Fecal carriage of ESBL-producing E. coli and K. pneumoniae in children in Guinea-Bissau: a hospital-based cross-sectional study

Antimicrobial resistance in community-acquired enteric pathogens among children aged ≤ 10-years in low-and middle-income countries: a systematic review and meta-analysis

Introduction

Antimicrobial resistance (AMR) is a global health priority. This systematic review summarizes the prevalence of AMR in enteric pathogens originating from the community, specifically among ≤10-year-old children in low-and middle-income countries (LMICs). In addition, it presents the proportions of pooled resistance in Campylobacter spp., Escherichia coli, Shigella spp., and Salmonella spp. (CESS) to clinically relevant antibiotics.

Methods

Six online repositories, namely PubMed, Medline, Web of Science, Cochrane Library, CABI, and EMBASE were searched for articles published between January 2005 and September 2024. Random-effects meta-analysis models were constructed to estimate the pooled AMR proportions for CESS pathogens, and a subgroup analysis by region was also carried out.

Results

A total of 64 publications from 23 LMICs met our inclusion criteria. The pooled estimates of E. coli AMR for clinically important antibiotics were as follows: sulfamethoxazole/trimethoprim (SXT) 71% [95%CI: 57-82%]; ampicillin (AMP) 56% [95%CI: 44-67%]; ciprofloxacin (CIP) 10% [95%CI: 5-20%]; and ceftriaxone (CRO) 8% [95%CI: 2-31%]. The proportions of AMR detected in Shigella spp. were AMP 76% [95%CI: 60-87%]; nalidixic acid (NA) 9% [95%CI: 2-31%]; CIP 3% [95%CI: 0-15%]; and CRO 2% [95%CI: 0-19%]. The proportions of Salmonella spp. AMR were AMP 55% [95%CI: 35-73%] and SXT 25% [95%CI: 15-38%]. The proportions of Campylobacter spp. AMR were erythromycin (ERY) 33% [95%CI: 12-64%] and CIP 27% [95%CI: 8-61%]. There was high variability in the regional subgroup analysis, with high interstudy and regional heterogeneity I2 ≥ 75%.

Conclusion

Our results shed light on drug-resistant enteric bacterial pathogens in young children, providing evidence that CESS pathogens are becoming increasingly resistant to clinically important antimicrobials. Regional differences in resistance patterns between these community isolates highlight the need for strong national and regional surveillance to detect regional variations and inform treatment and appropriate antibiotic stewardship programs. The limitations of our findings include high regional variability, significant interstudy heterogeneity, and underrepresentation of certain LMICs.

Systematic review registration

https://inplasy.com/inplasy-2024-2-0051/, registration number: INPLASY202420051.

Fecal carriage of ESBL-producing E. coli and genetic characterization in rural children and livestock in the Somali region, Ethiopia: a one health approach

BACKGROUND

The emergence and spread of Extended-Spectrum Beta-Lactamase (ESBL)-producing Escherichia coli pose significant challenges for treatment of infections globally. This challenge is exacerbated in sub-Saharan African countries, where the prevalence of ESBL-producing E. coli is high. This, combined with the lack of a strong and supportive healthcare system, leads to increased morbidity and mortality due to treatment failures. Notably, studies in Ethiopia have primarily focused on hospital settings, leaving a gap in understanding ESBL prevalence in rural communities, where human-animal proximity may facilitate microbial exchange.

METHODS

We conducted a community-based study in the rural Somali region of Ethiopia, simultaneously examining the fecal carriage of ESBL-producing E. coli in children aged 2-5 years and their livestock (cattle, camel, goat). Fecal samples from 366 children and 243 animals underwent phenotypic screening for ESBL-producing E. coli. Following phenotypic confirmation, ESBL resistance genes were identified via conventional PCR. Whole-genome sequencing (WGS) was performed on a subset of isolates from human feces.

RESULTS

We found that 43% (159/366) of children and 3.7% (9/244) of livestock harbored ESBL-producing E. coli. The ESBL gene blaCTX-M-15 was predominant in human (82.7%, 120/145) and livestock (100%) isolates. In the 48 human E. coli isolates subjected to WGS, a high diversity resulting in 40 sequence types (STs) was observed. Among these, ST-2353 was the most prevalent (5/48), followed by ST-10 and ST-48 (3/48) and ST-38, ST-450, and ST-4750 (2/48). These STs were associated with multiple resistance genes, such as blaCTX-M-15, blaTEM-1B, blaOXA-1, blaCTX-M-14 and blaTEM-35.

CONCLUSION

We report a high prevalence of ESBL E. coli in rural children, which outnumbers its prevalence in livestock. These isolates displayed a high diversity of sequence types (STs) with ST-2353 being the dominant ST. Our study is the first to report the association of ST-2353 with multi-drug resistance genes in Ethiopia. Further research using an integrated approach including other domains such as water and food products is needed to truly understand and combat AMR transmission and acquisition in this region.

