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Mogeni P, Soge OO, Tickell KD, Tornberg SN, Pascual R, Wakatake E, Diakhate MM, Rwigi D, Kariuki K, Kariuki S, Singa BO, Fang FC, Walson JL, Pavlinac PB. β-Lactamase and Macrolide Resistance Gene Carriage in Escherichia coli Isolates Among Children Discharged From Inpatient Care in Western Kenya: A Cross-sectional Study. Open Forum Infect Dis 2024; 11:ofae307. [PMID: 38938894 PMCID: PMC11210497 DOI: 10.1093/ofid/ofae307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/30/2024] [Indexed: 06/29/2024] Open
Abstract
Background Antimicrobial resistance (AMR) is a global threat to infectious disease control, particularly among recently hospitalized children. We sought to determine the prevalence and mitigating factors of resistance in enteric Escherichia coli among children discharged from health facilities in western Kenya. Methods Between June 2016 and November 2019, children aged 1 to 59 months were enrolled at the point of discharge from the hospital. E coli was isolated by microbiological culture from rectal swabs at baseline. β-Lactamases and macrolide resistance-conferring genes were detected by polymerase chain reaction. A modified Poisson regression model was used to assess the predictors mph(A) and CTX-M-type extended-spectrum β-lactamase (ESBL). Results Of the 238 children whose E coli isolates were tested, 91 (38.2%) and 109 (45.8%) had detectable CTX-M-type ESBL and mph(A) genes, respectively. Antibiotic treatment during hospitalization (adjusted prevalence ratio [aPR], 2.47; 95% CI, 1.12-5.43; P = .025), length of hospitalization (aPR, 1.42; 95% CI, 1.00-2.01; P = .052), and the practice of open defecation (aPR, 2.47; 95% CI, 1.40-4.36; P = .002) were independent predictors for CTX-M-type ESBL and mph(A) genes. Pneumococcal vaccination was associated with a 43% lower likelihood of CTX-M-type ESBL (aPR, 0.57; 95% CI, .38-.85; P = .005), while measles vaccination was associated with a 32% lower likelihood of mph(A) genes (aPR, 0.68; 95% CI, .49-.93; P = .017) in E coli isolates. Conclusions Among children discharged from the hospital, history of vaccination, shorter hospital stay, lack of in-hospital antibiotic exposure, and improved sanitation were associated with a lower likelihood of AMR genes. To mitigate the continued spread of AMR, AMR control programs should consider strategies beyond antimicrobial stewardship, including improvements in sanitation, increased vaccine coverage, and the development of novel vaccines.
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Affiliation(s)
- Polycarp Mogeni
- Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Olusegun O Soge
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Kirkby D Tickell
- Department of Global Health, University of Washington, Seattle, Washington, USA
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
| | - Stephanie N Tornberg
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Rushlenne Pascual
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Erika Wakatake
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Mame M Diakhate
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Doreen Rwigi
- Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Kevin Kariuki
- Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Samuel Kariuki
- Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Benson O Singa
- Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Ferric C Fang
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Judd L Walson
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Patricia B Pavlinac
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
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Rwigi D, Nyerere AK, Diakhate MM, Kariuki K, Tickell KD, Mutuma T, Tornberg SN, Soge OO, Walson JL, Singa B, Kariuki S, Pavlinac PB, Mogeni P. Phenotypic and molecular characterization of β-lactamase-producing Klebsiella species among children discharged from hospital in Western Kenya. BMC Microbiol 2024; 24:135. [PMID: 38654237 PMCID: PMC11040804 DOI: 10.1186/s12866-024-03284-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The emergence and spread of β-lactamase-producing Klebsiella spp. has been associated with a substantial healthcare burden resulting in therapeutic failures. We sought to describe the proportion of phenotypic resistance to commonly used antibiotics, characterize β-lactamase genes among isolates with antimicrobial resistance (AMR), and assess the correlates of phenotypic AMR in Klebsiella spp. isolated from stool or rectal swab samples collected from children being discharged from hospital. METHODS We conducted a cross-sectional study involving 245 children aged 1-59 months who were being discharged from hospitals in western Kenya between June 2016 and November 2019. Whole stool or rectal swab samples were collected and Klebsiella spp. isolated by standard microbiological culture. β-lactamase genes were detected by PCR whilst phenotypic antimicrobial susceptibility was determined using the disc diffusion technique following standard microbiology protocols. Descriptive analyses were used to characterize phenotypic AMR and carriage of β-lactamase-producing genes. The modified Poisson regression models were used to assess correlates of phenotypic beta-lactam resistance. RESULTS The prevalence of β-lactamase carriage among Klebsiella spp. isolates at hospital discharge was 62.9% (154/245). Antibiotic use during hospitalization (adjusted prevalence ratio [aPR] = 4.51; 95%CI: 1.79-11.4, p < 0.001), longer duration of hospitalization (aPR = 1.42; 95%CI: 1.14-1.77, p < 0.002), and access to treated water (aPR = 1.38; 95%CI: 1.12-1.71, p < 0.003), were significant predictors of phenotypically determined β-lactamase. All the 154 β-lactamase-producing Klebsiella spp. isolates had at least one genetic marker of β-lactam/third-generation cephalosporin resistance. The most prevalent genes were blaCTX-M 142/154 (92.2%,) and blaSHV 142/154 (92.2%,) followed by blaTEM 88/154 (57.1%,) and blaOXA 48/154 (31.2%,) respectively. CONCLUSION Carriage of β-lactamase producing Klebsiella spp. in stool is common among children discharged from hospital in western Kenya and is associated with longer duration of hospitalization, antibiotic use, and access to treated water. The findings emphasize the need for continued monitoring of antimicrobial susceptibility patterns to inform the development and implementation of appropriate treatment guidelines. In addition, we recommend measures beyond antimicrobial stewardship and infection control within hospitals, improved sanitation, and access to safe drinking water to mitigate the spread of β-lactamase-producing Klebsiella pathogens in these and similar settings.
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Affiliation(s)
- Doreen Rwigi
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya.
- Center for Microbiology Research (CMR), Kenya Medical Research Institute (KEMRI), Nairobi, Kenya.
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
| | - Andrew K Nyerere
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Mame M Diakhate
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Kevin Kariuki
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Center for Microbiology Research (CMR), Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Kirkby D Tickell
- Department of Global Health, University of Washington, Seattle, Washington, USA
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Timothy Mutuma
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Center for Microbiology Research (CMR), Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | | | - Olusegun O Soge
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Judd L Walson
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of International Health, Johns Hopkins University, Baltimore, MD, USA
| | - Benson Singa
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Samuel Kariuki
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Center for Microbiology Research (CMR), Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Patricia B Pavlinac
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Polycarp Mogeni
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya.
- Department of Global Health, University of Washington, Seattle, Washington, USA.
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Ruef M, Emonet S, Merglen A, Dewez JE, Obama BM, Catho G, Andrey DO, Kowalski M, Harbarth S, Combescure C, Wagner N, Galetto-Lacour A. Carriage of third-generation cephalosporin-resistant and carbapenem-resistant Enterobacterales among children in sub-Saharan Africa: a systematic review and meta-analysis. EClinicalMedicine 2024; 70:102508. [PMID: 38500839 PMCID: PMC10945212 DOI: 10.1016/j.eclinm.2024.102508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/09/2024] [Accepted: 02/16/2024] [Indexed: 03/20/2024] Open
Abstract
Background The increasing resistance of Enterobacterales to third-generation cephalosporins and carbapenems in sub-Saharan Africa (SSA) is a major public health concern. We did a systematic review and meta-analysis of studies to estimate the carriage prevalence of Enterobacterales not susceptible to third-generation cephalosporins or carbapenems among paediatric populations in SSA. Methods We performed a systematic literature review and meta-analysis of cross-sectional and cohort studies to estimate the prevalence of childhood (0-18 years old) carriage of extended-spectrum cephalosporin-resistant Enterobacterales (ESCR-E) or carbapenem-resistant Enterobacterales (CRE) in SSA. Medline, EMBASE and the Cochrane Library were searched for studies published from 1 January 2005 to 1 June 2022. Studies with <10 occurrences per bacteria, case reports, and meta-analyses were excluded. Quality and risk of bias were assessed using the Newcastle-Ottawa scale. Meta-analyses of prevalences and odds ratios were calculated using generalised linear mixed-effects models. Heterogeneity was assessed using I2 statistics. The protocol is available on PROSPERO (CRD42021260157). Findings Of 1111 studies examined, 40 met our inclusion criteria, reporting on the carriage prevalence of Enterobacterales in 9408 children. The pooled carriage prevalence of ESCR-E was 32.2% (95% CI: 25.2%-40.2%). Between-study heterogeneity was high (I2 = 96%). The main sources of bias pertained to participant selection and the heterogeneity of the microbiological specimens. Carriage proportions were higher among sick children than healthy ones (35.7% vs 16.9%). The pooled proportion of nosocomial acquisition was 53.8% (95% CI: 32.1%-74.1%) among the 922 children without ESCR-E carriage at hospital admission. The pooled odds ratio of ESCR-E carriage after antibiotic treatment within the previous 3 months was 3.20 (95% CI: 2.10-4.88). The proportion of pooled carbapenem-resistant for Enterobacterales was 3.6% (95% CI: 0.7%-16.4%). Interpretation This study suggests that ESCR-E carriage among children in SSA is frequent. Microbiology capacity and infection control must be scaled-up to reduce the spread of those multidrug-resistant microorganisms. Funding There was no funding source for this study.
