Evidence Of Co-infection Research Articles

COVID-19 bacteremic co-infection is a major risk factor for mortality, ICU admission, and mechanical ventilation

BackgroundRecent single-center reports have suggested that community-acquired bacteremic co-infection in the context of Coronavirus disease 2019 (COVID-19) may be an important driver of mortality; however, these reports have not been validated with a multicenter, demographically diverse, cohort study with data spanning the pandemic.MethodsIn this multicenter, retrospective cohort study, inpatient encounters were assessed for COVID-19 with community-acquired bacteremic co-infection using 48-h post-admission blood cultures and grouped by: (1) confirmed co-infection [recovery of bacterial pathogen], (2) suspected co-infection [negative culture with ≥ 2 antimicrobials administered], and (3) no evidence of co-infection [no culture]. The primary outcomes were in-hospital mortality, ICU admission, and mechanical ventilation. COVID-19 bacterial co-infection risk factors and impact on primary outcomes were determined using multivariate logistic regressions and expressed as adjusted odds ratios with 95% confidence intervals (Cohort, OR 95% CI, Wald test p value).ResultsThe studied cohorts included 13,781 COVID-19 inpatient encounters from 2020 to 2022 in the University of Alabama at Birmingham (UAB, n = 4075) and Ochsner Louisiana State University Health—Shreveport (OLHS, n = 9706) cohorts with confirmed (2.5%), suspected (46%), or no community-acquired bacterial co-infection (51.5%) and a comparison cohort consisting of 99,170 inpatient encounters from 2010 to 2019 (UAB pre-COVID-19 pandemic cohort). Significantly increased likelihood of COVID-19 bacterial co-infection was observed in patients with elevated ≥ 15 neutrophil-to-lymphocyte ratio (UAB: 1.95 [1.21–3.07]; OLHS: 3.65 [2.66–5.05], p < 0.001 for both) within 48-h of hospital admission. Bacterial co-infection was found to confer the greatest increased risk for in-hospital mortality (UAB: 3.07 [2.42–5.46]; OLHS: 4.05 [2.29–6.97], p < 0.001 for both), ICU admission (UAB: 4.47 [2.87–7.09], OLHS: 2.65 [2.00–3.48], p < 0.001 for both), and mechanical ventilation (UAB: 3.84 [2.21–6.12]; OLHS: 2.75 [1.87–3.92], p < 0.001 for both) across both cohorts, as compared to other risk factors for severe disease. Observed mortality in COVID-19 bacterial co-infection (24%) dramatically exceeds the mortality rate associated with community-acquired bacteremia in pre-COVID-19 pandemic inpatients (5.9%) and was consistent across alpha, delta, and omicron SARS-CoV-2 variants.ConclusionsElevated neutrophil-to-lymphocyte ratio is a prognostic indicator of COVID-19 bacterial co-infection within 48-h of admission. Community-acquired bacterial co-infection, as defined by blood culture-positive results, confers greater increased risk of in-hospital mortality, ICU admission, and mechanical ventilation than previously described risk factors (advanced age, select comorbidities, male sex) for COVID-19 mortality, and is independent of SARS-CoV-2 variant.

Evolutionary analysis of rabies virus isolates from Georgia.

Genetic relationships between rabies virus (RABV) isolates recovered from dogs, jackals, and cattle in Georgia and their closest relatives were investigated by comparing their nucleoprotein (N) gene sequences. Multiple isolates from dogs and cattle were found to share identical N gene sequences, indicating a risk of dog-to-cattle rabies transmission in Georgia. Exhibiting population-selective sweeps, expansion, and genetic recombination, evolutionary analysis of Georgian RABV isolates (all belonging to the cosmopolitan clade) and isolates from Russia, Turkey, and elsewhere provided further evidence for coinfections with different rabies virus strains and transborder transmission.

