Carbapenem-resistant gram-negative bacterial infections and risk factors for acquisition in a Kenyan intensive care unit.

BACKGROUND: Carbapenem-resistant Gram-negative bacteria (CR-GNB) are a critical public health threat globally; however, there are inadequate surveillance data, especially in intensive care units (ICU), to inform infection prevention and control in many resource-constrained settings. Here, we assessed the prevalence of CR-GNB infections and risk factors for acquisition in a Kenyan ICU. METHODS: A hospital-based cross-sectional study design was adopted, recruiting 162 patients clinically presenting with bacterial infection after 48 h of ICU admission, from January to October 2022 at the Nairobi West Hospital, Kenya. Demographics and clinical data were collected by case report form. The type of sample collected, including blood, tracheal aspirate, ascitic tap, urine, stool, and sputum depended on the patient's clinical presentation and were transported to the hospital Microbiology laboratory in a cool box for processing within 2 h. The samples were analyzed by cultured and BD Phoenix system used for isolates' identity and antimicrobial susceptibility. RESULTS: CR-GNB infections prevalence was 25.9% (42/162), with Klebsiella pneumoniae (35.7%, 15/42) and Pseudomonas aeruginosa (26.2%, 11/42) predominating. All isolates were multidrug-resistant (MDR). P. aeruginosa and A. baumannii were 100% colistin-resistant, while K. pneumoniae (33.3%) was tigecycline-resistant. History of antibiotics (aOR = 3.40, p = 0.005) and nasogastric tube (NGT) use (aOR = 5.84, p = < 0.001) were the risk factors for infection. CONCLUSION: Our study highlights high MDR- and CR-GNB infections in ICU, with prior antibiotic exposure and NGT use as risk factors, and diminishing clinical value of colistin and tigecycline. In this study setting and beyond, strict implementation of antimicrobial stewardship programs and adherence to infection prevention and control through monitoring, evaluation and feedback are warranted to curb CR-GNB infections, especially among the risk groups.

Asymptomatic gastrointestinal carriage of multidrug-resistant carbapenemase-producing Enterobacteriaceae among children under five years in a Kenyan hospital.

Objectives: Asymptomatic gastrointestinal carriage of carbapenem-resistant Enterobacteriaceae (CRE) is a threat to global health in developing countries with inadequate safe drinking water, poor hygiene, and weak antimicrobial stewardship; however, epidemiological data to guide CRE infection prevention and control is limited in these settings. We assessed asymptomatic CRE and carbapenem-producing Enterobacteriaceae (CPE) fecal carriage rates and associated risk factors among hospitalized children aged under 5 years. Methods: We adopted a cross-sectional study at Mama Lucy Kibaki Hospital in Nairobi-City County, Kenya, between June and September 2022. We collected demographic and clinical characteristics using a structured questionnaire and clinical reports and analyzed stool/rectal swab samples by standard and automated bacteriological methods. Results: Asymptomatic CRE and CPE fecal carriage rate was 2.25% (6/267), with six isolates recovered, predominated by Escherichia coli (33.33%) and Enterobacter cloacae subsp dissolvens (33.33%). Third-generation cephalosporin and ciprofloxacin resistance were highest in Citrobacter farmer and E. cloacae subsp cloacae. All CRE and CPE were multidrug-resistant, and except E. cloacae subsp cloacae, were 100% colistin-resistant. Conclusions: Asymptomatic gastrointestinal carriage of multidrug-resistant-CRE among hospitalized children under 5 years, presents a substantial public health threat. This calls for continuous surveillance including molecular characterization of isolates, to inform infection prevention and antimicrobial stewardship adherence in line with local and global plans on AMR.

Extended-spectrum ß-lactamase- producing gram-negative bacterial infections in severely ill COVID-19 patients admitted in a national referral hospital, Kenya.