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Affiliation(s)
- Micaela Ruef
- Children’s Hospital, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Stephane Emonet
- Division of Infectious Diseases, Hospital of Valais, Sion, and Faculty of Medicine, Geneva, Switzerland
| | - Arnaud Merglen
- Division of General Paediatrics, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Juan Emmanuel Dewez
- Medical Department, Médecins Sans Frontières, Operational Centre Geneva, Geneva, Switzerland
| | - Basilice Minka Obama
- Paediatric Infectious Diseases Unit, Children’s Hospital, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Regional Hospital Centre for Ebolowa, Cameroon
| | - Gaud Catho
- Infectious Diseases Division, Central Institute, Hospital of Valais, Switzerland
- Infection Control Division, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Diego O. Andrey
- Division of Infectious Diseases, Department of Medicine and Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Morgane Kowalski
- Children’s Hospital, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Stephan Harbarth
- Infection Control Programme and World Health Organization Collaborating Centre on Infection Prevention and Control and Antimicrobial Resistance, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Christophe Combescure
- Centre for Clinical Research, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Noémie Wagner
- Medical Department, Médecins Sans Frontières, Operational Centre Geneva, Geneva, Switzerland
- Paediatric Infectious Diseases Unit, Children’s Hospital, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Annick Galetto-Lacour
- Division of Paediatric Emergency Medicine, Children’s Hospital, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
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Mabena FC, Olwagen CP, Phosa M, Ngwenya IK, Van der Merwe L, Khan A, Mwamba TM, Mpembe R, Magobo RE, Govender NP, Velaphi SC, Madhi SA. Bacterial and Candida Colonization of Neonates in a Regional Hospital in South Africa. Pediatr Infect Dis J 2024; 43:263-270. [PMID: 38381956 DOI: 10.1097/inf.0000000000004177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
BACKGROUND Neonatal colonization with multidrug-resistant (MDR) Enterobacter spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterococcus faecium (ESKAPE) and Candida spp. often precedes invasive hospital-acquired infections. We investigated the prevalence and dynamics of neonatal ESKAPE and Candida spp. colonization from hospital admission until discharge (or death) and followed up for invasive disease. METHODS Prospective longitudinal surveillance for neonatal ESKAPE and Candida spp. colonization was conducted over 6 months at a South African regional hospital. Neonates enrolled at birth had swabs (nasal, 2× skin and rectal) collected within 24 hours and every 48-96 hours thereafter, until discharge or death. ESKAPE and Candida spp. were cultured for and antimicrobial susceptibility was performed on bacterial isolates. Whole-genome sequencing was undertaken on paired samples with the same bacterial species from colonizing and invasive disease episodes in the same child. RESULTS Of 102 enrolled neonates, 79% (n = 81) were colonized by ≥1 ESKAPE organism by time of discharge or death. Forty-four percent (36/81) were colonized within 24 hours of birth. Common colonizers were K. pneumoniae (70%; n = 57) and Enterobacter spp. (43%; n = 35). Almost all MDR organisms (93%) were Gram-negative. Forty-two (45%, 42/93) newborns acquired Candida spp. (skin only) colonization, commonly Candida parapsilosis (69%; n = 29). For 2 children with K. pneumoniae colonization and sepsis, the bloodstream and colonizing isolates were genetically different, whereas the single A. baumannii colonizing and blood isolate pair were genetically identical. CONCLUSIONS We report a high prevalence of MDR ESKAPE and Candida spp. colonization in a regional neonatal unit. Interventions to reduce the high incidence of hospital-acquired neonatal infections should include reducing high colonization rates.
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Affiliation(s)
- Fikile C Mabena
- From the Faculty of Health Science, South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand
- Department of Paediatrics and Child Health, University of the Witwatersrand
| | - Courtney P Olwagen
- From the Faculty of Health Science, South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand
| | - Matshie Phosa
- From the Faculty of Health Science, South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand
| | - Innocent K Ngwenya
- From the Faculty of Health Science, South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand
| | - Lara Van der Merwe
- From the Faculty of Health Science, South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand
| | - Aaliyah Khan
- From the Faculty of Health Science, South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand
| | - Tshiama M Mwamba
- Division of the National Health Laboratory Service, Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases
| | - Ruth Mpembe
- Division of the National Health Laboratory Service, Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases
| | - Rindidzani E Magobo
- Division of the National Health Laboratory Service, Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases
| | - Nelesh P Govender
- Division of the National Health Laboratory Service, Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases
- School of Pathology, University of the Witwatersrand
| | | | - Shabir A Madhi
- From the Faculty of Health Science, South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand
- Infectious Disease and Oncology Research Institute, University of the Witwatersrand, Johannesburg, South Africa
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Hounmanou YMG, Wanyana A, Alafi S, Wabwire-Mangen F, Christensen H, Olsen JE, Byarugaba DK. Whole strains vs MGEs in short and longterm transmission of ESBL genes between healthcare and community settings in Uganda. Sci Rep 2023; 13:10229. [PMID: 37353515 PMCID: PMC10290109 DOI: 10.1038/s41598-023-35879-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/25/2023] [Indexed: 06/25/2023] Open
Abstract
Multidrug-resistant ESBL-producing Escherichia coli are a leading cause of infections in hospital and community settings. Based on samples from two hospitals in Uganda and households of inpatients we tested the hypothesis that ESBL E. coli and/or their resistance determinants could spread within the healthcare and community settings through discharged patients that were still colonized. We used bacterial culture, susceptibility testing whole genome sequencing and detailed bioinformatics analysis to test the above hypothesis. Genome analysis revealed presence of predominantly blaCTX-M-15 and blaOXA-1 genes with a total resistome with genes belonging to 14 different classes of antimicrobials. Short-term cases of strain sharing were reported within each setting and strains from the two settings were found to cluster together based on their overall resistome. Long-term horizontal transfer of ESBL genes by various IncF and IncY types of plasmids shared between healthcare and community settings was demonstrated. Based on hybrid assembly, plasmid reconstruction and phylogenetic analyses, our study suggests that while the dissemination of AMR between healthcare and community settings in the short-term is possible at whole strain level, the long-term transmission between healthcare and communities is sustained by the transfer of plasmids circulating across niches and disseminating related resistomes.
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Affiliation(s)
- Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Agnes Wanyana
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Stephen Alafi
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Fred Wabwire-Mangen
- School of Public Health, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Denis Karuhize Byarugaba
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda.
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Venne DM, Hartley DM, Malchione MD, Koch M, Britto AY, Goodman JL. Review and analysis of the overlapping threats of carbapenem and polymyxin resistant E. coli and Klebsiella in Africa. Antimicrob Resist Infect Control 2023; 12:29. [PMID: 37013626 PMCID: PMC10071777 DOI: 10.1186/s13756-023-01220-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/18/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Enterobacterales are among the most serious antimicrobial resistance (AMR) threats. Emerging resistance to polymyxins raises the specter of untreatable infections. These resistant organisms have spread globally but, as indicated in WHO reports, the surveillance needed to identify and track them is insufficient, particularly in less resourced countries. This study employs comprehensive search strategies with data extraction, meta-analysis and mapping to help address gaps in the understanding of the risks of carbapenem and polymyxin resistance in the nations of Africa. METHODS Three comprehensive Boolean searches were constructed and utilized to query scientific and medical databases as well as grey literature sources through the end of 2019. Search results were screened to exclude irrelevant results and remaining studies were examined for relevant information regarding carbapenem and/or polymyxin(s) susceptibility and/or resistance amongst E. coli and Klebsiella isolates from humans. Such data and study characteristics were extracted and coded, and the resulting data was analyzed and geographically mapped. RESULTS Our analysis yielded 1341 reports documenting carbapenem resistance in 40 of 54 nations. Resistance among E. coli was estimated as high (> 5%) in 3, moderate (1-5%) in 8 and low (< 1%) in 14 nations with at least 100 representative isolates from 2010 to 2019, while present in 9 others with insufficient isolates to support estimates. Carbapenem resistance was generally higher among Klebsiella: high in 10 nations, moderate in 6, low in 6, and present in 11 with insufficient isolates for estimates. While much less information was available concerning polymyxins, we found 341 reports from 33 of 54 nations, documenting resistance in 23. Resistance among E. coli was high in 2 nations, moderate in 1 and low in 6, while present in 10 with insufficient isolates for estimates. Among Klebsiella, resistance was low in 8 nations and present in 8 with insufficient isolates for estimates. The most widespread associated genotypes were, for carbapenems, blaOXA-48, blaNDM-1 and blaOXA-181 and, for polymyxins, mcr-1, mgrB, and phoPQ/pmrAB. Overlapping carbapenem and polymyxin resistance was documented in 23 nations. CONCLUSIONS While numerous data gaps remain, these data show that significant carbapenem resistance is widespread in Africa and polymyxin resistance is also widely distributed, indicating the need to support robust AMR surveillance, antimicrobial stewardship and infection control in a manner that also addresses broader animal and environmental health dimensions.