Evidence of co-infections during Delta and Omicron SARS-CoV-2 variants co-circulation through prospective screening and sequencing

ObjectivesTo describe Delta/Omicron SARS-CoV-2 variants co-infection detection and confirmation during the fifth wave of COVID-19 pandemics in France in 7 immunocompetent and epidemiologically unrelated patients. MethodsSince December 2021, the surveillance of Delta/Omicron SARS-CoV-2 variants of concern (VOC) circulation was performed through prospective screening of positive-samples using single nucleotide polymorphism (SNP) PCR assays targeting SARS-CoV-2 S-gene mutations K417N (Omicron specific) and L452R (Delta specific). Samples showing unexpected mutational profiles were further submitted to whole genome sequencing (WGS) using three different primer sets. ResultsBetween weeks 49-2021 and 02-2022, SARS-CoV-2 genome was detected in 3831 respiratory samples, of which 3237 (84.5%) were screened for VOC specific SNPs. Unexpected mutation profiles suggesting a dual Delta/Omicron population were observed in 7 nasopharyngeal samples (0.2%). These co-infections were confirmed by WGS. For 2 patients, the sequence analyses of longitudinal samples collected 7 to 11 days apart showed that Delta or Omicron can outcompete the other variant during dual infection. Additionally, for one of these samples, a recombination event between Delta and Omicron was detected. ConclusionsThis work demonstrates that SARS-CoV-2 Delta/Omicron co-infections are not rare in high virus co-circulation periods. Moreover, co-infections can further lead to genetic recombination which may generate new chimeric variants with unpredictable epidemic or pathogenic properties that could represent a serious health threat.

P30 Bacterial coinfection and prescribing trends in SARS-CoV-2 infection in two UK hospitals

ObjectivesTo describe antibiotic prescribing and early bacterial and fungal coinfection in patients admitted to two London hospitals with COVID-19.MethodsA retrospective review of adults with PCR-confirmed SARS-CoV-2 infection admitted between 9 February and 10 May 2020. Demographics, critical care unit (CCU) admission, antibiotic prescribing and microbiology results within 10 days of COVID-19 diagnosis were analysed.ResultsIn total, 1155 patients were identified; 32.9% (380) died during admission and 12.4% (143) had positive microbiology. After excluding likely contaminants, 6.9% (80) had evidence of coinfection. The most common organisms isolated from blood cultures were Escherichia coli 9.5% (7), Klebsiella pneumoniae 4.0% (3), and MSSA 2.7% (2). Organisms isolated from lower respiratory tract samples included Candida albicans 44.4% (12), Staphylococcus aureus 22.2% (6), Klebsiella species 11.0% (3), Pseudomonas aeruginosa 11.0% (3) and Citrobacter species 11% (3). Legionella and pneumococcal urinary antigen tests were positive in 0/117 and 2/71 episodes, respectively. Patients admitted to CCU during their inpatient stay were more likely to have positive microbiology compared with patients managed outside CCU (26.2% versus 11.0%, P<0.001). Ninety-one percent (1051) of all patients received antibiotics. Clarithromycin (24.2% total antibiotic use) and amoxicillin (21%) were most frequently used, followed by piperacillin/tazobactam (12.6%), gentamicin (10.6%), co-amoxiclav (9.3%) and meropenem (3.2%). Patients given piperacillin/tazobactam or meropenem had a higher length of stay and mortality.ConclusionsBacterial coinfection in COVID-19 is uncommon, but more frequent in patients requiring CCU admission. Antibiotic use was widespread, despite lack of microbiological evidence of coinfection. When present, infection was more likely due to Gram-negative bacteria. Future local clinical and antimicrobial guidelines should reflect these findings.

Evidence of Coinfections between SARS-CoV-2 and Select Arboviruses in Guerrero, Mexico, 2020-2021.

