Pathogen Outbreaks Research Articles

Pseudomonas aeruginosa infection in augmented care: the molecular ecology and transmission dynamics in four large UK hospitals

Pseudomonas aeruginosa is a common opportunistic pathogen and molecular typing in outbreaks has linked patient acquisition to contaminated hospital water systems. To elucidate the role of P.aeruginosa transmission rates in non-outbreak augmented care settings in the UK. Over a 16-week period, all water outlets in augmented care units of four hospitals were sampled for P.aeruginosa and clinical isolates were collected. Outlet and clinical P.aeruginosa isolates underwent whole-genome sequencing (WGS), which with epidemiological data identified acquisition from water as definite (level 1), probable (level 2), possible (level 3), and no evidence (level 4). Outlets were positive in each hospital on all three occasions: W (16%), X (2.5%), Y (0.9%) and Z (2%); and there were 51 persistently positive outlets in total. WGS identified likely transmission (at levels 1, 2 and 3) from outlets to patients in three hospitals for P.aeruginosa positive patients: W (63%), X (54.5%) and Z (26%). According to the criteria (intimate epidemiological link and no phylogenetic distance), approximately 5% of patients in the study 'definitely' acquired their P.aeruginosa from their water outlets in the intensive care unit. This study found extensive evidence of transmission from the outlet to the patients particularly in the newest hospital (W), which had the highest rate of positive outlets. The overall findings suggest that water outlets are the most likely source of P.aeruginosa nosocomial infections in some settings, and that widespread introduction of control measures would have a substantial impact on infections.

In Search of Patient Zero: Visual Analytics of Pathogen Transmission Pathways in Hospitals.

Pathogen outbreaks (i.e., outbreaks of bacteria and viruses) in hospitals can cause high mortality rates and increase costs for hospitals significantly. An outbreak is generally noticed when the number of infected patients rises above an endemic level or the usual prevalence of a pathogen in a defined population. Reconstructing transmission pathways back to the source of an outbreak - the patient zero or index patient - requires the analysis of microbiological data and patient contacts. This is often manually completed by infection control experts. We present a novel visual analytics approach to support the analysis of transmission pathways, patient contacts, the progression of the outbreak, and patient timelines during hospitalization. Infection control experts applied our solution to a real outbreak of Klebsiella pneumoniae in a large German hospital. Using our system, our experts were able to scale the analysis of transmission pathways to longer time intervals (i.e., several years of data instead of days) and across a larger number of wards. Also, the system is able to reduce the analysis time from days to hours. In our final study, feedback from twenty-five experts from seven German hospitals provides evidence that our solution brings significant benefits for analyzing outbreaks.

Lytic characterization and application of listerial endolysins PlyP40 and PlyPSA in queso fresco

Queso fresco (QF) is a fresh Hispanic-style cheese that is commonly associated with the human foodborne pathogen Listeria monocytogenes and outbreaks of listeriosis in the United States. Endolysins, cell wall hydrolases derived from bacteriophages, are promising candidates for controlling bacterial pathogens in food systems. In this study, we characterized the lytic capabilities of 2 endolysins, PlyP40 and PlyPSA, under varying conditions (pH, temperature, salt concentration) and compared their activities with those of the previously described endolysin PlyP100. We showed that PlyP40 was effective, showing at least a 33% reduction in cellular debris, against a broader range of Listeria than PlyPSA, which showed little lytic activity toward Listeria strains not from serovar 4. Both endolysins were also capable of maintaining lytic activity to varying extents at refrigeration temperature. The effect of salt concentration and pH differed between PlyP40 and PlyPSA. Furthermore, we added the endolysins to QF and monitored their ability to control L. monocytogenes contamination over 28 d of cold storage. Both PlyP40 and PlyPSA were capable of lowering QF inoculum cell counts compared with the control; however, both were less effective than the previously characterized PlyP100. Further characterization of endolysins will continue to open opportunities to optimization and implementation in a variety of food matrices for controlling pathogen contamination.