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Affiliation(s)
- Danielle M Venne
- Center on Medical Product Access, Safety and Stewardship, Georgetown University, 3900 Reservoir Road, Washington, DC, 20057, USA
| | - David M Hartley
- James M. Anderson Center for Health Systems Excellence, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Marissa D Malchione
- Center on Medical Product Access, Safety and Stewardship, Georgetown University, 3900 Reservoir Road, Washington, DC, 20057, USA
- Sabin Vaccine Institute, Influenza Vaccine Innovation, 2175 K St NW, Washington, DC, 20037, USA
| | - Michala Koch
- Center on Medical Product Access, Safety and Stewardship, Georgetown University, 3900 Reservoir Road, Washington, DC, 20057, USA
| | - Anjali Y Britto
- Center on Medical Product Access, Safety and Stewardship, Georgetown University, 3900 Reservoir Road, Washington, DC, 20057, USA
| | - Jesse L Goodman
- Center on Medical Product Access, Safety and Stewardship, Georgetown University, 3900 Reservoir Road, Washington, DC, 20057, USA.
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Edwards T, Williams CT, Olwala M, Andang'o P, Otieno W, Nalwa GN, Akindolire A, Cubas-Atienzar AI, Ross T, Tongo OO, Adams ER, Nabwera H, Allen S. Molecular surveillance reveals widespread colonisation by carbapenemase and extended spectrum beta-lactamase producing organisms in neonatal units in Kenya and Nigeria. Antimicrob Resist Infect Control 2023; 12:14. [PMID: 36814315 PMCID: PMC9945588 DOI: 10.1186/s13756-023-01216-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
OBJECTIVES Neonatal sepsis, a major cause of death amongst infants in sub-Saharan Africa, is often gut derived. Gut colonisation by Enterobacteriaceae producing extended spectrum beta-lactamase (ESBL) or carbapenemase enzymes can lead to antimicrobial-resistant (AMR) or untreatable infections. We sought to explore the rates of colonisation by ESBL or carbapenemase producers in two neonatal units (NNUs) in West and East Africa. METHODS Stool and rectal swab samples were taken at multiple timepoints from newborns admitted to the NNUs at the University College Hospital, Ibadan, Nigeria and the Jaramogi Oginga Odinga Teaching and Referral Hospital, Kisumu, western Kenya. Samples were tested for ESBL and carbapenemase genes using a previously validated qPCR assay. Kaplan-Meier survival analysis was used to examine colonisation rates at both sites. RESULTS In total 119 stool and rectal swab samples were taken from 42 infants admitted to the two NNUs. Colonisation with ESBL (37 infants, 89%) was more common than with carbapenemase producers (26, 62.4%; P = 0.093). Median survival time before colonisation with ESBL organisms was 7 days and with carbapenemase producers 16 days (P = 0.035). The majority of ESBL genes detected belonged to the CTX-M-1 (36/38; 95%), and CTX-M-9 (2/36; 5%) groups, and the most prevalent carbapenemase was blaNDM (27/29, 93%). CONCLUSIONS Gut colonisation of neonates by AMR organisms was common and occurred rapidly in NNUs in Kenya and Nigeria. Active surveillance of colonisation will improve the understanding of AMR in these settings and guide infection control and antibiotic prescribing practice to improve clinical outcomes.
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Affiliation(s)
- Thomas Edwards
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK.
| | | | - Macrine Olwala
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Jomo Kenyatta Highway Kaloleni Kisumu KE Central, Maseno, Kenya
| | - Pauline Andang'o
- Department of Public Health, School of Public Health and Community Development, Maseno University, Maseno, Kenya
| | - Walter Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Jomo Kenyatta Highway Kaloleni Kisumu KE Central, Maseno, Kenya
| | - Grace N Nalwa
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Jomo Kenyatta Highway Kaloleni Kisumu KE Central, Maseno, Kenya
| | | | - Ana I Cubas-Atienzar
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Toby Ross
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Emily R Adams
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Helen Nabwera
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Stephen Allen
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
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Villinger D, Schultze TG, Musyoki VM, Inwani I, Aluvaala J, Okutoyi L, Ziegler AH, Wieters I, Stephan C, Museve B, Kempf VAJ, Masika M. Genomic transmission analysis of multidrug-resistant Gram-negative bacteria within a newborn unit of a Kenyan tertiary hospital: A four-month prospective colonization study. Front Cell Infect Microbiol 2022; 12:892126. [PMID: 36093198 PMCID: PMC9452910 DOI: 10.3389/fcimb.2022.892126] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/05/2022] [Indexed: 11/23/2022] Open
Abstract
Objective Multidrug-resistant organisms (MDRO), especially carbapenem-resistant organisms (CRO), represent a threat for newborns. This study investigates the colonization prevalence of these pathogens in a newborn unit at a Kenyan tertiary hospital in an integrated approach combining routine microbiology, whole genome sequencing (WGS) and hospital surveillance data. Methods The study was performed in the Kenyatta National Hospital (KNH) in 2019 over a four-month period and included 300 mother-baby pairs. A total of 1,097 swabs from newborns (weekly), mothers (once) and the hospital environment were taken. Routine clinical microbiology methods were applied for surveillance. Of the 288 detected MDRO, 160 isolates were analyzed for antimicrobial resistance genes and phylogenetic relatedness using whole genome sequencing (WGS) and bioinformatic analysis. Results In maternal vaginal swabs, MDRO detection rate was 15% (n=45/300), including 2% CRO (n=7/300). At admission, MDRO detection rate for neonates was 16% (n=48/300), including 3% CRO (n=8/300) with a threefold increase for MDRO (44%, n=97/218) and a fivefold increase for CRO (14%, n=29/218) until discharge. Among CRO, K. pneumoniae harboring blaNDM-1 (n=20) or blaNDM-5 (n=16) were most frequent. WGS analysis revealed 20 phylogenetically related transmission clusters (including five CRO clusters). In environmental samples, the MDRO detection rate was 11% (n=18/164), including 2% CRO (n=3/164). Conclusion Our study provides a snapshot of MDRO and CRO in a Kenyan NBU. Rather than a large outbreak scenario, data indicate several independent transmission events. The CRO rate among newborns attributed to the spread of NDM-type carbapenemases is worrisome.