ABSTRACT.We provide evidence of concurrent and close sequential infections between SARS-CoV-2 and select arboviruses—namely, chikungunya virus (CHIKV); dengue viruses 1, 2, and 3 (DENV1–3), and Zika virus (ZIKV)—in patients in Guerrero, southwest Mexico, in 2020–2021. The study population consisted of 176 febrile patients with laboratory evidence of SARS-CoV-2 infection. Sera from all patients were serologically and antigenically tested for seven arboviruses known to occur in Guerrero. Eighteen patients contained CHIKV IgM, six of whom also contained CHIKV RNA. Another 16 patients contained flavivirus antigen. The flaviviruses responsible for the infections were identified by plaque reduction neutralization test as DENV1 (two patients), DENV2 (five patients), DENV3 (three patients), ZIKV (three patients), and an undetermined flavivirus (three patients). In summary, we identified patients in Guerrero, Mexico, with concurrent or recent sequential infections between SARS-CoV-2 and select arboviruses, exemplifying the importance of performing differential diagnosis in regions where these viruses cocirculate.

Urinary antigen testing for respiratory infection during COVID-19: The microbiologist as a diagnostic steward

The use of antimicrobials in the management of community-acquired COVID-19 is commonplace but evidence for coinfection with common bacterial pathogens to justify their use is lacking. We undertook a retrospective review of all respiratory cultures, blood cultures and urinary antigen tests in COVID-19 patients looking for co-infection with Streptococcus pneumoniae and Legionella pneumophila, and specifically to judge the utility of urinary antigen testing. 2674 GSTT patients were included who had a positive RT-PCR test for SARS-CoV-2 performed at GSTT between 03-March-2020 and 31-Jan-2021 and who had at least one other microbiology sample for review.

Occurrence of maize yellow mosaic virus and evidence of co-infection with maize lethal necrosis viruses in Bomet County, Kenya

Maize Lethal Necrosis (MLN) disease is caused by synergistic interaction between maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV). However, some East African countries have detected maize infecting polerovirus named maize yellow mosaic virus (MaYMV) also known as maize yellow dwarf virus (MYDV-RMV) co-infecting maize with MLN viruses. Maize yellow dwarf virus occurrence and distribution in different parts of Kenya are not yet elucidated. This study aimed to establish the occurrence of MaYMV in maize and sorghum in Bomet County, MLN hotspot region in Kenya. Maize (n=90) and sorghum (n=19) samples were collected from East and Central sub-counties of Bomet County in 2019/2020. Reverse transcription-polymerase chain reaction (RT-PCR) protocol was developed and optimized for screening the samples using specific primers. Amplicons of 600, 250 and 169 bp were generated for MaYMV, MCMV and SCMV, respectively. The analysis revealed 56% (62/109) of the samples tested positive for MaYMV co-infecting maize with MLN viruses. Sanger sequencing of representative samples confirmed the presence of MaYMV. BLASTN analysis showed 95-100% sequence identity to MaYMV/MYDV-RMV hence confirmed the occurrence of MaYMV infecting maize and sorghum in Bomet County whose impacts is a potential threat to food security. Key words: Occurrence, co-infection, maize lethal necrosis, maize yellow mosaic virus, maize chlorotic mottle virus, sugarcane mosaic virus.

Bartonella spp. seroprevalence in tick-exposed Swedish patients with persistent symptoms

BackgroundBartonella spp. are emerging pathogens transmitted by arthropod vectors, possibly including ticks. We have investigated signs of bartonellosis in Swedish patients with presumed tick-bite exposure and symptom duration of at least 6 months.MethodsSerological testing for Bartonella henselae and Bartonella quintana was performed in 224 patients. Symptoms, tick exposure, evidence of co-infection and previous treatments were evaluated. Seropositive patients were compared to a matched group (twofold larger and negative serology) from the same study cohort.ResultsSeroprevalence was 7% for B. henselae and 1% for B. quintana, with one patient testing positive to both agents. Tick bites were reported by 63% of the patients in the seropositive group and 88% in the seronegative group and presumed tick exposure was more common in the seronegative group. Animal contact was equally common in both groups, along with reported symptoms. The most common symptoms were fatigue, muscular symptoms, arthralgia and cognitive symptoms. Exposure to co-infections was evenly distributed in the seropositive and seronegative groups.ConclusionsAntibodies to Bartonella were more common in this cohort of patients than in cohorts of healthy Swedish blood donors in previous studies but lower than those in blood donors from southern Europe. Positive Bartonella serology was not linked to any specific symptom, nor to (suspected) tick-bite exposure.Graphical abstract

Intra-host evolution during SARS-CoV-2 prolonged infection.