Neonatal Colonization With Antibiotic-Resistant Pathogens in Low- and Middle-Income Countries: A Systematic Review and Meta-Analysis

Importance

In low- and middle-income countries (LMICs), neonatal bacterial infections are mainly caused by Enterobacterales species and Staphylococcus aureus, which are also the leading causes of mortality directly attributable to antimicrobial resistance. As bacterial colonization often precedes infection, better knowledge of colonization is crucial to prevent antibiotic-resistant neonatal sepsis.

Objective

To synthesize current evidence on the prevalence of and factors associated with colonization with third-generation cephalosporin-resistant Enterobacterales (3GCRE), carbapenem-resistant Enterobacterales (CRE), and methicillin-resistant S aureus (MRSA) during the first 3 months of life in LMICs.

Data Sources

PubMed, Scopus, Web of Science, and the World Health Organization Global Index Medicus were searched for articles published from January 1, 2000, through July 29, 2024.

Study Selection

Included studies were conducted in LMICs and reported prevalence rates or factors associated with colonization with 3GCRE, CRE, or MRSA in neonates and infants up to 3 months of age. Outbreak reports were excluded.

Data Extraction and Synthesis

Data extraction and risk-of-bias assessment using a Joanna Briggs Institute tool were performed by 2 independent reviewers. Pooled prevalence for each pathogen was computed using a random-effects model. Reporting followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guideline.

Main Outcomes and Measures

Prevalence of and factors associated with 3GCRE, CRE, and MRSA colonization.

Results

Of the 3147 articles identified in the search, 67 studies (51 for 3GCRE and CRE and 16 for MRSA) including 17 152 individuals were eligible. The pooled prevalence of 3GCRE colonization was 30.2% (95% CI, 21.4%-40.7%; τ2 = 1.48; I2 = 95.1%), varying from 18.2% (95% CI, 10.8%-29.1%) in nonhospitalized individuals to 48.2% (95% CI, 36.4%-60.2%) in hospitalized individuals. The prevalence of CRE colonization was 2.6% (95% CI, 0.7%-8.8%; τ2 = 7.79; I2 = 95.6%), while it was 2.7% (95% CI, 1.0%-6.7%; τ2 = 2.58; I2 = 93.5%) for MRSA. Increased risk of colonization with 3GCRE was associated with hospital birth (odds ratio [OR], 1.87; 95% CI, 1.33-2.64), neonatal antibiotic use (OR, 2.96; 95% CI, 1.43-6.11), and prolonged rupture of membranes (OR, 3.86; 95% CI, 2.19-6.84).

Conclusions and Relevance

In this systematic review and meta-analysis of antibiotic-resistant pathogen carriage in individuals aged 0 to 3 months, the pooled prevalence was substantial despite a limited exposure period. Although high heterogeneity between studies limited extrapolation of results, the findings highlight the need for further investigation to identify transmission routes and to design targeted and effective preventive measures.

Carriage of third-generation cephalosporin-resistant and carbapenem-resistant Enterobacterales among children in sub-Saharan Africa: a systematic review and meta-analysis

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.

ESBL-producing Enterobacteriaceae in a rural Rwandan community: Carriage among community members, livestock, farm products and environment

OBJECTIVES

Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) are spreading globally. However, respective data from African communities including livestock and environmental specimens are rare. In a rural community of southern Rwanda, we assessed intestinal carriage of ESBL-PE among residents and livestock as well as presence in household specimens and examined associated factors.

METHODS

Samples of humans and livestock (both rectal swabs), soil, water, vegetables and animal products were collected within 312 community households in Sovu, Southern Rwanda. Specimens were screened for ESBL-PE on chromogenic agar, and susceptibility to common antibiotics was determined by disc diffusion assays. Socio-demographic information was collected with questionnaires focusing on the socio-economic background, alimentation, living conditions, hygiene measures and medical history of the participants.

RESULTS

Data and specimens from 312 randomly selected households including 617 human beings, 620 livestock and of approximately each 300 kitchen vegetables, animal products, soil and drinking water were analysed. Overall, 14.8% of 2508 collected samples were positive for ESBL-PE; figures were highest for humans (37.9%) and livestock (15.6%), lower for vegetables (3.8%) and animal products (3.3%), and lowest for soil (1.6%) and water (0.6%). Most detected ESBL-PE were Escherichia coli (93.5%) in addition to Klebsiella pneumoniae (6.5%). Cross-resistance to ampicillin-sulbactam, ciprofloxacin and co-trimoxazole was common. Logistic regression identified increasing age, another ESBL-PE positive household member, prolonged time for fetching water, current diarrhoea and the ability to pay school fees as independent predictors of intestinal ESBL-PE carriage among community members.