Study on pathogenicity and characterization of disease causing fungal community associated with cultured fish of Kashmir valley, India

Cultured fisheries of developing countries are continously challenged by a number of pathogenic microbes. Among microbial diseases, fungal and fungal like pathogen outbreaks lead to negative social and economic impacts on stakeholders. The cultured fisheries of Kashmir valley are also facing challenge from fungal pathogens, leading to tremendous socio-economic lossess to the fish farmer community hence, yearns to boost the sector with efficient management strategy. Our study was aimed at investigating the diversity of fungal communities infecting cultured rainbow trout and carp fish species. We employed classical microbiology, macro and micro morphological characteristics, and molecular analysis (multilocus typing) for fungal identification. Also histopathological approach was used to examine the pathogenicity patterns of diverse fungal groups. The study revealed that the infection in fish was predisposed to both superficial as well as visceral organs. However, skin, gills and head were predominantly infected compared to internal organs. The microbiological investigation of infected fish by culture dependent approach helped us to obtain the total of 250 fungal isolates. Out of these isolates, 21 different species were identified belonging to three diverse fungal groups which mostly included 14 species among Ascomycetes, 03 species of Oomycetes and 04 species of Zygomycetes. The majority of fungi which were infectious to cultured fish of valley are biotrophic or opportunistic soil fungi, and some of them being exclusive pathogens of fish.

Pathogen detection with electrochemical biosensors: Advantages, challenges and future perspectives.

Detection of pathogens, e.g., bacteria and viruses, is still a big challenge in analytical medicine due to their vast number and variety. Developing strategies for rapid, inexpensive, specific, and sensitive detection of the pathogens using nanomaterials, integrating with microfluidics devices, amplification methods, or even combining these strategies have received significant attention. Especially, after the health-threatening COVID-19 outbreak, rapid and sensitive detection of pathogens became very critical. Detection of pathogens could be realized with electrochemical, optical, mass sensitive, or thermal methods. Among them, electrochemical methods are very promising by bringing different advantages, i.e., they exhibit more versatile detection schemes and real-time quantification as well as label-free measurements, which provides a broader application perspective. In this review, we discuss the recent advances for the detection of bacteria and viruses using electrochemical biosensors. Moreover, electrochemical biosensors for pathogen detection were broadly reviewed in terms of analyte, bio-recognition and transduction elements. Different fabrication techniques, detection principles, and applications of various pathogens with the electrochemical biosensors were also discussed.

Induction of Trained Immunity by Recombinant Vaccines.

Vaccines represent an important strategy to protect humans against a wide variety of pathogens and have even led to eradicating some diseases. Although every vaccine is developed to induce specific protection for a particular pathogen, some vaccine formulations can also promote trained immunity, which is a non-specific memory-like feature developed by the innate immune system. It is thought that trained immunity can protect against a wide variety of pathogens other than those contained in the vaccine formulation. The non-specific memory of the trained immunity-based vaccines (TIbV) seems beneficial for the immunized individual, as it may represent a powerful strategy that contributes to the control of pathogen outbreaks, reducing morbidity and mortality. A wide variety of respiratory viruses, including respiratory syncytial virus (hRSV) and metapneumovirus (hMPV), cause serious illness in children under 5 years old and the elderly. To address this public health problem, we have developed recombinant BCG vaccines that have shown to be safe and immunogenic against hRSV or hMPV. Besides the induction of specific adaptive immunity against the viral antigens, these vaccines could generate trained immunity against other respiratory pathogens. Here, we discuss some of the features of trained immunity induced by BCG and put forward the notion that recombinant BCGs expressing hRSV or hMPV antigens have the capacity to simultaneously induce specific adaptive immunity and non-specific trained immunity. These recombinant BCG vaccines could be considered as TIbV capable of inducing simultaneously the development of specific protection against hRSV or hMPV, as well as non-specific trained-immunity-based protection against other pathogenic viruses.