Long-term infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents a challenge to virus dispersion and the control of coronavirus disease 2019 (COVID-19) pandemic. The reason why some people have prolonged infection and how the virus persists for so long are still not fully understood. Recent studies suggested that the accumulation of intra-host single nucleotide variants (iSNVs) over the course of the infection might play an important role in persistence as well as emergence of mutations of concern. For this reason, we aimed to investigate the intra-host evolution of SARS-CoV-2 during prolonged infection. Thirty-three patients who remained reverse transcription polymerase chain reaction (RT-PCR) positive in the nasopharynx for on average 18 days from the symptoms onset were included in this study. Whole-genome sequences were obtained for each patient at two different time points. Phylogenetic, populational, and computational analyses of viral sequences were consistent with prolonged infection without evidence of coinfection in our cohort. We observed an elevated within-host genomic diversity at the second time point samples positively correlated with cycle threshold (Ct) values (lower viral load). Direct transmission was also confirmed in a small cluster of healthcare professionals that shared the same workplace by the presence of common iSNVs. A differential accumulation of missense variants between the time points was detected targeting crucial structural and non-structural proteins such as Spike and helicase. Interestingly, longitudinal acquisition of iSNVs in Spike protein coincided in many cases with SARS-CoV-2 reactive and predicted T cell epitopes. We observed a distinguishing pattern of mutations over the course of the infection mainly driven by increasing A→U and decreasing G→A signatures. G→A mutations may be associated with RNA-editing enzyme activities; therefore, the mutational profiles observed in our analysis were suggestive of innate immune mechanisms of the host cell defense. Therefore, we unveiled a dynamic and complex landscape of host and pathogen interaction during prolonged infection of SARS-CoV-2, suggesting that the host’s innate immunity shapes the increase of intra-host diversity. Our findings may also shed light on possible mechanisms underlying the emergence and spread of new variants resistant to the host immune response as recently observed in COVID-19 pandemic.

Detection and Molecular Characterization of Two Gammaherpesviruses from Pantesco Breed Donkeys during an Outbreak of Mild Respiratory Disease.

Equid and asinine gammaherpesviruses (GHVs; genus Percavirus) are members of the Herpesviridae family. Though GHVs have been reported in horse populations, less studies are available on gammaherpesviral infections in donkeys. This study reports the co-infection with two GHVs in Pantesco breed donkeys, an endangered Italian donkey breed. Samples (n = 124) were collected on a breeding farm in Southern Italy from 40 donkeys, some of which were healthy or presented erosive tongue lesions and/or mild respiratory signs. Samples were analysed by using a set of nested PCRs targeting the DNA polymerase, glycoprotein B, and DNA-packaging protein genes, and sequence and phylogenetic analyses were performed. Twenty-nine donkeys (72.5%) tested positive, and the presence of Equid gammaherpesvirus 7 and asinine herpesvirus 5 was evidenced. In 11 animals, we found evidence for co-infection with viruses from the two species. Virions with herpesvirus-like morphology were observed by electron microscopic examination, and viruses were successfully isolated in RK-13-KY cell monolayers. The histological evaluation of tongue lesions revealed moderate lympho-granulocytic infiltrates and rare eosinophilic inclusions. The detection of GHVs in this endangered asinine breed suggests the need long-life monitoring within conservation programs and reinforces the need for further investigations of GHV’s pathogenetic role in asinine species.