BACKGROUND: Bacterial infections in COVID-19 patients, especially those caused by multidrug-resistant gram-negative strains, are associated with increased morbidity, hospital stay and mortality. However, there is limited data on the epidemiology of extended-spectrum ß-lactamase (ESBL)-producing bacteria in COVID-19 patients. Here, we assessed the prevalence and the factors associated with ESBL-producing gram-negative bacterial (GNB) infections among severely ill COVID-19 patients admitted in Kenyatta National Hospital (KNH), Kenya. METHODS: We adopted a descriptive cross-sectional study design for patients admitted between October 2021 and February 2022, purposively recruiting 120 SARS-CoV- 2 infected participants based on clinical presentation. Demographics and clinical characteristics data were collected using structured questionnaires and case report forms. Clinical samples were collected and analyzed by standard microbiological methods in the KNH Microbiology laboratory and the Centre for Microbiology Research, Kenya Medical Research Institute. RESULTS: GNB infections prevalence was 40.8%, majorly caused by ESBL-producers (67.3%) predominated by Klebsiella pneumoniae (45.5%). Generally, 73% of the ESBL producers harboured our target ESBL genes, mainly CTX-M-type (59%, 17/29) in K. pneumoniae (76.9%, 20/26). GNB harbouring TEM-type (83%, 10/12) and SHV-type (100%, 7/7) genes showed ESBLs phenotypes and inhibitor resistance, mainly involving clavulanate, but most of them remained susceptible to tazobactam (60%, 6/10). SHV-type genes carrying ESBL producers showed resistance to both cefotaxime (CTX) and ceftazidime (CAZ) (K. pneumoniae), CAZ (E. coli) or CTX (E. cloacae complex and K. pneumoniae). About 87% (20/23) of isolates encoding CTX-M-type ß-lactamases displayed CTX/ceftriaxone (CRO) resistance phenotype. About 42% of isolates with CTX-M-type ß-lactamases only hydrolyzed ceftazidime (CAZ). Isolates with OXA-type ß-lactamases were resistant to CTX, CAZ, CRO, cefepime and aztreonam. Patients with comorbidities were 10 times more likely to have an ESBL-producing GNB infection (aOR = 9.86, 95%CI 1.30 - 74.63, p = 0.003). CONCLUSION: We report a high prevalence of ESBL-GNB infections in severely ill COVID-19 patients, predominantly due to Klebsiella pneumoniae harbouring CTX-M type ESBL genes. The patient's underlying comorbidities increased the risk of ESBL-producing GNB infection. In COVID-19 pandemic, enhanced systematic and continuous surveillance of ESBL-producing GNB, strict adherence to infection control measures and antimicrobial stewardship policies are warranted in the current study setting.

Multidrug-resistant Gram-negative bacterial infections and associated factors in a Kenyan intensive care unit: a cross-sectional study.

BACKGROUND: Patients admitted to intensive care units (ICU) are at risk of Gram-negative bacteria (GNB) infections, especially those caused by multidrug-resistant (MDR) isolates, increasing morbidity, mortality, and healthcare costs. However, epidemiological surveillance data on MDR bacteria to inform infection prevention and control (IPCs) interventions is limited in our study setting. Here we assessed the prevalence and factors associated with GNB infections in ICU- patients admitted in our study setting. METHODS: This was a hospital-based cross-sectional study among patients admitted to ICU at the Nairobi West Hospital, Kenya, between January and October 2022. Altogether, we recruited 162 patients, excluding those hospitalized for less than 48 h and declining consent, and collected demographics and clinical data by case report form. Blood, wound and throat swab, ascetic tap, stool, urine, tracheal aspirate, and sputum samples were collected cultured. Isolates identity and antimicrobial susceptibility were elucidated using the BD Phoenix system. RESULTS: The prevalence of GNB infections was 55.6%, predominated by urinary tract infections (UTIs). We recovered 13 GNB types, with Escherichia coli (33.3%) and Klebsiella pneumoniae (31.1%) as the most common isolates. Factors associated with GNB infections were a history of antibiotic use (aOR = 4.23, p = 0.001), nasogastric tube use (NGT, aOR = 3.04, p = 0.013), respiratory tract (RT, aOR = 5.3, p = 0.005) and cardiovascular (CV, aOR = 5.7, p = 0.024) conditions. 92% of the isolates were MDR,predominantly Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. CONCLUSION: We report a high prevalence of MDR-GNB infections, predominated by UTI, in ICU, whereby patients with a history of antibiotic use, using the NGT, and having RT and CV conditions were at increased risk. To improve the management of ICU-admitted patients, continuous education, training, monitoring, evaluation and feedback on infection prevention and control are warranted in our study setting.