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Affiliation(s)
- David Villinger
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Competence for Infection Control, Frankfurt, Hesse, Germany
| | - Tilman G. Schultze
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Competence for Infection Control, Frankfurt, Hesse, Germany
| | - Victor M. Musyoki
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Irene Inwani
- Pediatrics Department, Kenyatta National Hospital, Nairobi, Kenya
| | - Jalemba Aluvaala
- Pediatrics Department, Kenyatta National Hospital, Nairobi, Kenya
| | - Lydia Okutoyi
- Quality Health Department, Kenyatta National Hospital, Nairobi, Kenya
| | - Anna-Henriette Ziegler
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
| | - Imke Wieters
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- Center of Internal Medicine/Infectious Diseases Unit, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
| | - Christoph Stephan
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- Center of Internal Medicine/Infectious Diseases Unit, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
| | - Beatrice Museve
- Department of Laboratory Medicine, Kenyatta National Hospital, Nairobi, Kenya
| | - Volkhard A. J. Kempf
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Competence for Infection Control, Frankfurt, Hesse, Germany
- *Correspondence: Volkhard A. J. Kempf, ; Moses Masika,
| | - Moses Masika
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- *Correspondence: Volkhard A. J. Kempf, ; Moses Masika,
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9
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Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries. Nat Microbiol 2022; 7:1337-1347. [PMID: 35927336 PMCID: PMC9417982 DOI: 10.1038/s41564-022-01184-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/23/2022] [Indexed: 12/29/2022]
Abstract
Early development of the microbiome has been shown to affect general health and physical development of the infant and, although some studies have been undertaken in high-income countries, there are few studies from low- and middle-income countries. As part of the BARNARDS study, we examined the rectal microbiota of 2,931 neonates (term used up to 60 d) with clinical signs of sepsis and of 15,217 mothers screening for blaCTX-M-15, blaNDM, blaKPC and blaOXA-48-like genes, which were detected in 56.1%, 18.5%, 0% and 4.1% of neonates’ rectal swabs and 47.1%, 4.6%, 0% and 1.6% of mothers’ rectal swabs, respectively. Carbapenemase-positive bacteria were identified by MALDI-TOF MS and showed a high diversity of bacterial species (57 distinct species/genera) which exhibited resistance to most of the antibiotics tested. Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae/E. cloacae complex, the most commonly found isolates, were subjected to whole-genome sequencing analysis and revealed close relationships between isolates from different samples, suggesting transmission of bacteria between neonates, and between neonates and mothers. Associations between the carriage of antimicrobial resistance genes (ARGs) and healthcare/environmental factors were identified, and the presence of ARGs was a predictor of neonatal sepsis and adverse birth outcomes. Analysis of gut microbiota of mothers and its neonates—as part of the BARNARDS study—reveals associations between β-lactamase gene carriage and neonatal sepsis risk in low-income settings.
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10
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Gastrointestinal colonization of Extended-Spectrum Beta lactamase producing bacteria among children below five years of age hospitalized with fever in Dar es Salaam, Tanzania. J Glob Antimicrob Resist 2022; 30:107-114. [PMID: 35667646 DOI: 10.1016/j.jgar.2022.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/16/2022] [Accepted: 05/26/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Gastrointestinal colonization of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) is of concern because prior colonization increases risk for subsequent infections. To date, the link between ESBL-PE fecal carriage and the risk of subsequent ESBL-PE infection has not been well established, and information on carriage of such pathogens among children with invasive infections such as blood stream infections (BSI) remains to be explored worldwide. METHODS This cross-sectional study was conducted among childrenunder the age of 5 years admitted for febrile illness in Dar es Salaam, Tanzania, between March 2017 and July 2018. We used rectal swabs to screen for ESBL-PE using selective media, ChromID® ESBL. Bacterial isolates were identified by MALDI-TOF.Blood cultures were drawn from all children. Antimicrobial susceptibility testingwas done using disk diffusion method. ESBL alleles were identified by Real-Time PCR and sequencing. RESULTS The overall prevalence of ESBL-PE carriage was 56% (112/200) and washighestamong children 4-6 months old (17/21, 81%) (p =0.05). Children with BSI had high ESBL-PE carriage (78.4%) compared to those without BSI (53.1%)(p=0.02; AOR 3.4, 95% CI1.20-9.58).The most common isolate was E.coli (64/112, 45%). Sixteen pairs of ESBL-PEisolates(from the gut and from blood)had similar antimicrobial susceptibility profile. We detectedblaCTX-M gene in 97% of all phenotypically detected ESBL-PE; among those,blaCTX-M-15 was dominant (99%). CONCLUSIONS We report a high prevalence of ESBL-PEfecal carriage among children with BSI in Tanzania. Colonization of ESBL-PEwasa risk factor for ESBL-BSI.
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11
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Sands K, Spiller OB, Thomson K, Portal EAR, Iregbu KC, Walsh TR. Early-Onset Neonatal Sepsis in Low- and Middle-Income Countries: Current Challenges and Future Opportunities. Infect Drug Resist 2022; 15:933-946. [PMID: 35299860 PMCID: PMC8921667 DOI: 10.2147/idr.s294156] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/17/2022] [Indexed: 12/18/2022] Open
Abstract
Neonatal sepsis is defined as a systemic infection within the first 28 days of life, with early-onset sepsis (EOS) occurring within the first 72h, although the definition of EOS varies in literature. Whilst the global incidence has dramatically reduced over the last decade, neonatal sepsis remains an important cause of neonatal mortality, highest in low- and middle-income countries (LMICs). Symptoms at the onset of neonatal sepsis can be subtle, and therefore EOS is often difficult to diagnose from clinical presentation and laboratory testing and blood cultures are not always conclusive or accessible, especially in resource limited countries. Although the World Health Organisation (WHO) currently advocates a ß-lactam, and gentamicin for first line treatment, availability and cost influence the empirical antibiotic therapy administered. Antibiotic treatment of neonatal sepsis in LMICs is highly variable, partially caused by factors such as cost of antibiotics (and who pays for them) and access to certain antibiotics. Antimicrobial resistance (AMR) has increased considerably over the past decade and this review discusses current microbiology data available in the context of the diagnosis, and treatment for EOS. Importantly, this review highlights a large variability in data availability, methodology, availability of diagnostics, and aetiology of sepsis pathogens.
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Affiliation(s)
- Kirsty Sands
- Ineos Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, UK
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Owen B Spiller
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Kathryn Thomson
- Ineos Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, UK
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | | | | | - Timothy R Walsh
- Ineos Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, UK
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
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12
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Tornberg-Belanger SN, Rwigi D, Mugo M, Kitheka L, Onamu N, Ounga D, Diakhate MM, Atlas HE, Wald A, McClelland RS, Soge OO, Tickell KD, Kariuki S, Singa BO, Walson JL, Pavlinac PB. Antimicrobial resistance including Extended Spectrum Beta Lactamases (ESBL) among E. coli isolated from kenyan children at hospital discharge. PLoS Negl Trop Dis 2022; 16:e0010283. [PMID: 35358186 PMCID: PMC9015121 DOI: 10.1371/journal.pntd.0010283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 04/18/2022] [Accepted: 02/27/2022] [Indexed: 12/04/2022] Open
Abstract
Background Children who have been discharged from hospital in sub-Saharan Africa remain at substantial risk of mortality in the post-discharge period. Antimicrobial resistance (AMR) may be an important factor. We sought to determine the prevalence and risk factors associated with AMR in commensal Escherichia coli(E. coli) from Kenyan children at the time of discharge. Methodology/Principle findings Fecal samples were collected from 406 children aged 1–59 months in western Kenya at the time of discharge from hospital and cultured for E. coli. Susceptibility to ampicillin, ceftriaxone, cefotaxime, ceftazidime, cefoxitin, imipenem, ciprofloxacin, gentamicin, combined amoxicillin/clavulanic acid, trimethoprim-sulfamethoxazole, azithromycin, and chloramphenicol was determined by disc diffusion according to guidelines from the Clinical and Laboratory Standards Institute (CLSI). Poisson regression was used to determine associations between participant characteristics and the presence of extended-spectrum beta-lactamases (ESBL) producing E. coli. Non-susceptibility to ampicillin (95%), gentamicin (44%), ceftriaxone (46%), and the presence of ESBL (44%) was high. Receipt of antibiotics during the hospitalization was associated with the presence of ESBL (aPR = 2.23; 95% CI: 1.29–3.83) as was being hospitalized within the prior year (aPR = 1.32 [1.07–1.69]). Open defecation (aPR = 2.02; 95% CI: 1.39–2.94), having a toilet shared with other households (aPR = 1.49; 95% CI: 1.17–1.89), and being female (aPR = 1.42; 95% CI: 1.15–1.76) were associated with carriage of ESBL E. coli Conclusions/Significance AMR is common among isolates of E. coli from children at hospital discharge in Kenya, including nearly half having detectable ESBL. Children who have been hospitalized in sub-Saharan Africa remain at a high risk of death and morbidity for at least 6 months following discharge. These children may harbor AMR in commensal bacteria following hospitalization, which may be associated with poor outcomes. There are limited data describing AMR and risk factors that are associated with AMR carriage at hospital discharge. In this cross-sectional study of Kenyan children under 5 years of age discharged from hospitals, we found AMR to be high. Children who received antibiotics in the hospital, had limited access to improved sanitation, and who were female had the highest prevalence of ESBL-producing E. coli.