Prevalence of Human Papillomavirus Genotypes in Pterygia from Thai Individuals

ABSTRACT Purpose Pterygium, a common ocular growth, has an unknown pathogenesis and aetiology. Environmental factors such as ultraviolet light, genetic factors and viral infections may be implicated in the development of pterygia. Human papillomavirus (HPV), an oncogenic virus, has previous been detected in individuals with pterygia. The aim of this study was to assess the prevalence of HPV genotypes in pterygia from Thai individuals. Methods DNA was extracted from 389 pterygia. HPV was detected by nested PCR and HPV genotyping was conducted using reverse hybridization. The DNA sequences of HPV-L1 genes were analyzed. Results HPV was detected in only 6.8% (25/389) of pterygia from Thai individuals. The majority (16/25, 64%) of strains were genotyped as HPV-16 and the remainder (9/25, 36%) could not be typed. Four pterygia showed evidence of coinfection by HPV-16 and either HPV-18 (2/25, 8%) or HPV-58 (2/25, 8%). Nine of 11 samples showed the same HPV-16 L1 gene sequence that was identical to a HPV-16 reference sequence in GenBank. The remaining two samples each bore silent single nucleotide mutations (T1078G and T1081A) that did not result in amino acid changes. Conclusion HPV, especially HPV-16, may be one of the pathogens causing pterygia in Thai individuals. Genotyping data suggested that HPV-16 from pterygia may be similar in sequence to HPV-16 causing cervical cancer.

Antimicrobial stewardship program in COVID-19 era: Ruin of the reign?

COVID-19 is the most important matter in the medical field worldwide in 2020. Although COVID-19 is a viral disease, the threshold to antibiotic prescription for COVID-19 patients is low, partly because of WHO recommendations and previous experiences from influenza, despite the lack of strong evidence of co-infection or superimposed bacterial infection in COVID-19 patients. Antibiotic stewardship program (ASP) could play an important role in this period, otherwise, we will face a crisis of superbugs in the early future.&#x0D; Keywords: COVID-19, Antibiotic stewardship program (ASP), Superbugs

Widespread zoophagy and detection of Plasmodium spp. in Anopheles mosquitoes in southeastern Madagascar

BackgroundMalaria is a top cause of mortality on the island nation of Madagascar, where many rural communities rely on subsistence agriculture and livestock production. Understanding feeding behaviours of Anopheles in this landscape is crucial for optimizing malaria control and prevention strategies. Previous studies in southeastern Madagascar have shown that Anopheles mosquitoes are more frequently captured within 50 m of livestock. However, it remains unknown whether these mosquitoes preferentially feed on livestock. Here, mosquito blood meal sources and Plasmodium sporozoite rates were determined to evaluate patterns of feeding behaviour in Anopheles spp. and malaria transmission in southeastern Madagascar.MethodsAcross a habitat gradient in southeastern Madagascar 7762 female Anopheles spp. mosquitoes were collected. Of the captured mosquitoes, 492 were visibly blood fed and morphologically identifiable, and a direct enzyme-linked immunosorbent assay (ELISA) was used to test for swine, cattle, chicken, human, and dog blood among these specimens. Host species identification was confirmed for multiple blood meals using PCR along with Sanger sequencing. Additionally, 1,607 Anopheles spp. were screened for the presence of Plasmodium falciparum, P. vivax-210, and P. vivax 247 circumsporozoites (cs) by ELISA.ResultsCattle and swine accounted, respectively, for 51% and 41% of all blood meals, with the remaining 8% split between domesticated animals and humans. Of the 1,607 Anopheles spp. screened for Plasmodium falciparum, Plasmodium vivax 210, and Plasmodium vivax 247 cs-protein, 45 tested positive, the most prevalent being P. vivax 247, followed by P. vivax 210 and P. falciparum. Both variants of P. vivax were observed in secondary vectors, including Anopheles squamosus/cydippis, Anopheles coustani, and unknown Anopheles spp. Furthermore, evidence of coinfection of P. falciparum and P. vivax 210 in Anopheles gambiae sensu lato (s.l.) was found.ConclusionsHere, feeding behaviour of Anopheles spp. mosquitoes in southeastern Madagascar was evaluated, in a livestock rich landscape. These findings suggest largely zoophagic feeding behaviors of Anopheles spp., including An. gambiae s.l. and presence of both P. vivax and P. falciparum sporozoites in Anopheles spp. A discordance between P. vivax reports in mosquitoes and humans exists, suggesting high prevalence of P. vivax circulating in vectors in the ecosystem despite low reports of clinical vivax malaria in humans in Madagascar. Vector surveillance of P. vivax may be relevant to malaria control and elimination efforts in Madagascar. At present, the high proportion of livestock blood meals in Madagascar may play a role in buffering (zooprophylaxis) or amplifying (zoopotentiation) the impacts of malaria. With malaria vector control efforts focused on indoor feeding behaviours, complementary approaches, such as endectocide-aided vector control in livestock may be an effective strategy for malaria reduction in Madagascar.