Comparison of the chemical diversity ofVitis rotundifoliaandVitis viniferacv. ‘Cabernet Sauvignon’

Grapevine is one of the most important fruit plants in the world, mainly due to its grapes and related products, with a highly economic and cultural importance. Every year, vineyards are affected by several pathogen outbreaks and the only way to control them is through preventive applications of agrochemicals every 12 to 15 days. This approach is not sustainable and not always effective. TheVitisgenus comprise different species that exhibit varying levels of resistance to pathogens, thus the understanding of the innate resistance/susceptibility mechanisms of these differentVitisspecies is crucial to cope with these threats. In this work, an untargeted metabolomics approach was followed, using Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR-MS), to analyse the metabolic chemical diversity of twoVitisspecies:Vitis rotundifolia(resistant to pathogens) andV. viniferacv. ‘Cabernet Sauvignon’ (susceptible to pathogens). Chemical formulas from bothVitiswere used to build Van Krevelen diagrams and compositional space plots, which do not require full metabolite identification and provide an easy comparison method. Based only on these visualization tools, it was shown that theV. rotundifoliametabolome is more complex than the metabolome ofV. viniferacv. ‘Cabernet Sauvignon’. Moreover, the regions that present a higher density are associated to lipids, polyketides and carbohydrates. Also,V. rotundifoliametabolome presented a higher ratio O/C compounds.

Study of clinical features of patients with COVID-19 hospitalized in an educational hospital in Iran.

BACKGROUND:The outbreak of new pathogens or the resurgence of pathogens that have already spread is a serious challenge to public health. Coronavirus is a pathogen that seems to invade the human respiratory system in the first place. Coronaviruses form a large family and are so called because of the presence of crown like cristae on their surface.MATERIALS AND METHODS:This is a cross-sectional, descriptive study conducted to assess the status of patients with COVID-19 who were hospitalized in an educational hospital. For this purpose, 142 patients hospitalized in this hospital were followed up 2 weeks after discharge and were inquired about the symptoms they had upon admission to the hospital, the number of hospitalization days, the history of underlying disease, and so on. Descriptive data analysis was done with the SPSS software version 22.RESULTS:The findings of this research showed that overweight or obese people (about 66%) is more likely to contract the disease. It also seems that older people (37.3% older than 60 years old) and those with a history of diseases (69.6%) such as diabetes, high blood pressure, or heart disease are more prone to COVID-19. The most common symptoms of COVID-19 patients included fever (64.5%), shortness of breath (67.4%), and dry cough (50.4%).CONCLUSION:it seems that high risk group (obese people, old people, and people with a history of disease) is more likely to be infect with coronavirus so they should more careful than others. Another important issue is that policy-makers must play an active role in public awareness of dangers of COVID-19 and ways to prevent it.

Development of an Enteric Bacterial Enrichment Broth and Its Performance for Isolation of Clinically Significant Bacterial Pathogens from Stool

Background: Early detection and accurate identification of foodborne pathogen outbreaks is an important public health function. Increased clinical adoption of multiplex PCR assays or culture independent diagnostic tests (CIDT) correlates to more stool specimens sent to public health laboratories (PHL) for characterization. Isolation and confirmation of enteric bacterial pathogens can prove difficult to consistently recover. The purpose of this study was to evaluate the performance of a broad-use laboratory developed enrichment broth for isolation of Campylobacter, Salmonella, Shigella, and Yersinia strains from stool specimens. Methods: The study compared differences in positivity rates among media and enrichment combinations at specific time points. Comparison of direct inoculation (DI), enrichment using a lab-developed Enteric Bacterial Enrichment (EBE) broth and gold-standard isolation methods were conducted to test current utility of this established practice with stool specimens heat injured and non-injured. Results: A total of 234 spiked stool samples, 175 non-injured and 59 heat injured, were tested with varying bacterial concentrations. For non-injured stools, direct inoculation performed better for Campylobacter and Yersinia than enrichment. Conversely, Salmonella and Shigella recovery and limit of detection increased with enrichment. Campylobacter had the highest percent recovery while Shigella being the lowest from direct plating at 6-hour and 24-hour enrichment periods. Among broths, EBE performed the best for Yersinia and similar to Selenite broth for Salmonella and Shigella. Generally, heat injured stool had a significantly lower percent of recovery than non-heat injured with a higher limit of detection across organisms. Conclusion: Our data suggest there is an only utility for targeted enrichment of CIDT positive Salmonella stool specimens. We highlight the difficulties of formulating an enrichment broth capable of supporting a variety of enteric pathogens with standardized incubation. Increasing demands on PHL infrastructure warrant further examination of enhancing organism isolation and cost analyses for CIDT positive specimens.