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Affiliation(s)
- Stephanie N. Tornberg-Belanger
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (STB); (PBP)
| | - Doreen Rwigi
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Centre for Microbiology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Michael Mugo
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Centre for Microbiology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Lynnete Kitheka
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Centre for Microbiology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Nancy Onamu
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Derrick Ounga
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Mame M. Diakhate
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Hannah E. Atlas
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Anna Wald
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - R. Scott McClelland
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Olusegun O. Soge
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Kirkby D. Tickell
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Samuel Kariuki
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Centre for Microbiology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Benson O. Singa
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Judd L. Walson
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
- Department of Medicine (Allergy and Infectious Diseases), University of Washington, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Patricia B. Pavlinac
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail: (STB); (PBP)
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13
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Basu S, Copana R, Morales R, Anugulruengkitt S, Puthanakit T, Maramba-Lazarte C, Williams P, Musembi J, Boga M, Issack M, Hokororo A, Falade AG, Trehan I, Molyneux E, Arscott-Mills T, Alemayehu T, Bryant PA. Keeping It Real: Antibiotic Use Problems and Stewardship Solutions in Low- and Middle-income Countries. Pediatr Infect Dis J 2022; 41:S18-S25. [PMID: 35134036 PMCID: PMC8815843 DOI: 10.1097/inf.0000000000003321] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 12/28/2022]
Abstract
Antimicrobial resistance is a global health threat and there is an urgent need to manage antibiotic use to slow its development. However, antimicrobial stewardship interventions in low- and middle-income countries (LMIC) have been limited in terms of their resourcing, feasibility and effectiveness in the face of greater challenges in child mortality. We sought to gather together examples of antibiotic use problems faced by clinicians in LMIC, many of which are unique to these settings, and real-world antimicrobial stewardship solutions identified, with the goal of learning broader lessons that might be applicable across LMIC.
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Affiliation(s)
- Saurav Basu
- From the Department of Community Medicine, Maulana Azad Medical College, New Delhi, India
| | - Raul Copana
- Department of Pediatrics, Faculty of Medicine, San Simon University, Cochabamba, Bolivia
- Intensive Care Unit, Manuel A. Villarroel Childrens Hospotal, Cochabamba, Bolivia
| | - Ronaldo Morales
- Clinical Pharmacokinetics Center, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Suvaporn Anugulruengkitt
- Department of Pediatrics and
- Center of Excellence for Pediatric Infectious Diseases and Vaccines, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Thanyawee Puthanakit
- Department of Pediatrics and
- Center of Excellence for Pediatric Infectious Diseases and Vaccines, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Cecilia Maramba-Lazarte
- Division of Infectious and Tropical Diseases (INTROP), Department of Pediatrics, University of the Philippines College of Medicine-Philippine General Hospital, Manila, Philippines
- Department of Pharmacology and Toxicology, University of the Philippines, College of Medicine, Manila, Philippines
| | - Phoebe Williams
- Kenya Medical Research Institute (KEMRI/Wellcome Trust Research Programme), Department of Paediatrics, Kilifi, Kenya
- School of Public Health, Faculty of Medicine, The University of Sydney, Sydney, New South Wales, Australia
| | - John Musembi
- School of Public Health, Faculty of Medicine, The University of Sydney, Sydney, New South Wales, Australia
| | - Mwanamvua Boga
- School of Public Health, Faculty of Medicine, The University of Sydney, Sydney, New South Wales, Australia
| | - Mohammad Issack
- Bacteriology Department, Central Health Laboratory, Victoria Hospital, Quatre-Bornes, Mauritius
| | - Adolfine Hokororo
- Department of Paediatrics and Child Health, Catholic University of Health and Allied Sciences-Bugando, Mwanza, Tanzania
| | - Adegoke G. Falade
- Department of Paediatrics, College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Indi Trehan
- Departments of Pediatrics, Global Health, and Epidemiology, University of Washington, Seattle, Washington
| | - Elizabeth Molyneux
- Paediatric and Child Health Department, College of Medicine, Blantyre, Malawi
| | | | - Tinsae Alemayehu
- American Medical Center, and St. Paul’s Hospital Millennium Medical College, Department of Infectious Diseases and Travel Medicine, Addis Ababa, Ethiopia
| | - Penelope A. Bryant
- Consultant in Paediatric Infectious Diseases and Medical Lead, Hospital-in-the-Home, The Royal Children’s Hospital
- Group Leader and Clinician-Scientist Fellow, Clinical Paediatrics, Murdoch Children's Research Institute and
- Department of Paediatrics, University of Melbourne Parkville, Victoria, Australia
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14
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Dramowski A, Aucamp M, Beales E, Bekker A, Cotton MF, Fitzgerald FC, Labi AK, Russell N, Strysko J, Whitelaw A, Coffin S. Healthcare-Associated Infection Prevention Interventions for Neonates in Resource-Limited Settings. Front Pediatr 2022; 10:919403. [PMID: 35874586 PMCID: PMC9301049 DOI: 10.3389/fped.2022.919403] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
Healthcare-associated infections (HAIs) and antimicrobial-resistant (AMR) infections are leading causes of neonatal morbidity and mortality, contributing to an extended hospital stay and increased healthcare costs. Although the burden and impact of HAI/AMR in resource-limited neonatal units are substantial, there are few HAI/AMR prevention studies in these settings. We reviewed the mechanism of action and evidence supporting HAI/AMR prevention interventions, including care bundles, for hospitalized neonates in low- and middle-income countries (LMIC).
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Affiliation(s)
- Angela Dramowski
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marina Aucamp
- Infection Prevention and Control Service, Mowbray Maternity Hospital, Cape Town, South Africa
| | - Emily Beales
- Center for Neonatal and Pediatric Infection, St George's University of London, London, United Kingdom
| | - Adrie Bekker
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mark Frederic Cotton
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Felicity C Fitzgerald
- Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Appiah-Korang Labi
- Department of Medical Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Neal Russell
- Center for Neonatal and Pediatric Infection, St George's University of London, London, United Kingdom
| | - Jonathan Strysko
- Department of Paediatric and Adolescent Health, Princess Marina Hospital, Gaborone, Botswana.,Department of Global Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Andrew Whitelaw
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa.,National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Susan Coffin
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
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15
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Bloodstream Infections at Two Neonatal Intensive Care Units in Ghana: Multidrug Resistant Enterobacterales Undermine the Usefulness of Standard Antibiotic Regimes. Pediatr Infect Dis J 2021; 40:1115-1121. [PMID: 34561387 DOI: 10.1097/inf.0000000000003284] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Bloodstream infections (BSIs) are a major cause of morbidity and mortality in hospitalized neonates. Data on antibiotic resistance in neonatal BSIs and their impact on clinical outcomes in Africa are limited. METHODS We conducted a prospective cohort study at 2 tertiary level neonatal intensive care units (NICUs) in Ghana. All neonates admitted to the NICUs were included from October 2017 to September 2019. We monitored BSI rates and analyzed the effect of BSI and antibiotic resistance on mortality and duration of hospitalization. RESULTS Of 5433 neonates included, 3514 had at least one blood culture performed and 355 had growth of a total of 368 pathogenic microorganisms. Overall incidence of BSI was 1.0 (0.9-1.1) per 100 person days. The predominant organisms were Klebsiella pneumoniae 49.7% (183/368) and Streptococcus spp. 10.6% (39/368). In addition, 512 coagulase negative Staphylococci were isolated but considered probable contaminants. Among K. pneumoniae, resistance to gentamicin and amikacin was 91.8% and 16.4%, respectively, while carbapenem resistance was 4.4%. All-cause mortality among enrolled neonates was 19.7% (1066/5416). The mortality rate was significantly higher in neonates with BSI compared with culture-negative neonates in univariate analysis (27.9%, n = 99/355 vs. 16.5%, n = 520/3148; hazard ratio 1.4, 95% confidence interval 1.07-1.70) but not in multivariate analysis. CONCLUSION The diversity of etiologic agents and the high-risk of antibiotic resistance suggest that standard empirical treatment is unlikely to improve the outcome of BSIs in low and middle income. Such improvements will depend on access to reliable clinical microbiologic services.