Co-distribution of dengue and Chikungunya viruses in Aedes mosquitoes of Delhi, India.

In India, vector-borne diseases, dengue and chikungunya are major public health concerns. In recent decades, dengue outbreaks have been reported in almost every part of India. In 2016, India recorded 101388 dengue cases and 210 deaths, including 4337 cases and six deaths in Delhi, whereas Chikungunya outbreaks were reported from several states in 2006, with 1.3 million cases. The Dengue virus (DENV) and Chikungunya virus (CHIKV) are both transmitted by the same Aedes mosquito species. DENV and CHIKV co-infections have been reported in 13 of 98 countries, with both viruses being transmitted locally. The reasons for the sudden upsurge in cases of these diseases are undetermined. From March to December 2016, a study was carried out in 66 localities of Delhi in collaboration with the Municipal Corporation of Delhi. Localities were selected on the basis of confirmed dengue cases reported during the last five years and the study area was visited once a month. A door-to-door entomological survey was conducted to identify Aedes breeding in all water-filled containers in and around houses. Both immature and mature stages of Aedes mosquitoes were collected. Mosquitoes were pooled (n≤10 each for male and female) breeding site-wise and stored in Trizol at -80°C. The Chikungunya and dengue viruses were detected using a multiplex RT-PCR. A total of 981 Aedes mosquitos were distributed among 146 Pools, and DENV and CHIKV were detected using Multiplex Reverse Transcriptase-PCR. Chikungunya virus was identified in 19 pools of females captured adults, whereas dengue virus was found in 8 pools of females captured adults. There was no evidence of coinfection in any of the pools. In endemic areas, continuous surveillance for both dengue and Chikungunya viruses is required to identify and characterize these viral pathogens. This information will also help implement effective strategies to combat outbreaks produced by these emerging viral pathogens.

Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections.

BackgroundIn December 2019, an ongoing outbreak of pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/ 2019-nCoV) infection was initially reported in Wuhan, Hubei Province, China. Early in 2020, the World Health Organization (WHO) announced a new name for the 2019-nCoV-caused disease: coronavirus disease 2019 (COVID-19) and declared COVID-19 to be a Public Health Emergency of International Concern (PHEIC). Cellular co-infection is a critical determinant of viral fitness and infection outcomes and plays a crucial role in shaping the host immune response to infections.MethodsIn this study, 68 public next-generation sequencing data from SARS-CoV-2 infected patients were retrieved from the NCBI Sequence Read Archive database using SRA-Toolkit. Data screening was performed using an alignment-free method based on k-mer mapping and extension, fastv. Taxonomic classification was performed using Kraken 2 on all reads containing one or more virus sequences other than SARS-CoV-2.ResultsSARS-CoV-2 was identified in all except three patients. Influenza type A (H7N9) virus, human immunodeficiency virus, rhabdovirus, human metapneumovirus, Human adenovirus, Human herpesvirus 1, coronavirus NL63, parvovirus, simian virus 40, and hepatitis virus genomes sequences were detected in SARS-CoV-2 infected patients. Besides, a very diverse group of bacterial populations were observed in the samples.