CONCLUSIONS

ESBL-PE carriage is common in a rural Rwandan farming community. Carriage in livestock is not associated with human carriage. Associated factors suggest few addressable risk factors. The data indicate that in southern Rwanda, ESBL-PE are no longer primarily hospital-based but circulate in the community.

Horizontal transfer and driving factors of extended-spectrum β-lactamase-producing resistance genes in mice intestine after the ingestion of contaminated water

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) has been identified in various water environments, posing a serious risk to public health. However, whether and how ESBL-producing genes in water-derived E. coli can spread among mammalian gut microbiota via drinking water is largely unclear. To address this problem, horizontal transfer characterization of ESBL-producing genes in mice gut microbiota was determined after the oral ingestion of contaminated water by ESBL-producing E. coli, and then the driving factors were comprehensively examined from multiple different perspectives. The results showed that water-borne ESBL-producing E. coli can colonize in the mice intestine, the ESBL-producing genes can horizontally spread among gut microbiota, and the recipient bacteria include opportunistic pathogens Klebsiella pneumoniae and Salmonella enterica. This horizontal spread may be attributed to the intestinal micro-environment changes caused by the ingestion of contaminated water by ESBL-producing E. coli. These changes, including gut microbiota diversity, increased levels of inflammatory response and reactive oxygen species, cell membrane permeability, and expression levels of conjugative transfer-related genes, are all major driving factors for horizontal transfer of ESBL-producing genes in mice gut microbiota. Our findings highlight the potential for ESBL-producing E. coli to spread resistance genes to mammalian gut microbiota during ingestion of contaminated water.

Carriage of β-lactamase and carbapenemase-producing Enterobacteriaceae in hospitalized patients at debre tabor comprehensive specialized hospital

Background

Antimicrobial resistance has remained global public health threat. Carriage with drug-resistant bacterial pathogens, particularly beta-lactamase and carbapenemase-producing Enterobacteriaceae is among the most concerning. The purpose of this study was to look into the magnitude, antimicrobial resistance patterns, and associated risk factors among hospitalized patients.

Methods

A facility-based cross-sectional study was conducted on 383 hospitalized patients at Debre Tabor Comprehensive Specialized Hospital between September 2022 and May 2023. A pre-tested structured questionnaire was used to collect sociodemographic and clinical data. The data on the etiologic agent was collected using standard bacteriological techniques. Briefly, stool specimens were collected aseptically into sterile, leak-proof stool cups. The stool sample was inoculated onto MacConkey agar and incubated aerobically at 37 °C for 24 h. The species isolation and antimicrobial resistance patterns were then performed adhering to bacteriological procedures. In the analysis, a p-value of <0.05 was considered statistically significant.

Results

There were 383 study participants, and men made up the majority (55.6%). The study participants' mean age was 33 ± 18 years. Three hundred and seventy-seven (88%) of the study's participants had no previous history of antibiotic use. There were 102 (26.6%) and 21 (5.5%) cases of gastrointestinal carriage caused by Enterobacteriaceae that produce beta-lactamase and carbapenemase, respectively. In total, 175 isolates of Enterobacteriaceae were detected. E. coli (n = 89) and K. pneumoniae (n = 51) were the most frequently recovered. In this study, 46 (79.3%) and 8 (13.8%) isolates of E. coli that produce beta-lactamase were resistant to ampicillin and amoxicillin/clavulanic acid, respectively. Furthermore, participants who had previously used antibiotics experienced a two-fold increase in exposure to gastrointestinal tract carriage by carbapenemase-producing Enterobacteriaceae [AOR, 95% CI (2.01, 1.06-2.98), p = 0.001].

Conclusions

The emergence of drug-resistant pathogens is a growing concern. An increase in the prevalence of drug-resistant infections in hospitalized patients is warranting further investigation.

Source-tracking ESBL-producing bacteria at the maternity ward of Mulago hospital, Uganda

INTRODUCTION

Escherichia coli, Klebsiella pneumoniae and Enterobacter (EKE) are the leading cause of mortality and morbidity in neonates in Africa. The management of EKE infections remains challenging given the global emergence of carbapenem resistance in Gram-negative bacteria. This study aimed to investigate the source of EKE organisms for neonates in the maternity environment of a national referral hospital in Uganda, by examining the phenotypic and molecular characteristics of isolates from mothers, neonates, and maternity ward.