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16
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Zakir A, Regasa Dadi B, Aklilu A, Oumer Y. Investigation of Extended-Spectrum β-Lactamase and Carbapenemase Producing Gram-Negative Bacilli in Rectal Swabs Collected from Neonates and Their Associated Factors in Neonatal Intensive Care Units of Southern Ethiopia. Infect Drug Resist 2021; 14:3907-3917. [PMID: 34588786 PMCID: PMC8476106 DOI: 10.2147/idr.s333603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/15/2021] [Indexed: 12/14/2022] Open
Abstract
Background Currently extended-spectrum β-lactamase (ESβL) and carbapenemase producing gram-negative bacteria are the greatest concern among the neonatal population with very limited therapeutic options. The aim of this study was to assess the prevalence of ESβL and carbapenemase producing gram-negative bacilli, associated factors and antimicrobial resistance patterns among neonates in intensive care units. Methods An institutional-based cross-sectional study was conducted from February to June 2021 on 212 neonates in intensive care units. Risk factors data were collected by using a well-designed questionnaire. A rectal swab sample was collected using a sterile cotton swab and inoculated on MacConkey agar. Bacterial isolates were identified using various biochemical tests. ESβL and carbapenemase were first screened by indicator cephalosporins (cefotaxime (30µg) and ceftazidine (30µg)) and carbapenem (meropenem and ertapenem), respectively. ESβL and carbapenemase were confirmed by a double-disk synergy test and modified carbapenem inactivation methods, respectively. SPSS version 21.0 was used for data analysis. A P-value ≤ 0.05 was considered as statistically significant. Results The overall prevalence of ESβL-producing gram-negative bacilli was 72/212 (34%). The predominant ESβL-producing isolate was Klebsiella pneumoniae 23/72 (31.9%) followed by Escherichia coli 17/72 (23.6%). Five (2.4%) carbapenemase-producing gram-negative bacilli were isolated. ESβL-producing isolates showed a high resistance against ampicillin 72/72 (100%), augmentin 69/72 (95.8%) and gentamycin 57/72 (79.2%). The majority 63/72 (87.5%) of isolated ESβL-producing gram-negative bacilli were multi-drug resistant (MDR). Rectal carriage of ESβL by neonates showed a statistically significant association with endotracheal intubation (p = 0.001; AOR = 4.2; 96% CI = (1.8–9.5)), treatment with ampicillin+gentamycin (p = 0.004; AOR = 3.3; 95% CI = (1.5–7.6)) and staying in a neonatal intensive care unit (NICU) between 11 and 20 days (p = 0.042; AOR = 2; 95% CI = (1.0–4.5)). Conclusion A high prevalence of ESβL-producing bacterial isolates was observed for commonly used antibiotics which needs further attention. Therefore, continuous and regular follow-ups of drug resistance patterns is important for the proper treatment and management of ESβL and carbapenemase producing gram-negative bacilli.
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Affiliation(s)
- Abdurezak Zakir
- Department of Medical Microbiology, Arba Minch University, Arba Minch, Ethiopia
| | | | - Addis Aklilu
- Department of Medical Microbiology, Arba Minch University, Arba Minch, Ethiopia
| | - Yisiak Oumer
- Department of Medical Microbiology, Arba Minch University, Arba Minch, Ethiopia
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Dramowski A, Pillay S, Bekker A, Abrahams I, Cotton MF, Coffin SE, Whitelaw AC. Impact of 1% chlorhexidine gluconate bathing and emollient application on bacterial pathogen colonization dynamics in hospitalized preterm neonates - A pilot clinical trial. EClinicalMedicine 2021; 37:100946. [PMID: 34195575 PMCID: PMC8225683 DOI: 10.1016/j.eclinm.2021.100946] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Chlorhexidine gluconate (CHG) body washes and emollient application may modulate bacterial pathogen colonization and prevent neonatal hospital-acquired infections. METHODS This pilot, non-randomized, open-label trial, enrolled preterm neonates (1000-1500g; day 1-3 of life) at a tertiary hospital in Cape Town, South Africa. Participants were sequentially allocated to 4 trial arms (n=20 each): 1% aqueous CHG (CHG), 1% CHG plus emollient (CHG+EM), emollient only (EM) and standard of care (SOC: no antiseptic/emollient). Trial treatment/s were applied daily for 10 days (d) post-enrolment, documenting neonatal skin condition score. Anterior nose, neck, umbilical and perianal swabs for bacterial culture were collected at d1, d3, d10 and d16 post-enrolment, (±1 day), reporting pathogen acquisition rates and semi-quantitative bacterial colony counts. (ClinicalTrials.gov identifier: NCT03896893; trial status: closed). FINDINGS Eighty preterm neonates (mean gestational age 30 weeks [SD 2]) were enrolled between 4 March and 26 August 2019. The bacterial pathogen acquisition rate (comparing d1 and d16 swabs) varied from 33·9% [95%CI 22·9-47·0] at the umbilicus, 39·3% [95%CI 27·6-52·4] at the neck, to 71·4% [95%CI 58·5-81·7] at both the nose and perianal region. At d10, CHG babies had reduced bacterial density detected from neck, umbilicus, and perianal swabs compared to other groups (see Table 3). Following intervention cessation, colonization density was similar across all trial arms, but S. aureus colonization was more prevalent among EM and CHG+EM babies. Neonatal skin condition score improved in babies receiving emollient application (EM: -0·87 [95%CI 0·69-1·06] and CHG+EM: -0·73 [0·45-0·99]), compared to the SOC and CHG arms (Table 2); no CHG-related skin reactions occurred. INTERPRETATION Bacterial colonization density was significantly reduced in babies receiving 1% CHG washes but colonization levels rebounded rapidly post-intervention. Emollient application improved skin condition but was associated with higher rates of S. aureus colonization. FUNDING South African Medical Research Council; National Institutes of Health (TW010682).
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Key Words
- ACC, aerobic colony count
- AE, adverse event
- AMR, antimicrobial resistance
- ART, antiretroviral therapy
- BSI, bloodstream infection
- CFU, colony forming unit
- CHG, chlorhexidine gluconate
- CI, confidence interval
- EM, emollient
- ESBL, extended-spectrum B-lactamase
- HAI, healthcare-associated infection
- HIV, human immunodeficiency virus
- IPC, infection prevention and control
- KMC, kangaroo mother care
- LMIC, low-to-middle income countries
- NEC, necrotizing enterocolitis
- NICU, neonatal intensive care unit
- SD, standard deviation
- SOC, standard of care
- UIPC, Unit for Infection Prevention and Control
- UTI, urinary tract infection
- VLBW, very low birth weight
- bacterial colonization
- chlorhexidine gluconate
- d, day
- emollient
- hospital-acquired infection
- infection prevention
- nCPAP, nasal cannula positive airways pressure
- neonatal unit
- spp, species
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Affiliation(s)
- Angela Dramowski
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
- Corresponding author.
| | - Sheylyn Pillay
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University and National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Adrie Bekker
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Ilhaam Abrahams
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Mark F. Cotton
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Susan E. Coffin
- Division of Infectious Diseases, Children's Hospital of Philadelphia and Department of Paediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Andrew C. Whitelaw
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University and National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
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18
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Auguet OT, Niehus R, Gweon HS, Berkley JA, Waichungo J, Njim T, Edgeworth JD, Batra R, Chau K, Swann J, Walker SA, Peto TE, Crook DW, Lamble S, Turner P, Cooper BS, Stoesser N. Population-level faecal metagenomic profiling as a tool to predict antimicrobial resistance in Enterobacterales isolates causing invasive infections: An exploratory study across Cambodia, Kenya, and the UK. EClinicalMedicine 2021; 36:100910. [PMID: 34124634 PMCID: PMC8173267 DOI: 10.1016/j.eclinm.2021.100910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/16/2021] [Accepted: 04/30/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) in Enterobacterales is a global health threat. Capacity for individual-level surveillance remains limited in many countries, whilst population-level surveillance approaches could inform empiric antibiotic treatment guidelines. METHODS In this exploratory study, a novel approach to population-level prediction of AMR in Enterobacterales clinical isolates using metagenomic (Illumina) profiling of pooled DNA extracts from human faecal samples was developed and tested. Taxonomic and AMR gene profiles were used to derive taxonomy-adjusted population-level AMR metrics. Bayesian modelling, and model comparison based on cross-validation, were used to evaluate the capacity of each metric to predict the number of resistant Enterobacterales invasive infections at a population-level, using available bloodstream/cerebrospinal fluid infection data. FINDINGS Population metagenomes comprised samples from 177, 157, and 156 individuals in Kenya, the UK, and Cambodia, respectively, collected between September 2014 and April 2016. Clinical data from independent populations included 910, 3356 and 197 bacterial isolates from blood/cerebrospinal fluid infections in Kenya, the UK and Cambodia, respectively (samples collected between January 2010 and May 2017). Enterobacterales were common colonisers and pathogens, and faecal taxonomic/AMR gene distributions and proportions of antimicrobial-resistant Enterobacterales infections differed by setting. A model including terms reflecting the metagenomic abundance of the commonest clinical Enterobacterales species, and of AMR genes known to either increase the minimum inhibitory concentration (MIC) or confer clinically-relevant resistance, had a higher predictive performance in determining population-level resistance in clinical Enterobacterales isolates compared to models considering only AMR gene information, only taxonomic information, or an intercept-only baseline model (difference in expected log predictive density compared to best model, estimated using leave-one-out cross-validation: intercept-only model = -223 [95% credible interval (CI): -330,-116]; model considering only AMR gene information = -186 [95% CI: -281,-91]; model considering only taxonomic information = -151 [95% CI: -232,-69]). INTERPRETATION Whilst our findings are exploratory and require validation, intermittent metagenomics of pooled samples could represent an effective approach for AMR surveillance and to predict population-level AMR in clinical isolates, complementary to ongoing development of laboratory infrastructures processing individual samples.