Mammalian deltavirus without hepadnavirus coinfection in the neotropical rodent Proechimys semispinosus

Hepatitis delta virus (HDV) is a human hepatitis-causing RNA virus, unrelated to any other taxonomic group of RNA viruses. Its occurrence as a satellite virus of hepatitis B virus (HBV) is a singular case in animal virology for which no consensus evolutionary explanation exists. Here we present a mammalian deltavirus that does not occur in humans, identified in the neotropical rodent species Proechimys semispinosus The rodent deltavirus is highly distinct, showing a common ancestor with a recently described deltavirus in snakes. Reverse genetics based on a tandem minus-strand complementary DNA genome copy under the control of a cytomegalovirus (CMV) promoter confirms autonomous genome replication in transfected cells, with initiation of replication from the upstream genome copy. In contrast to HDV, a large delta antigen is not expressed and the farnesylation motif critical for HBV interaction is absent from a genome region that might correspond to a hypothetical rodent large delta antigen. Correspondingly, there is no evidence for coinfection with an HBV-related hepadnavirus based on virus detection and serology in any deltavirus-positive animal. No other coinfecting viruses were detected by RNA sequencing studies of 120 wild-caught animals that could serve as a potential helper virus. The presence of virus in blood and pronounced detection in reproductively active males suggest horizontal transmission linked to competitive behavior. Our study establishes a nonhuman, mammalian deltavirus that occurs as a horizontally transmitted infection, is potentially cleared by immune response, is not focused in the liver, and possibly does not require helper virus coinfection.

Prevalence of B. pertussis infection in children with clinically suspected pertussis.

Pertussis is an important cause of hospitalization in children. Limited data on pertussis have been reported from China. The aim of this study was to characterize clinically suspected pertussis attributable to Bordetella pertussis among children and determine factors associated with longer duration of hospital stay in B. pertussis infection. Two hundred and seventeen consecutive children with clinically suspected pertussis were prospectively enrolled in the study between Jan 2016 through Aug 2017. Variables assessed included demographics, clinical symptoms and laboratory findings. Cox proportional hazards regression model were used to predict variables associated with longer duration of hospital stay. Among the 217 patients with clinically suspected pertussis, B. pertussis was found in 106 (48.8%) patients. Of the 106 children with B. pertussis infection, 63 (59.4%) patients had coinfections with majority due to rhinovirus (HRV) (30.2%), Mycoplasma pneumoniae (29.2%) and human bocavirus (hBoV) (11.3%). Presence of coinfection [odds ratio (OR): 1.73, CI: 1.17-2.54], age≤3 months (OR: 1.51, CI: 1.09 to 2.27), and WBC count ≥30×109/L (OR: 1.66, CI: 1.07 to 2.84) were independently associated with a longer hospital stay. B. pertussis infection had a high coinfection rate with the majority of coinfections due to HRV, M. pneumoniae and hBoV. Presence of coinfection, Age ≤3 months and WBC count ≥30×109/L were associated with a longer hospital stay. Children admitted with pertussis need close monitoring when they had evidence of coinfection, Age ≤3 months, WBC count ≥30×109/L.

Coinfection of Severe Fever with Thrombocytopenia Syndrome and Scrub Typhus in Patients with Tick-Borne Illness.

Severe fever with thrombocytopenia syndrome (SFTS) and scrub typhus are the most common tick-borne diseases in South Korea. However, few studies have systematically examined the simultaneous presence of the two diseases. We found that two (4.9%) of 41 patients with suspected and confirmed SFTS had evidence of coinfection with scrub typhus. In addition, two (3.6%) of 55 suspected and confirmed scrub typhus patients were identified to have coinfection with SFTS. Our data suggest that diagnostic evaluation for coinfection in patients with tick-borne illness and empirical doxycycline treatment in patients with SFTS may be warranted in areas endemic for both diseases until coinfection with scrub typhus is ruled out.