METHODS

From August 2015 to August 2016, we conducted a cross-sectional study of pregnant women admitted for elective surgical delivery at Mulago hospital in Kampala, Uganda; we sampled (nose, armpit, groin) 137 pregnant women and their newborns (n = 137), as well as health workers (n = 67) and inanimate objects (n = 70 -beds, ventilator tubes, sinks, toilets, door-handles) in the maternity ward. Samples (swabs) were cultured for growth of EKE bacteria and isolates phenotypically/molecularly investigated for antibiotic sensitivity, as well as β-lactamase and carbapenemase activity. To infer relationships among the EKE isolates, spatial cluster analysis of phenotypic and genotypic susceptibility characteristics was done using the Ridom server.

RESULTS

Gram-negative bacteria were isolated from 21 mothers (15%), 15 neonates (11%), 2 health workers (3%), and 13 inanimate objects (19%); a total of 131 Gram-negative isolates were identified of which 104 were EKE bacteria i.e., 23 (22%) E. coli, 50 (48%) K. pneumoniae, and 31 (30%) Enterobacter. Carbapenems were the most effective antibiotics as 89% (93/104) of the isolates were susceptible to meropenem; however, multidrug resistance was prevalent i.e., 61% (63/104). Furthermore, carbapenemase production and carbapenemase gene prevalence were low; 10% (10/104) and 6% (6/104), respectively. Extended spectrum β-lactamase (ESBL) production occurred in 37 (36%) isolates though 61 (59%) carried ESBL-encoding genes, mainly blaCTX-M (93%, 57/61) implying that blaCTX-M is the ideal gene for tracking ESBL-mediated resistance at Mulago. Additionally, spatial cluster analysis revealed isolates from mothers, new-borns, health workers, and environment with similar phenotypic/genotypic characteristics, suggesting transmission of multidrug-resistant EKE to new-borns.

CONCLUSION

Our study shows evidence of transmission of drug resistant EKE bacteria in the maternity ward of Mulago hospital, and the dynamics in the ward are more likely to be responsible for transmission but not individual mother characteristics. The high prevalence of drug resistance genes highlights the need for more effective infection prevention/control measures and antimicrobial stewardship programs to reduce spread of drug-resistant bacteria in the hospital, and improve patient outcomes.

Acquisition and carriage of genetically diverse multi-drug resistant gram-negative bacilli in hospitalised newborns in The Gambia

BACKGROUND

This detailed genomic study characterised multi-drug resistant-Gram negative bacilli (MDR-GNB) carriage in neonates < 2 kg and paired mothers at a low-resource African hospital.

METHODS

This cross-sectional cohort study was conducted at the neonatal referral unit in The Gambia with weekly neonatal skin and peri-anal sampling and paired maternal recto-vaginal swabs. Prospective bacteriological culture used MacConkey agar with species identification by API20E and API20NE. All GNB isolates underwent whole genome sequencing on Illumina Miseq platform. Multi-Locus Sequence Typing and SNP-distance analysis identified strain type and relatedness.

RESULTS

135 swabs from 34 neonates and 21 paired mothers, yielded 137 GNB isolates, of which 112 are high quality de novo assemblies. Neonatal MDR-GNB carriage prevalence is 41% (14/34) at admission with 85% (11/13) new acquisition by 7d. Multiple MDR and ESBL-GNB species are carried at different timepoints, most frequently K. pneumoniae and E. coli, with heterogeneous strain diversity and no evidence of clonality. 111 distinct antibiotic resistance genes are mostly beta lactamases (Bla-AMPH, Bla-PBP, CTX-M-15, Bla-TEM-105). 76% (16/21) and 62% (13/21) of mothers have recto-vaginal carriage of ≥1 MDR-GNB and ESBL-GNB respectively, mostly MDR-E. coli (76%, 16/21) and MDR-K. pneumoniae (24%, 5/21). Of 21 newborn-mother dyads, only one have genetically identical isolates (E. coli ST131 and K. pneumoniae ST3476).

CONCLUSIONS

Gambian hospitalised neonates exhibit high MDR and ESBL-GNB carriage prevalence with acquisition between birth and 7d with limited evidence supporting mother to neonate transmission. Genomic studies in similar settings are required to further understand transmission and inform targeted surveillance and infection prevention policies.