Hypothesis: Immunotherapy by Selective Convalescent Blood Engineering to Stifle Diseases like COVID-19.

Current standard vaccine testing protocols take approximately 10-24 months of testing before a vaccine can be declared successful. Sometimes by the time a successful vaccine is out for public use, the outbreak may already be over. With no vaccine or antiviral drug available to treat the infected, we are left with the age-old methods of isolation, quarantine, and rest, to arrest such a viral outbreak. Convalescent blood therapy and covalent plasma therapy have often proved effective in reducing mortality, however, the role of innate and adaptive immune cells in these therapies have been overlooked. Antigen presenting cells (APCs), CD4+ T memory cells, CD8+ T memory cells, and memory B-Cells all play a vital role in sustainable defense and subsequent recovery. This report incorporates all these aspects by suggesting a novel treatment therapy called selective convalescent leukapheresis and transfusion (SCLT) and also highlights its potential in vaccination. The anticipated advantages of the proposed technique outweigh the cost, time, and efficiency of other available transfusion and vaccination processes. It is envisioned that in the future this new approach could serve as a rapid emergency response to subdue a pathogen outbreak and to stop it from becoming an epidemic, or pandemic.

The Role of Peridomestic Rodents as Reservoirs for Zoonotic Foodborne Pathogens.

Although rodents are well-known reservoirs and vectors for a number of zoonoses, the functional role that peridomestic rodents serve in the amplification and transmission of foodborne pathogens is likely underappreciated. Clear links have been identified between commensal rodents and outbreaks of foodborne pathogens throughout Europe and Asia; however, comparatively little research has been devoted to studying this relationship in the United States. In particular, regional studies focused on specific rodent species and their foodborne pathogen reservoir status across the diverse agricultural landscapes of the United States are lacking. We posit that both native and invasive species of rodents associated with food-production pipelines are likely sources of seasonal outbreaks of foodborne pathogens throughout the United States. In this study, we review the evidence that identifies peridomestic rodents as reservoirs for foodborne pathogens, and we call for novel research focused on the metagenomic communities residing at the rodent-agriculture interface. Such data will likely result in the identification of new reservoirs for foodborne pathogens and species-specific demographic traits that might underlie seasonal enteric disease outbreaks. Moreover, we anticipate that a One Health metagenomic research approach will result in the discovery of new strains of zoonotic pathogens circulating in peridomestic rodents. Data resulting from such research efforts would directly inform and improve upon biosecurity efforts, ultimately serving to protect our food supply.

Monitoring ash dieback (Hymenoscyphus fraxineus) in British forests using hyperspectral remote sensing

AbstractLarge‐scale dieback of ash trees (Fraxinus spp.) caused by the fungus Hymenoscyphus fraxineus is posing an immense threat to forest health in Europe, requiring effective monitoring at large scales. In this study, a pipeline was created to find ash trees and classify dieback severity using high‐resolution hyperspectral imagery of individual tree crowns (ITCs). Hyperspectral data were collected in four forest sites near Cambridge, UK, where 422 ITCs were manually delineated and labelled using field‐measurements of species and dieback severity (for ash trees). Four algorithms, namely linear discriminant analysis (LDA), principal components analysis coupled with LDA (PCA‐LDA), partial least squares discriminant analysis (PLS‐DA) and random forest (RF), were used to build classification models for species and dieback severity classification. The effect of dark‐pixel filtering on classification accuracy was evaluated. The best performing models were then coupled with automatic ITC segmentation to map species and ash dieback distribution over 16.8 hectares of woodland. We calculated and partitioned the coefficient of variation (CV) of the reflected ash spectra to find variable wavebands associated with dieback. PLS‐DA and LDA were most accurate for classifying ITC species identifies (overall accuracy >90%), whereas RF was most accurate for classifying ash dieback severity (overall accuracy 77%). Dark pixel filtering further increased the accuracy of species classification (+6%), but not disease classification. The reflectances of narrow blue (415 nm), red‐edge (680 nm) and NIR (760 nm) bands had high CV across disease classes and should be included if multispectral imagery were to be used to monitor ash dieback. The study demonstrates the possibility of using remote sensing to forward epidemiological research by monitoring forest pathogens in landscape scales, which would allow temperate forest managers to control pathogen outbreaks, assess associated impacts and restore affected forests much more effectively.

Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene.

Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.

Exposure to Zoonotic West Nile Virus in Long-Tailed Macaques and Bats in Peninsular Malaysia.

Simple SummaryThe role of wildlife animals, such as macaques and bats, in the spreading and maintenance of deadly zoonotic pathogens in nature are documented in several studies. The present study substantially highlights the first evidence of West Nile Virus (WNV) infection, a mosquito borne virus in the Malaysian macaques and bats. Of the 81 macaques sampled, 24 of the long-tailed macaques were seropositive to WNV, indicating that they were exposed to the virus in the past. The long-tailed macaques were found in the mangrove forests located in the Central, Southern, and West Peninsular Malaysia. Meanwhile, five out of 41 bats (Lesser Short-nosed Fruit Bats, Lesser Sheath-tailed Bats, and Thai Horseshoe Bats) that were found in the caves from Northern Peninsular Malaysia showed susceptibility to WNV. Therefore, a constant bio surveillance of WNV in the wildlife in Malaysia is a proactive attempt. This study was aligned with the Malaysian government’s mission under the Malaysia Strategy for Emerging Diseases and Public Health Emergencies (MYSED) II (2017–2021) and the Ministry of Health priorities in order to enhance the regional capability to rapidly and accurately survey, detect, diagnose, and report outbreaks of pathogens and diseases of security concern.The role of wildlife such as wild birds, macaques, and bats in the spreading and maintenance of deadly zoonotic pathogens in nature have been well documented in many parts of the world. One such pathogen is the mosquitoes borne virus, namely the West Nile Virus (WNV). Previous research has shown that 1:7 and 1:6 Malaysian wild birds are WNV antibody and RNA positive, respectively, and bats in North America may not be susceptible to the WNV infection. This study was conducted to determine the status of WNV in Malaysian macaques and bats found in mangrove forests and caves, respectively. Archive sera and oropharyngeal swabs from long-tailed macaques were subjected to the antibody detection using WNV competitive enzyme-linked immunosorbent assay (c-ELISA) and WNV RNA using RT-PCR, respectively, while the archive oropharyngeal and rectal swabs from bats were subjected to RT-PCR without serological analysis due to the unavailability of serum samples. The analysis revealed a WNV seropositivity of 29.63% (24/81) and none of the macaques were positive for WNV RNA. Meanwhile, 12.2% (5/41) of the bats from Pteropodidae, Emballonuridae, and Rhinolophidae families tested positive for WNV RNA. Here, we show a high WNV antibody prevalence in macaques and a moderate WNV RNA in various Malaysian bat species, suggesting that WNV circulates through Malaysian wild animals and Malaysian bat species may be susceptible to the WNV infection.

Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis

SummaryBackgroundWhole-genome sequencing (WGS) can be used in genomic epidemiology investigations to confirm or refute outbreaks of bacterial pathogens, and to support targeted and efficient infection control interventions. We aimed to define a genetic relatedness cutoff, quantified as a number of single-nucleotide polymorphisms (SNP), for meticillin-resistant Staphylococcus aureus (MRSA), above which recent (ie, within 6 months) patient-to-patient transmission could be ruled out.MethodsWe did a retrospective genomic and epidemiological analysis of MRSA data from two prospective observational cohort studies in the UK to establish SNP cutoffs for genetic relatedness, above which recent transmission was unlikely. We used three separate approaches to calculate these thresholds. First, we applied a linear mixed model to estimate the S aureus substitution rate and 95th percentile within-host diversity in a cohort in which multiple isolates were sequenced per individual. Second, we applied a simulated transmission model to this same genomic dataset. Finally, in a second cohort, we determined the genetic distance (ie, the number of SNPs) that would capture 95% of epidemiologically linked cases. We applied the three approaches to both whole-genome and core-genome sequences.FindingsIn the linear mixed model, the estimated substitution rate was roughly 5 whole-genome SNPs (wgSNPs) or 3 core-genome SNPs (cgSNPs) per genome per year, and the 95th percentile within-host diversity was 19 wgSNPs or 10 cgSNPs. The combined SNP cutoffs for detection of MRSA transmission within 6 months per this model were thus 24 wgSNPs or 13 cgSNPs. The simulated transmission model suggested that cutoffs of 17 wgSNPs or 12 cgSNPs would detect 95% of MRSA transmission events within the same timeframe. Finally, in the second cohort, cutoffs of 22 wgSNPs or 11 cgSNPs captured 95% of epidemiologically linked cases within 6 months.InterpretationOn the basis of our results, we propose conservative cutoffs of 25 wgSNPs or 15 cgSNPS above which transmission of MRSA within the previous 6 months can be ruled out. These cutoffs could potentially be used as part of a genomic sequencing approach to the management of outbreaks of MRSA in conjunction with traditional epidemiological techniques.FundingUK Department of Health, Wellcome Trust, UK National Institute for Health Research.

Laboratory-confirmed bloodstream infections in two large neonatal units in sub-Saharan Africa

BackgroundEpidemiological data on neonatal bloodstream infections (BSI) in sub-Saharan Africa are extremely limited. MethodsA comparative analysis of laboratory-confirmed neonatal BSI episodes was conducted retrospectively in two large neonatal units in Botswana and South Africa (January 1 to December 31, 2017). Routine laboratory and ward register data were used to determine BSI rates, the pathogen spectrum, and BSI outcomes. ResultsIn 2017, the Princess Marina Hospital (PMH) and Tygerberg Hospital (TBH) neonatal units admitted 1187 and 2826 neonates, respectively. The BSI incidence rate was 12.1/1000 patient-days (95% confidence interval (CI) 10.2–14.3) at PMH and 3.5/1000 patient-days (95% CI 2.9–4.1) at TBH (p < 0.0001). Most BSI episodes were hospital-acquired (260/284; 91.6%). The blood culture contamination rate was substantially higher at PMH than TBH (152/1116 (13.6%) vs 122/2559 (4.8%); p < 0.001). The crude mortality rate in neonates with BSI was 21.2% (53/250) and significantly higher at TBH than PMH (38/128 (29.7%) vs 15/122 (12.3%), p = 0.001). Factors independently associated with death were birth weight <1500 g (adjusted odds ratio (aOR) 2.8, 95% CI 1.3–6.4; p = 0.02) and male sex (aOR 2.1, 95% CI 1.1–3.7; p = 0.01). Klebsiella pneumoniae was the dominant BSI pathogen in both units, accounting for two-thirds of BSI, and was associated with a large infection outbreak at PMH. Antibiotic resistance rates were substantial in both neonatal units, particularly for K. pneumoniae (98/122 (80.3%), extended-spectrum beta-lactamase (ESBL)-producers) and Staphylococcus aureus (22/33 (66.7%), methicillin-resistant). ConclusionsBSI rates and associated mortality were substantial in these two neonatal units in sub-Saharan Africa. ESBL-producing K. pneumoniae remains a leading BSI and outbreak pathogen.

Label-Free Immunoassay for Multiplex Detections of Foodborne Bacteria in Chicken Carcass Rinse with Surface Plasmon Resonance Imaging.

The frequent outbreaks of foodborne pathogens have stimulated the demand of biosensors capable of rapid and multiplex detection of contaminated food. In this study, surface plasmon resonance imaging (SPRi) was used in simultaneous label-free detection of multiple foodborne pathogens, mainly Salmonella spp. and Shiga-toxin producing Escherichia coli (STEC), in commercial chicken carcass rinse. The antibodies were immobilized on the same SPRi sensor chip as a label-free immunoassay. Their immobilization concentrations were optimized to be ranging from 0.25 to 1.0 mg/mL, and independent of pH values. This label-free immunoassay achieved 106 colony-forming unit (CFU)/mL limit of detection for Salmonella, which was further improved to 1.0 CFU/mL with overnight bacteria enrichment. The injected samples with different bacteria, Salmonella Enteritidis, STEC, and Listeria monocytogenes, have been identified by the same biochip. Moreover, the SPRi signals revealed complex interference effects among coexisting bacteria species in heterogeneous bacteria solutions. This SPRi-based immunoassay demonstrates the great potential in high-throughput screening of multiple pathogenic bacteria coexisting in chicken carcass rinse. The reliability of antibody immobilization and cross-reactions of different antibodies on the same biochip are the major challenges of practical application of SPRi.