Multidrug resistant bacterial infections in severely ill COVID-19 patients admitted in a national referral and teaching hospital, Kenya.

BACKGROUND: Bacterial infections are a common complication in patients with seasonal viral respiratory tract infections and are associated with poor prognosis, increased risk of intensive care unit admission and 29-55% mortality. Yet, there is limited data on the burden of bacterial infections among COVID-19 patients in Africa, where underdeveloped healthcare systems are likely to play a pertinent role in the epidemiology of the COVID-19 pandemic. Here, we evaluated the etiologies, antimicrobial resistance profiles, risk factors, and outcomes of bacterial infections in severely ill COVID-19 patients. METHODS: A descriptive cross-sectional study design was adopted in severely ill COVID-19 patients at Kenyatta National Hospital, Kenya, from October to December 2021. We used a structured questionnaire and case report forms to collect sociodemographics, clinical presentation, and hospitalization outcome data. Blood, nasal/oropharyngeal swabs and tracheal aspirate samples were collected based on the patient's clinical presentation and transported to the Kenyatta National Hospital microbiology laboratory for immediate processing following the standard bacteriological procedures. RESULTS: We found at least one bacterial infection in 44.2% (53/120) of the patients sampled, with a 31.7% mortality rate. Pathogens were mainly from the upper respiratory tract (62.7%, 42/67), with gram-negative bacteria dominating (73.1%, 49/67). Males were about three times more likely to acquire bacterial infection (p = 0.015). Those aged 25 to 44 years (p = 0.009), immunized against SARS-CoV-2 (p = 0.027), and admitted to the infectious disease unit ward (p = 0.031) for a short length of stay (0-5 days, p < 0.001) were more likely to have a positive outcome. Multidrug-resistant isolates were the majority (64.3%, 46/67), mainly gram-negative bacteria (69.6%, 32/46). The predominant multidrug-resistant phenotypes were in Enterococcus cloacae (42.9%, 3/7), Klebsiella pneumonia (25%, 4/16), and Escherichia coli (40%, 2/5). CONCLUSION: Our findings highlight a high prevalence of multidrug-resistant bacterial infections in severely ill COVID-19 patients, with male gender as a risk factor for bacterial infection. Elderly Patients, non-SARS-CoV-2 vaccination, intensive care unit admission, and long length of hospital stay were associated with poor outcomes. There is a need to emphasize strict adherence to infection and prevention at KNH-IDU and antimicrobial stewardship in line with local and global AMR control action plans.

Multidrug-Resistant Shigellosis among Children Aged below Five Years with Diarrhea at Banadir Hospital in Mogadishu, Somalia.

Globally, shigellosis remains the second leading cause of diarrhea-associated deaths among children under five years of age, and the infections are disproportionately higher in resource-limited settings due to overcrowding, poor sanitation, and inadequate safe drinking water. The emergence and global spread of multidrug-resistant (MDR) Shigella are exacerbating the shigellosis burden. We adopted a cross-sectional study design to determine the distribution and antimicrobial susceptibility (AST) patterns of Shigella serogroups among children aged below five years presenting with diarrhea at Banadir Hospital in Mogadishu, Somalia, from August to October 2019. Stool and rectal swab samples were collected from 180 children consecutively enrolled using a convenient sampling technique and processed following standard bacteriological methods. AST was determined using the Kirby-Bauer disc diffusion method and interpreted as per the Clinical Laboratory Standard Institute (2018) guidelines. Shigellosis prevalence was 20.6% (37/180), and S. flexneri (26/37 (70.3%)) was the predominant serogroup. All the serogroups were 100% resistant to ampicillin (AMP), trimethoprim-sulfamethoxazole (SXT), and tetracycline (TE). Ceftriaxone (CRO) resistance was the highest among S. sonnei (66.7%) isolates. 19.2% of S. flexneri and S. sonnei (50%) serogroups were resistant to ciprofloxacin (CIP), but all S. dysenteriae type 1 isolates remained (100%) susceptible. Forty percent of CIP-susceptible S. dysenteriae type 1 were resistant to CRO. Seven MDR Shigella phenotypes were identified, dominated by those involving resistance to AMP, SXT, and TE (100%). Our findings showed a high prevalence of shigellosis with S. flexneri as the most predominant serogroup among children under five years of age in Banadir Hospital, Somalia. AMP and SXT are no longer appropriate treatments for shigellosis in children under five years in Banadir Hospital. MDR Shigella strains, including those resistant to CIP and CRO, have emerged in Somalia, posing a public health challenge. Therefore, there is an urgent need for AMR surveillance and continuous monitoring to mitigate the further spread of the MDR Shigella strains in Banadir Hospital and beyond.