High level of colonization with 3rd-generation cephalosporin-resistant Enterobacterales in African community settings, Ghana

A cross-sectional survey was conducted in eight Ghanaian communities to investigate the extent of intestinal colonization with 3^rd-generation cephalosporin-resistant Enterobacterales. The study collected faecal samples and corresponding lifestyle data from 736 healthy residents to assess the occurrence of cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae, with a focus on genotypes of plasmid-mediated ESBLs, AmpCs, and carbapenemases. The results showed that 371 participants (50.4%) carried 3^rd-generation cephalosporin-resistant E. coli (n=362) and K. pneumoniae (n=9). Most of these were ESBL-producing E. coli (n=352, 94.9%), carrying CTX-M genes (96.0%, n=338/352), mostly for CTX-M-15 (98.9%, n=334/338). Nine participants (1.2%) carried AmpC-producing E. coli that harboured bla_DHA-1 or blaCMY-2 genes, and two participants (0.3%) each carried a carbapenem-resistant E. coli that harboured both bla_NDM-1 and bla_CMY-2. Quinolone-resistant O25b: ST131 E. coli were recovered from six participants (0.8%) and were all CTX-M-15 ESBL-producers. Having a household toilet facility was significantly associated with a reduced risk of intestinal colonization (adjusted odds ratio, 0.71; 95% CI, 0.48-0.99; P-value=0.0095) in multivariate analysis. These findings raise serious public health concerns, and effective control of the spread of antibiotic-resistant bacteria is possible by providing better sanitary conditions for communities.

Fecal Carriage of Extended-Spectrum β-Lactamases and pAmpC Producing Enterobacterales in an Iranian Community: Prevalence, Risk Factors, Molecular Epidemiology, and Antibiotic Resistance

This study aimed to determine the prevalence and risk factors associated with intestinal carriage of extended-spectrum β-lactamases producing Enterobacterales (ESBL-PE) and plasmid-mediated AmpC β-lactamase producing Enterobacterales (AmpC-PE) in healthy children in Ardabil, Iran. A total of 305 fecal samples were collected. Isolates underwent antimicrobial susceptibility testing, phenotypic and genotypic identification of β-lactamase production, and epidemiologic molecular typing. In total, 21.5%, 1.5%, and 1.2% of volunteers were extended-spectrum β-lactamase (ESBL)-, AmpC-, and simultaneous ESBL/AmpC-PE carriers, respectively. Escherichia coli was the predominant ESBL producing bacterium (70.2%) found in ESBL-PE colonized subjects. Beyond ESBL positive isolates, bla _CTX-M group genes were the most common type (75.6%) and bla _TEM (non-bla _TEM-1 and non- bla _TEM-2) were in the second place (25.6%). Among bla _CTX-M genes, bla _CTX-M-1 (55.3%) and bla _CTX-M-15 (55.3%) were the most predominant types with equal prevalence. Some isolates were multi-enzyme producers. bla _CIT and bla _DHA genes were common AmpC type enzyme encoding genes found in AmpC-PE isolates. Most isolates produced both enzymes at the same time. The number of students in the classes was statistically associated with ESBL-PE intestinal carriage (p < 0.05). Moreover, 46 (65.7%), 3 (60%), 4 (100%), and 98 (39.8%) ESBL-, AmpC-, ESBL/AmpC, and non-ESBL/AmpC-PE isolates were multidrug-resistant, respectively. Overall, regardless of β-lactam antibiotics, 62% and 59.5% of isolates were resistant to co-trimoxazole and tetracycline, respectively. The majority of ESBL producing E. coli isolates (69.2%) belonged to phylogroup A. According to Enterobacterial repetitive intergenic consensus polymerase chain reaction, there was no clonal relatedness between isolates. This study showed a high rate of multi-resistant ESBL-PE intestinal carriage among healthy individuals in Iran.

Extended Spectrum β-Lactamase Producing Lactose Fermenting Bacteria Colonizing Children with Human Immunodeficiency Virus, Sickle Cell Disease and Diabetes Mellitus in Mwanza City, Tanzania: A Cross-Sectional Study

Rectal carriage of extended spectrum β-lactamase-lactose fermenters (ESBL-LF) is the major risk factor for the development of subsequent endogenous infections. This study determined the patterns and factors associated with the rectal carriage of ESBL-LF among children with Human Immunodeficiency Virus (HIV), Diabetes Mellitus (DM), and Sickle Cell Disease (SCD) attending clinics at different health care facilities in the city of Mwanza, Tanzania. A cross-sectional study was conducted among children living with HIV (n = 236), DM (n = 42) and SCD (n = 126) between July and September 2021. Socio-demographic and clinical data were collected using a structured questionnaire. Rectal swabs/stool samples were collected and processed to detect the rectal carriage of ESBL-LF following laboratory standard operating procedures (SOPs). Descriptive statistical analysis was conducted using STATA 13.0. The overall prevalence of ESBL-LF carriage was 94/404 (23.3%). Significantly higher resistance was observed to ampicillin, trimethoprim-sulfamethoxazole, and tetracycline among Enterobacteriaceae isolated from HIV infected children than in non-HIV infected children (p < 0.05). The commonest ESBL allele 45/62 (72.6%) detected was blaCTX-M. Generally, a parent’s low education level was found to be associated with ESBL-LF colonization among children living with HIV; (OR 4.60 [95%CI] [1.04−20], p = 0.044). A higher proportion of ESBL-LF from DM 10/10 (100%) carried ESBL genes than ESBL-LF from HIV 37/56 (66.1%) and SCD 15/28 (53.6%), p = 0.02. There is a need to collect more data regarding trimethoprim-sulfamethoxazole (SXT) prophylaxis and antibiotic resistance to guide the decision of providing SXT prophylaxis in HIV-infected children especially at this time, when testing and treatment is carried out.