1703. Bacterial or Fungal Co-Infection in Patients with Mucormycosis

BackgroundThere is a growing concern on infections with multiple organisms including fungi in patients with mucormycosis. However, limited data are available on co-infection in patients with mucormycosis.MethodsPatients with proven mucormycosis were retrospectively enrolled at a tertiary hospital from July 2009 to January 2019. Proven mucormycosis was defined as positive fungal culture result for mucormycosis from a sterile biopsy specimen and/or histologic evidence of tissue invasion of hyphae with positive mucormycosis immunohistochemistry test result. We reviewed other pathogens isolated from sterile or non-sterile sites before and after 7 days from the biopsy for infected tissue that suggested invasive fungal infection.ResultsA total of 61 patients with proven mucormycosis were analyzed. The primary site of infection was as follows; lung (n = 38, 62.3%), rhino-sinus (n = 21, 34.4%), and orbito-cerebral (n = 15, 24.6%). Based on sterile culture results, 4 patients (6.6%) had the evidence of co-infection with other fungi including Candida species (from 3 cases; C. albicans from 1, C. glabrata from 1 and C. krusei from 1), A. flavus (1), and F. solani (1), and 23 patients (37.7%) had the evidence of co-infection with bacteria including E. faecium (VRE) (8), P. aeruginosa (5),coagulase-negative staphylococci (5), methicillin-susceptible S. aureus (4) and others. Based on non-sterile culture results, 10 patients (16.4%) had the evidence of co-infection with fungi other than mucormycosis including Aspergillus species (5, A. fumigatus from 1, Aspergillus not fumigatus from 1 and A. oryzae from 1), Candida species (5, C. albicans from 2, C. tropicalis from 2 and C. glabrata from 1), Penicillium species (1), S. cerevisiae (1) and P. jirovecii (1), and 24 patients (39.3%) had evidence of bacterial co-infection including S. maltophilia (5), methicillin-resistant S. aureus (5), E. faecium (VSE) (3), K. pneumonia (3), P. aeruginosa (3), and others.ConclusionBacterial or fungal co-infections appear to frequently occur as appreciated before in patients with mucormycosis. These data provide us important information to select empirical antifungal and antibacterial agents. Disclosures All authors: No reported disclosures.

Avian influenza H9N2 subtype in Ghana: virus characterization and evidence of co-infection

ABSTRACTBetween November 2017 and February 2018, Ghanaian poultry producers reported to animal health authorities a dramatic increase in mortality rate and a relevant drop in egg production in several layer hen farms. Laboratory investigations revealed that the farms had been infected by the H9N2 influenza subtype. Virological and molecular characterization of the viruses identified in Ghana is described here for the first time. Whole genome analysis showed that the viruses belong to the G1-lineage and cluster with viruses identified in North and West Africa. The low pathogenicity of the virus was confirmed by the intravenous pathogenicity index assay. Further investigations revealed co-infection with infectious bronchitis virus of the GI-19 lineage, which very likely explained the severity of the disease observed during the outbreaks. The H9N2 outbreaks in Ghana highlight the importance of performing a differential diagnosis and an in-depth characterization of emerging viruses. In addition, the detection of a potentially zoonotic subtype, such as the H9N2, in a region where highly pathogenic avian influenza H5Nx is currently circulating highlights the urgency of implementing enhanced monitoring strategies and supporting improved investments in regional diagnostic technologies.RESEARCH HIGHLIGHTSInfluenza A H9N2 subtype was detected in layer hens in Ghana in 2017–2018Whole genome characterization of seven H9N2 viruses was performedPhylogenetic trees revealed that the H9N2 viruses belong to the G1 lineageThe HA protein possesses the amino acid mutations 226L and 155TCo-infection with infectious bronchitis virus of the GI-19 lineage was identified