Structural and functional analysis of an anchorless fibronectin-binding protein FBPS from Gram-positive bacterium Streptococcus suis.

The anchorless fibronectin-binding proteins (FnBPs) are a group of important virulence factors for which the structures are not available and the functions are not well defined. In this study we performed comprehensive studies on a prototypic member of this group: the fibronectin-/fibrinogen-binding protein from Streptococcus suis (FBPS). The structures of the N- and C-terminal halves (FBPS-N and FBPS-C), which together cover the full-length protein in sequence, were solved at a resolution of 2.1 and 2.6 Å, respectively, and each was found to be composed of two domains with unique folds. Furthermore, we have elucidated the organization of these domains by small-angle X-ray scattering. We further showed that the fibronectin-binding site is located in FBPS-C and that FBPS promotes the adherence of S suis to host cells by attaching the bacteria via FBPS-N. Finally, we demonstrated that FBPS functions both as an adhesin, promoting S suis attachment to host cells, and as a bacterial factor, activating signaling pathways via ß1 integrin receptors to induce chemokine production.

In vitro assembly of Ebola virus nucleocapsid-like complex expressed in E. coli.

Ebola virus (EBOV) harbors an RNA genome encapsidated by nucleoprotein (NP) along with other viral proteins to form a nucleocapsid complex. Previous Cryo-eletron tomography and biochemical studies have shown the helical structure of EBOV nucleocapsid at nanometer resolution and the first 450 amino-acid of NP (NPΔ451-739) alone is capable of forming a helical nucleocapsid-like complex (NLC). However, the structural basis for NP-NP interaction and the dynamic procedure of the nucleocapsid assembly is yet poorly understood. In this work, we, by using an E. coli expression system, captured a series of images of NPΔ451-739 conformers at different stages of NLC assembly by negative-stain electron microscopy, which allowed us to picture the dynamic procedure of EBOV nucleocapsid assembly. Along with further biochemical studies, we showed the assembly of NLC is salt-sensitive, and also established an indispensible role of RNA in this process. We propose the diverse modes of NLC elongation might be the key determinants shaping the plasticity of EBOV virions. Our findings provide a new model for characterizing the self-oligomerization of viral nucleoproteins and studying the dynamic assembly process of viral nucleocapsid in vitro.

Structures of the Zika Virus Envelope Protein and Its Complex with a Flavivirus Broadly Protective Antibody.

Zika virus (ZIKV), a mosquito-borne flavivirus, is a current global public health concern. The flavivirus envelope (E) glycoprotein is responsible for virus entry and represents a major target of neutralizing antibodies for other flaviviruses. Here, we report the structures of ZIKV E protein at 2.0 Å and in complex with a flavivirus broadly neutralizing murine antibody 2A10G6 at 3.0 Å. ZIKV-E resembles all the known flavivirus E structures but contains a unique, positively charged patch adjacent to the fusion loop region of the juxtaposed monomer, which may influence host attachment. The ZIKV-E-2A10G6 complex structure reveals antibody recognition of a highly conserved fusion loop. 2A10G6 binds to ZIKV-E with high affinity in vitro and neutralizes currently circulating ZIKV strains in vitro and in mice. The E protein fusion loop epitope represents a potential candidate for therapeutic antibodies against ZIKV.