Clonal spread of PER-1 and OXA-23 producing extensively drug resistant Acinetobacter baumannii during an outbreak in a burn intensive care unit in Tunisia.

Extensively drug resistant Acinetobacter baumannii (XDR-Ab), has emerged as an important pathogen in several outbreaks. The aim of our study was to investigate the eventual genetic relatedness of XDR-Ab strains recovered from burn patients and environment sites in the largest Tunisian Burn Intensive Care Unit (BICU) and to characterize β-lactamase encoding genes in these strains. Between March 04th, 2019 and April 22nd, 2019 an outbreak of XDR-Ab was suspected. Environmental screening was done. All isolates were screened by simplex PCR for β-lactamase genes. Genetic relatedness was determined by pulsed field gel electrophoresis (PFGE) of ApaI-digested total DNA. During the study period, 21 strains of A. baumannii were isolated in burn patients, mainly in blood culture (n = 7) and central vascular catheter (n = 6). All strains were susceptible to colistin but resistant to imipenem (n = 23), ciprofloxacin (n = 23), amikacin (n = 22), tigecyclin (n = 5) and rifampicin (n = 4). The blaOXA-51-like, blaOXA23, and blaADC genes were present in all strains. These resistance determinants were associated with blaPER-1 in 10 strains. The ISAba1 was inserted upstream of blaOXA-23 in all isolates. PFGE revealed two major clusters A (n = 11) and B (n = 5). This is the first description in Tunisia of clonally related PER-1 producing XDR-Ab in burn patients with probable environmental origin.

The Genus Ochrobactrum as Major Opportunistic Pathogens.

Ochrobactrum species are non-enteric, Gram-negative organisms that are closely related to the genus Brucella. Since the designation of the genus in 1988, several distinct species have now been characterised and implicated as opportunistic pathogens in multiple outbreaks. Here, we examine the genus, its members, diagnostic tools used for identification, data from recent Ochrobactrum whole genome sequencing and the pathogenicity associated with reported Ochrobactrum infections. This review identified 128 instances of Ochrobactrum spp. infections that have been discussed in the literature. These findings indicate that infection review programs should consider investigation of possible Ochrobactrum spp. outbreaks if these bacteria are clinically isolated in more than one patient and that Ochrobactrum spp. are more important pathogens than previously thought.

The use of military planning techniques to manage outbreaks of novel infections in acute inpatient settings: development of an 'infection control estimate' (ICE).

Outbreaks of infection create unique challenges to healthcare leaders and members of infection control teams who lead efforts to manage, control and resolve outbreaks. This is especially true during outbreaks of novel pathogens which may require atypical control methods reflecting the unknowns inherent in such situations. Healthcare providers within the UK have adopted various structures and models of infection prevention and control (IPC) service reflecting the individual needs of different organisations. As such, the roles and responsibilities of IPC practitioners vary between organisations. Variations in models of care combined with challenges created by outbreaks of novel infections may make algorithm based approaches to outbreak management less effective and potentially prone to missing key actions or considerations which may improve outcomes. Here we suggest the application of a widely established military planning technique, developed to aid decision making in combat environments, to the management of outbreaks of novel infection in acute hospital settings. The technique can be applied at all levels within an IPC hierarchy regardless of role or responsibility and may improve the coherency and efficacy of outbreak management efforts made by IPC teams. The technique may also be applied to outbreaks of known infections; however, in order to demonstrate the flexibility of the model, a novel infection has been used to illustrate its potential value in outbreak management when knowledge is limited.