Antimicrobial Resistance Patterns of Bacterial and Fungal Isolates in COVID-19

Background: The pattern of bacterial infection in coronavirus disease 2019 (COVID-19) patients differ worldwide. Objectives: This study aimed to determine the patterns of bacterial infections and the antibiotic resistance profile by VITEK 2 (bioMérieux, France) in the culture of blood samples from hospitalized patients with COVID-19. Methods: This retrospective descriptive cross-sectional was conducted on a total of 25 patients with critical COVID-19 admitted to Imam Reza Hospital in Mashhad, Iran, during the first three COVID-19 peaks (2019 - 2020). Results: Among Gram-positive bacteria, two strains isolated from Staphylococcus aureus were methicillin-resistant S. aureus at a concentration of > 2 μg/mL. Enterococcus was vancomycin-resistant Enterococcus at a concentration of higher than 4 μg/mL (the minimum inhibitory concentration [MIC] ≥ 32). Among Gram-negative bacteria, three strains of Acinetobacter baumannii complex were extensively drug-resistant. Conclusions: There is evidence of the remarkable increase of various antibiotics’ MIC during the COVID-19 pandemic, which highlights the impact of the use of steroids on the risk of developing antimicrobial resistance during the COVID-19 pandemic.

Antimicrobial Resistance Rates and Surveillance in Sub-Saharan Africa: Where Are We Now?

Introduction

Although antimicrobials have traditionally been used to treat infections and improve health outcomes, resistance to commonly used antimicrobials has posed a major challenge. An estimated 700,000 deaths occur globally every year as a result of infections caused by antimicrobial-resistant pathogens. Antimicrobial resistance (AMR) also contributes directly to the decline in the global economy. In 2019, sub-Saharan Africa (SSA) had the highest mortality rate (23.5 deaths per 100,000) attributable to AMR compared to other regions.

Methods

We searched PubMed for articles relevant to AMR in pathogens in the WHO-GLASS list and in other infections of local importance in SSA. In this review, we focused on AMR rates and surveillance of AMR for these priority pathogens and some of the most encountered pathogens of public health significance. In addition, we reviewed the implementation of national action plans to mitigate against AMR in countries in SSA.

Results and Discussion

The SSA region is disproportionately affected by AMR, in part owing to the prevailing high levels of poverty, which result in a high burden of infectious diseases, poor regulation of antimicrobial use, and a lack of alternatives to ineffective antimicrobials. The global action plan as a strategy for prevention and combating AMR has been adopted by most countries, but fewer countries are able to fully implement country-specific action plans, and several challenges exist in many settings.

Conclusion

A concerted One Health approach will be required to ramp up implementation of action plans in the region. In addition to AMR surveillance, effective implementation of infection prevention and control, water, sanitation, and hygiene, and antimicrobial stewardship programs will be key cost-effective strategies in helping to tackle AMR.

Five-Year Survey of Asymptomatic Colonization with Multidrug-Resistant Organisms in a Romanian Tertiary Care Hospital

Purpose

To determine the rate of carriage of multidrug-resistant organisms (MDROs) between 2015 and 2019 among patients admitted to the National Institute of Infectious Diseases “Prof. Dr. Matei Balș,” from Bucharest, Romania.

Methods

Nasal, throat, and rectal/perirectal screening swabs were collected either immediately or during the first 24 hours of admission and sent to the microbiology laboratory where the following MDROs were identified: methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), extended-spectrum β-lactamase (ESBL)-producing Enterobacterales, carbapenem-resistant/carbapenemase-producing Enterobacterales (CRE/CPE), multidrug-resistant/extended drug-resistant Acinetobacter baumannii (MDR/XDR-AB), and multidrug-resistant/extended drug-resistant Pseudomonas aeruginosa (MDR/XDR-PA).

Results

A total of 5083 unique patients were screened for MRSA and 5008 for VRE, ESBL/CRE/CPE, MDR/XDR-AB, and MDR/XDR-PA. MRSA was detected in 8.24% of patients, VRE in 17.67%, ESBL Enterobacterales in 25.85%, and CPE in 6.13%. MDR/XDR-AB was found in 1.59% and MDR/XDR-PA in 1.91% of patients. The rates of carriage increased between 2015 and 2019 for MRSA (7.23–7.6%), VRE (9–16.68%), CPE (1.15–6.77%), MDR/XDR-PA (1.15–1.91%), and MDR/XDR-AB (1.15–2.04%). OXA-48-type carbapenemase was predominant in Klebsiella pneumoniae (68.62%) and Escherichia coli (89.47%). CPE bacteria other than Klebsiella pneumoniae and Escherichia coli identified in our study carried mostly metallo-beta-lactamase (n = 28, 84.85%).

