes including recreation, exhibition, and racing. As farm, performance, and companion animals, horses are a unique species from a zoonotic disease risk perspective, and the risks of subclinical infections spreading among horses can pose challenges. Using a nanoscale real-time PCR platform, we investigated the prevalence of 14 enteric pathogens, 11 Escherichia coli genes, and 9 respiratory pathogens in fecal samples from 97 apparently healthy horses at a multi-day horse event. In addition, sugar flotation test was performed for fecal parasites. E. coli f17 was commonly detected, prevalent in 59% of horses, followed closely by Streptococcus equi subsp. zooepidemicus (55%). Additional pathogens recognized included betacoronavirus, Campylobacter jejuni, Cryptosporidium sp., E. coli O157, equine adenovirus 1, equine rhinitis B virus, and others. The use of PCR data may overestimate the true prevalence of these pathogens but provides a sensitive overview of common pathogens present in healthy horses. Our results prompt the continued need for practical biosecurity measures at horse shows, both to protect individuals interacting with these horses and to minimize transmission among horses.

Rates of bacterial co-infections and antimicrobial use in COVID-19 patients: a retrospective cohort study in light of antibiotic stewardship.

The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. Bacterial co-infections are associated with unfavourable outcomes in respiratory viral infections; however, microbiological and antibiotic data related to COVID-19 are sparse. Adequate use of antibiotics in line with antibiotic stewardship (ABS) principles is warranted during the pandemic. We performed a retrospective study of clinical and microbiological characteristics of 140 COVID-19 patients admitted between February and April 2020 to a German University hospital, with a focus on bacterial co-infections and antimicrobial therapy. The final date of follow-up was 6 May 2020. Clinical data of 140 COVID-19 patients were recorded: The median age was 63.5 (range 17-99) years; 64% were males. According to the implemented local ABS guidelines, the most commonly used antibiotic regimen was ampicillin/sulbactam (41.5%) with a median duration of 6 (range 1-13) days. Urinary antigen tests for Legionella pneumophila and Streptococcus peumoniae were negative in all cases. In critically ill patients admitted to intensive care units (n = 50), co-infections with Enterobacterales (34.0%) and Aspergillus fumigatus (18.0%) were detected. Blood cultures collected at admission showed a diagnostic yield of 4.2%. Bacterial and fungal co-infections are rare in COVID-19 patients and are mainly prevalent in critically ill patients. Further studies are needed to assess the impact of antimicrobial therapy on therapeutic outcome in COVID-19 patients to prevent antimicrobial overuse. ABS guidelines could help in optimising the management of COVID-19. Investigation of microbial patterns of infectious complications in critically ill COVID-19 patients is also required.

First report on Cryptosporidium parvum, Escherichia coli K99, rotavirus and coronavirus in neonatal lambs from north-center region, Algeria.

The etiology of neonatal diarrhea is multifactorial and remains one of the greatest health problems in sheep livestock farming. Faecal samples from 559 neonatal lambs aged less than 30 days from 30 sheepfolds located in the north-center region of Algeria were screened with pathogen-specific antigen ELISA for Cryptosporidium parvum, Escherichia coli K99, rotavirus, and coronavirus. Of the 559 lambs, 312 (58.81 %), 155 (27.72 %), 72 (12.88 %) and 20 (3.57 %) were positives for C. parvum, E. coli K99, rotavirus and coronavirus antigens, respectively. The prevalence of C. parvum was the highest (p < 0.0001). C. parvum, E. coli K99, rotavirus and coronavirus were observed in 23 (76.66 %), 17 (56.66 %), 9 (30 %) and 3 (10 %) sheepfolds, respectively. Compared to age, the prevalence of C. parvum was highest during the second and third week of age (p < 0.001). In contrast, other pathogens were found to be more frequent in lambs aged ≤7 days (p < 0.001). The number of lambs with diarrhea was 280 (50.09 %) of which 280 (100 %), 127 (45.35 %), 52 (18.57 %) and 10 (3.57 %) were found to be infected with C. parvum, E. coli K99, rotavirus and coronavirus, respectively (p < 0.0001). In various combinations, mixed infections were detected only with C. parvum. This is the first report of C. parvum, E. coli K99, rotavirus, and coronavirus in ≤30-days old neonatal lambs in Algeria. Special attention should be given to the first colostrum feeding, hygiene of the farm, prevention and control measures for a better prevention of neonatal diarrhea in lambs.