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Affiliation(s)
- Olga Tosas Auguet
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Rene Niehus
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Hyun Soon Gweon
- School of Biological Sciences, University of Reading, Reading, UK
- Centre for Ecology & Hydrology, Wallingford, UK
| | - James A. Berkley
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- The Childhood Acute Illness and Nutrition (CHAIN) Network, Nairobi, Kenya
| | | | - Tsi Njim
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Jonathan D. Edgeworth
- Centre for Clinical Infection and Diagnostics Research (CIDR), Department of Infectious Diseases, King's College London, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research (CIDR), Department of Infectious Diseases, King's College London, London, UK
| | - Kevin Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jeremy Swann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah A. Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and Antimicrobial Resistance, Oxford, UK
| | - Tim E.A. Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and Antimicrobial Resistance, Oxford, UK
| | - Derrick W. Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and Antimicrobial Resistance, Oxford, UK
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Cambodia-Oxford Medical Research Unit, Microbiology Department, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Ben S. Cooper
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and Antimicrobial Resistance, Oxford, UK
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Bayleyegn B, Fisaha R, Kasew D. Fecal carriage of extended spectrum beta-lactamase producing Enterobacteriaceae among HIV infected children at the University of Gondar Comprehensive Specialized Hospital Gondar, Ethiopia. AIDS Res Ther 2021; 18:19. [PMID: 33882946 PMCID: PMC8061171 DOI: 10.1186/s12981-021-00347-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/12/2021] [Indexed: 12/31/2022] Open
Abstract
Background Human immunodeficiency virus (HIV) and extended spectrum beta lactamase (ESBL) producing Enterobacteriaceae infections are the major challenges in sub-Saharan Africa. Data on the carriage rate of ESBL producing Enterobacteriaceae among HIV infected children is lacking in Ethiopia. Hence this study was aimed to investigate fecal carriage of ESBL producing Enterobacteriaceae among HIV infected children at the University of Gondar comprehensive Specialized Hospital. Methods A cross-sectional study was conducted among HIV infected children from January to April 2020. Stool specimens were collected from 161 study participants by convenient sampling and cultured on MacConkey agar. Biochemical identification, antimicrobial susceptibility testing including ESBL production were carried out. Data were analyzed by SPSS version-20 and P-value < 0.05 on multivariate logistic regression analysis was regarded as statistically significant. Results From a total of 161 study participants male to female ratio was 1:1.1. Moreover; 96.3% of participants were in HIV stage-I and 90.1% had at least a year highly active antiretroviral therapy exposure. A total of 186 Enterobacteriaceae, with E. coli 60% and K. pneumonia 16.13% predominance were isolated from 161 participants. Majority of isolates were most resistant to amoxicillin (95.1%) and sensitive to CHL (94.1%), CXT (91.4%) and CAZ (91.4%). There were 71(38.17%) multidrug resistant isolates, 13 of which were also ESBL producers. The overall ESBL carriage rate was 32/161 (19.9%). History of antibiotic use was the independent factor associated with ESBL carriage (AOR 3.23 (95% CI 1.054–9.88)) and P-value of 0.04. Conclusion ESBL carriage rate of HIV infected children was considerable. Previous antibiotic use was the independent factor. Regular screening for antibiotic resistance on HIV patients before prescription and large-scale antibiotic resistance survey including healthy community may be important.
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20
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Tompkins K, Juliano JJ, van Duin D. Antimicrobial Resistance in Enterobacterales and Its Contribution to Sepsis in Sub-saharan Africa. Front Med (Lausanne) 2021; 8:615649. [PMID: 33575265 PMCID: PMC7870712 DOI: 10.3389/fmed.2021.615649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
Antibiotic resistant Enterobacterales (formerly Enterobactereaceae) are a growing threat to Sub-Saharan Africa. Genes causing antibiotic resistance are easily spread between the environment and humans and infections due to drug resistant organisms contribute to sepsis mortality via delayed time to appropriate antimicrobial therapy. Additionally, second or third-line antibiotics are often not available or are prohibitively expensive in resource-constrained settings leading to limited treatment options. Lack of access to water and sanitation facilities, unregulated use of antibiotics, and malnutrition are contributors to high rates of antibiotic resistance in the region. Improvements in the monitoring of drug resistant infections and antibiotic stewardship are needed to preserve the efficacy of antibiotics for the future.
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Affiliation(s)
- Kathleen Tompkins
- Division of Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Jonathan J Juliano
- Division of Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States.,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States.,Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - David van Duin
- Division of Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
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21
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Nadimpalli ML, Bourke CD, Robertson RC, Delarocque-Astagneau E, Manges AR, Pickering AJ. Can breastfeeding protect against antimicrobial resistance? BMC Med 2020; 18:392. [PMID: 33317529 PMCID: PMC7737306 DOI: 10.1186/s12916-020-01862-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/19/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The proportion of infections among young children that are antimicrobial-resistant is increasing across the globe. Newborns may be colonized with enteric antimicrobial-resistant pathogens early in life, which is a risk factor for infection-related morbidity and mortality. Breastfeeding is actively promoted worldwide for its beneficial impacts on newborn health and gut health. However, the role of breastfeeding and human milk components in mitigating young children's carriage of antimicrobial-resistant pathogens and antibiotic resistance genes has not been comprehensively explored. MAIN BODY Here, we review how the act of breastfeeding, early breastfeeding, and/or human milk components, such as the milk microbiota, secretory IgA, human milk oligosaccharides, antimicrobial peptides, and microRNA -bearing extracellular vesicles, could play a role in preventing the establishment of antimicrobial-resistant pathogens in young children's developing gut microbiomes. We describe findings from recent human studies that support this concept. CONCLUSION Given the projected rise in global morbidity and mortality that will stem from antimicrobial-resistant infections, identifying behavioral or nutritional interventions that could decrease children's susceptibility to colonization with antimicrobial-resistant pathogens may be one strategy for protecting their health. We suggest that breastfeeding and human milk supplements deserve greater attention as potential preventive measures in the global effort to combat antimicrobial resistance, particularly in low- and middle-income settings.
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Affiliation(s)
- Maya L Nadimpalli
- Department of Civil and Environmental Engineering, Tufts University, Science & Engineering Complex, Anderson Hall, Room 204, 200 College Avenue, Medford, MA, USA. .,Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA.
| | - Claire D Bourke
- Centre for Genomics and Child Health, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK.,Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Ruairi C Robertson
- Centre for Genomics and Child Health, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK
| | - Elisabeth Delarocque-Astagneau
- Université Paris-Saclay, UVSQ, Inserm, CESP, Team Anti-infective Evasion and Pharmacoepidemiology, 78180 Montigny, France.,AP-HP, GHU Paris Saclay University, Raymond Poincaré Hospital, Epidemiology and Public Health Department, 92380 Garches, France
| | - Amee R Manges
- School of Population and Public Health, The University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Amy J Pickering
- Department of Civil and Environmental Engineering, Tufts University, Science & Engineering Complex, Anderson Hall, Room 204, 200 College Avenue, Medford, MA, USA.,Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA
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22
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Mwandigha AM, Kamori D, Kibwana UO, Masoud S, Manyahi J, Majigo M. Fecal carriage and factors associated with extended-spectrum β-lactamase-producing Enterobacteriaceae among pregnant women at the tertiary referral hospital, Tanzania. Trop Med Health 2020; 48:84. [PMID: 33061787 PMCID: PMC7545914 DOI: 10.1186/s41182-020-00271-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023] Open
Abstract
Background Infections due to extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) are increasing worldwide. Evidence indicates that fecal carriage of ESBL-E in pregnancy predisposes women to potential life-threatening urinary tract infections and subsequently increasing the risk of neonatal infections. There is limited data regarding fecal carriage of ESBL-E and associated factors among pregnant women in Tanzania. We aimed to address the gap by determining the proportion of pregnant women with ESBL-E fecal carriage and identify the related factors. Methodology A hospital-based cross-sectional study was conducted at Muhimbili National Hospital in Dar es Salaam, Tanzania. A total of 182 pregnant women at the gestational age of 37 weeks and above were enrolled. Participants’ socio-demographic, clinical, and hygienic information were collected by using a well-structured questionnaire. Rectal swabs were collected and processed for isolation of ESBL-E. The extended-spectrum β-lactamase production and antibiotic susceptibility test (AST) were performed using a double-disc synergy test and Kirby-Bauer disc diffusion method, respectively. Results A total of 117 (64.3%) pregnant women were found to carry ESBL-E. Factors such as self-prescription of antibiotic medication during pregnancy, low education level, and toilet sharing were independently associated with ESBL-E fecal carriage. Five ESBL-E species that were isolated include Escherichia coli (84.6%), Klebsiella pneumoniae (8.9%), Klebsiella oxytoca (3.3%), Citrobacter spp. (1.6%), and Enterobacter spp. (1.6%). ESBL-E isolates demonstrated high resistance to aztreonam and sulphamethoxazole-trimethoprim. Conclusion This study has revealed a relatively high fecal carriage of ESBL-E among pregnant women, suggesting that there is a need for routine screening among that population. We recommend further studies to explore comprehensively the factors associated with high fecal carriage of ESBL-E in pregnancy and the potential transmission kinetics to their newborn babies.