Conclusion

In this study, 37% of the unique patients screened over five years were found to be MDRO carriers. The proportion of VRE and CPE rectal carriers increased significantly between 2015 and 2019. The most frequently isolated carbapenemase was the OXA-48 type.

Gastrointestinal colonization of Extended-Spectrum Beta lactamase producing bacteria among children below five years of age hospitalized with fever in Dar es Salaam, Tanzania

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 detectedbla_CTX-M gene in 97% of all phenotypically detected ESBL-PE; among those,bla_CTX-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.

Transmission routes of antibiotic resistant bacteria: a systematic review

Background

Quantification of acquisition routes of antibiotic resistant bacteria (ARB) is pivotal for understanding transmission dynamics and designing cost-effective interventions. Different methods have been used to quantify the importance of transmission routes, such as relative risks, odds ratios (OR), genomic comparisons and basic reproduction numbers. We systematically reviewed reported estimates on acquisition routes’ contributions of ARB in humans, animals, water and the environment and assessed the methods used to quantify the importance of transmission routes.

Methods

PubMed and EMBASE were searched, resulting in 6054 articles published up until January 1st, 2019. Full text screening was performed on 525 articles and 277 are included.

Results

We extracted 718 estimates with S. aureus (n = 273), E. coli (n = 157) and Enterobacteriaceae (n = 99) being studied most frequently. Most estimates were derived from statistical methods (n = 560), mainly expressed as risks (n = 246) and ORs (n = 239), followed by genetic comparisons (n = 85), modelling (n = 62) and dosage of ARB ingested (n = 17). Transmission routes analysed most frequently were occupational exposure (n = 157), travelling (n = 110) and contacts with carriers (n = 83). Studies were mostly performed in the United States (n = 142), the Netherlands (n = 87) and Germany (n = 60). Comparison of methods was not possible as studies using different methods to estimate the same route were lacking. Due to study heterogeneity not all estimates by the same method could be pooled.

Conclusion

Despite an abundance of published data the relative importance of transmission routes of ARB has not been accurately quantified. Links between exposure and acquisition are often present, but the frequency of exposure is missing, which disables estimation of transmission routes’ importance. To create effective policies reducing ARB, estimates of transmission should be weighed by the frequency of exposure occurrence.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07360-z.

High Fecal Carriage of Multidrug Resistant Bacteria in the Community among Children in Northwestern Tanzania

Colonization of multidrug resistant (MDR) bacteria is associated with subsequent invasive infections in children with comorbidities. This study aimed to determine the resistance profile and factors associated with MDR pathogen colonization among HIV−and HIV+ children below five years of age in Mwanza, Tanzania. A total of 399 (HIV− 255 and HIV+ 144) children were enrolled and investigated for the presence of MDR bacteria. The median [IQR] age of children was 19 (10–36) months. Out of 27 Staphylococcus aureus colonizing the nasal cavity, 16 (59.5%) were methicillin resistant while 132/278 (47.2%) of Enterobacteriaceae from rectal swabs were resistant to third generation cephalosporins, with 69.7% (92/132) exhibiting extended spectrum beta lactamase (ESBL) phenotypes. The proportion of resistance to gentamicin, amoxicillin/clavulanic acid and meropenem were significantly higher among HIV+ than HIV− children. A history of antibiotic use in the last month OR 2.62 [1.1, 6.9] (p = 0.04) and history of a relative admitted from the same household in the past three months OR 3.73 [1.1, 13.2] (p = 0.03) independently predicted ESBL rectal colonization. HIV+ children had significantly more fecal carriage of isolates resistant to uncommonly used antibiotics. There is a need to strengthen antimicrobial stewardship and Infection Prevention and Control (IPC) programs to prevent the emergence and spread of MDR pathogens in children.

Extended-Spectrum Beta-Lactamase- and Carbapenemase-Producing Enterobacteriaceae Family of Bacteria from Diarrheal Stool Samples in Northwest Ethiopia

Background

Resistance among the commensal flora is a serious threat because they are highly populated ecosystems like the gut, maybe a source of extraintestinal infections. Infections due to extended-spectrum beta-lactamase (ESBL)- and carbapenemase (CPM)-producing Enterobacteriaceae family of bacteria impose a major global issue because they are usually resistant to multiple antimicrobial agents. Data on the fecal ESBL- and CPM-producing group of bacteria in developing countries including Ethiopia are limited mainly due to resource constraints. Thus, this study aimed to determine the prevalence of multidrug-resistant (MDR)-, ESBL-, and CPM-producing Enterobacteriaceae family of bacteria from diarrheal stool samples at the University Hospital, Northwest Ethiopia.