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Affiliation(s)
- Ambele M Mwandigha
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Doreen Kamori
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Upendo O Kibwana
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Salim Masoud
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Joel Manyahi
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Mtebe Majigo
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
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23
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Eberhart M, Grisold A, Lavorato M, Resch E, Trobisch A, Resch B. Extended-spectrum beta-lactamase (ESBL) producing Enterobacterales in stool surveillance cultures of preterm infants are no risk factor for necrotizing enterocolitis: a retrospective case-control study over 12 years. Infection 2020; 48:853-860. [PMID: 32462287 PMCID: PMC7674344 DOI: 10.1007/s15010-020-01453-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/22/2020] [Indexed: 12/17/2022]
Abstract
Purpose Microbial dysbiosis has been found preceding necrotizing enterocolitis (NEC) in preterm infants; thus, we aimed to investigate whether there is evidence that neonates with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) positive stool cultures are at higher risk for NEC at the NICU. Methods We included very preterm inborn infants of ≤ 32 weeks of gestational age being fecal carriers of ESBL-E and compared them with 1:1 matched (gestational age, birth weight, gender and year) controls tested negative for ESBL-E in the stool between 2005 and 2016. An association with NEC was defined as the first detection of ESBL-E before or at the time of definite diagnosis of NEC. Results During the study period, we diagnosed 217 infants with a total of 270 ESBL-E. We identified ten different species with ESBL-producing Klebsiella oxytoca being the most common one (46%) followed by Klebsiella pneumoniae (19%), and Citrobacter freundii (17%). Ten out of 217 infants had any kind of NEC in the case group compared to two of the controls (p < 0.01), but only four cases with predefined criteria were associated with NEC ≥ stage IIa (1.8 vs. 0.5%, p = 0.089, OR 4.1, CI95% 0.45–36.6). NEC mortality rate was 2/8 (25%). Conclusions We observed a threefold increase of ESBL-E in stool surveillance cultures during study time and germs were dominated by ESBL-producing Klebsiella spp. There was no evidence that preterm infants colonized with ESBL-E in the stool were at higher risk for definite NEC.
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Affiliation(s)
- Martin Eberhart
- Research Unit for Neonatal Infectious Diseases and Epidemiology, Medical University of Graz, Graz, Austria
| | - Andrea Grisold
- D&R Institute of Hygiene Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Michela Lavorato
- Research Unit for Neonatal Infectious Diseases and Epidemiology, Medical University of Graz, Graz, Austria
- Policlinico Umberto I Hospital, Sapienza University of Rome, Rome, Italy
| | - Elisabeth Resch
- Research Unit for Neonatal Infectious Diseases and Epidemiology, Medical University of Graz, Graz, Austria
- Division of Neonatology, Department of Paediatrics and Adolescent Medicine, Medical University of Graz, Auenbruggerplatz 34/2, 8036, Graz, Austria
| | - Andreas Trobisch
- Research Unit for Neonatal Infectious Diseases and Epidemiology, Medical University of Graz, Graz, Austria
- Division of Neonatology, Department of Paediatrics and Adolescent Medicine, Medical University of Graz, Auenbruggerplatz 34/2, 8036, Graz, Austria
| | - Bernhard Resch
- Research Unit for Neonatal Infectious Diseases and Epidemiology, Medical University of Graz, Graz, Austria.
- Division of Neonatology, Department of Paediatrics and Adolescent Medicine, Medical University of Graz, Auenbruggerplatz 34/2, 8036, Graz, Austria.
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Impact of chlorhexidine baths on suspected sepsis and bloodstream infections in hospitalized neonates in Zambia. Int J Infect Dis 2020; 96:54-60. [PMID: 32304821 DOI: 10.1016/j.ijid.2020.03.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/10/2020] [Accepted: 03/18/2020] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION Sepsis is the leading cause of infectious morbidity and mortality among hospitalized neonates. In high-resource pediatric and adult intensive care units, use of aqueous chlorhexidine (CHG) solution has been associated with reduced risk of bloodstream infections (BSI). OBJECTIVES To assess the impact of bathing of neonates with 2% CHG on BSI, suspected sepsis, and mortality in a low-income country neonatal care unit. METHODS We conducted a secondary analysis of data from the Sepsis Prevention in Neonates in Zambia (SPINZ) study, a prospective observational cohort study performed at a large public referral hospital in Lusaka, Zambia. The SPINZ study assessed the impact of an infection control bundle (consisting of alcohol hand rub, SMS hygiene reminders, enhanced environmental cleaning, and CHG baths for babies ≥1.5 kg) on sepsis, BSI, and all-cause mortality. Episodic shortages in study staffing resulted in some enrolled babies not receiving a CHG bath. Using Longitudinal Targeted Maximum Likelihood Estimation and Cox proportional hazards regression to adjust for observed confounding, we estimated the causal effect of receiving a CHG bath within the first 3 days of life on suspected sepsis, BSI, and death among inborn babies enrolled during the study implementation and intervention phases. RESULTS The majority of inborn, enrolled babies ≥1.5 kg received a CHG bath within 3 days of NICU admission (864 of 1233, 70%). We found that CHG bathing reduced the hazard rate of BSI among inborn babies ≥1.5 kg by a factor of 0.58 (p = 0.10, 95% CI: 0.31, 1.11), corresponding to an absolute risk reduction of 9.6 percentage points within a week of admission (p = 0.002, 95% CI: 3.4-15.7 percentage points). We did not find a statistically significant effect of CHG bathing on culture-negative sepsis (p = 0.54) or death (p = 0.85). CONCLUSION In our single center study, CHG bathing at admission was associated with a reduced risk of BSI due to a pathogenic organism after adjusting for potential confounding. Our results suggest that CHG may be an effective intervention for preventing neonatal sepsis in high-risk, low-income country settings.
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Extended-spectrum beta-lactamases and plasmid diversity in urinary isolates of Escherichia coli in Croatia: a nation-wide, multicentric, retrospective study. Folia Microbiol (Praha) 2020; 65:649-667. [PMID: 31953747 DOI: 10.1007/s12223-019-00769-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 12/30/2019] [Indexed: 10/25/2022]
Abstract
In recent years, a dramatic increase in the prevalence of Escherichia coli strains producing extended-spectrum β-lactamases (ESBLs) has been observed - both in the community and in healthcare settings. This multicentric study aimed to characterize ESBLs produced by E. coli isolates causing hospital-onset and community urinary tract infections, as well as to compare their antimicrobial sensitivity patterns, β-lactamase content and plasmid types. Phenotypic tests for the detection of ESBLs and plasmid-mediated AmpC β-lactamases were initially pursued, followed by molecular detection of resistance genes, plasmid characterization, genotyping with pulsed-field gel electrophoresis and whole genome sequencing (WGS). The isolates exhibited high level of resistance to expanded-spectrum cephalosporins (ESC) and carried CTX-M (cefotaximase-Munich) or TEM (Temoniera) β-lactamases. All six representative isolates subjected to WGS belonged to the widespread clone ST131. In conclusion, our study demonstrated dissemination of group 1 CTX-M positive E. coli in different geographic regions of Croatia, but also different components of the health care systems (hospitals, nursing homes and the community) and confirmed the switch from SHV-2 (suphydril variant) and SHV-5 ESBLs to the nation-wide predominance of group 1 CTX-M β-lactamases. Different plasmids were shown to be associated with the dissemination of blaCTX-M genes in different geographic regions of Croatia.
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