Materials and Methods

A hospital-based cross-sectional study was conducted involving a total of 384 study participants having gastrointestinal complaints from January to April 2019. A diarrheal stool sample was aseptically collected and inoculated on a MacConkey agar plate. After getting pure colonies, biochemical and antimicrobial susceptibility testing was done following standard microbiological techniques. ESBL production was screened using ceftazidime and cefotaxime and confirmed using a combined disk diffusion test. Carbapenemases were screened by meropenem disk and confirmed by the modified carbapenem inactivation method. Data were checked, cleaned, and entered using Epi Info version 7.1 and transferred to SPSS version 20 for analysis.

Result

A total of 404 Enterobacteriaceae groups of bacteria were isolated from 384 diarrheal stool samples. The overall prevalence of fecal MDR-, ESBL-, and CPM-producing group of Enterobacteriaceae was 196 (48.5%), 66 (16.3%), and 4 (1%), respectively. Of the total ESBL-producing Enterobacteriaceae, E. coli (41/66 (62.1%)) and K. pneumoniae (18/66 (27.3%)) were the most predominant isolates. One half of CPE has been observed in Citrobacter species and the rest in E. coli (25%) and P. vulgaris (25%). Conclusion and Recommendation. Finding the high rate of ESBL-producing Enterobacteriaceae and CPE requires strict infection control measures and careful selection of empirical therapy in the study area. Therefore, active surveillance with large sample size and better infection prevention control is needed.

OUP accepted manuscript

Objectives

The widespread intestinal carriage of ESBL-producing Escherichia coli (ESBL E. coli) among both patients and healthy individuals is alarming. However, the global prevalence and trend of this MDR bacterium in healthcare settings remains undetermined. To address this knowledge gap, we performed a comparative meta-analysis of the prevalence in community and healthcare settings.

Methods

Our systematic review included 133 articles published between 1 January 2000 and 22 April 2021 and indexed in PubMed, EMBASE or Google Scholar. A random-effects meta-analysis was performed to obtain the global pooled prevalence (community and healthcare settings). Subgroup meta-analyses were performed by grouping studies using the WHO regions and 5 year intervals of the study period.

Results

We found that 21.1% (95% CI, 19.1%–23.2%) of inpatients in healthcare settings and 17.6% (95% CI, 15.3%–19.8%) of healthy individuals worldwide carried ESBL E. coli in their intestine. The global carriage rate in healthcare settings increased 3-fold from 7% (95% CI, 3.7%–10.3%) in 2001–05 to 25.7% (95% CI, 19.5%–32.0%) in 2016–20, whereas in community settings it increased 10-fold from 2.6% (95% CI, 1.2%–4.0%) to 26.4% (95% CI, 17.0%–35.9%) over the same period.

Conclusions

The global and regional human intestinal ESBL E. coli carriage is increasing in both community and healthcare settings. Carriage rates were generally higher in healthcare than in community settings. Key relevant health organizations should perform surveillance and implement preventive measures to address the spread of ESBL E. coli in both settings.

Prevalence and patient related factors associated with Extended-Spectrum Beta-Lactamase producing Escherichia coli and Klebsiella pneumoniae carriage and infection among pediatric patients in Tanzania

Extended-Spectrum Beta-Lactamase (ESBL) producing Enterobacteriaceae (EPE) is increasing worldwide, though less documented in low-income settings. Here we determined the prevalence of EPE infection and carriage, and patient factors associated with EPE-carriage among pediatric patients in three health care levels in Tanzania. Between January and April 2016, 350 febrile children (median age 21 months) seeking care at a university or a regional referral hospital, or a health centre in Moshi municipality, Tanzania, were included. Socio-demographic characteristics were collected using a questionnaire. Rectal swabs and blood cultures were collected from all children (n = 350) and urinary samples from 259 children at admission. ESBL-phenotype and antimicrobial susceptibility were determined for Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E. coli) isolates. Only one EPE case (E. coli) in blood and four in urine (one E. coli and three K. pneumoniae) were found, whereas (n = 90, 26%) of the children were colonized in feces (ESBL-E. coli; n = 76, ESBL-K. pneumoniae, n = 14). High resistance rates were seen in fecal ESBL-E. coli (n = 76) against trimethoprim-sulfamethoxazole (n = 69, 91%), gentamicin (n = 51, 67%), ciprofloxacin (n = 39, 51%) and chloramphenicol (n = 27, 35%) whereas most isolates were sensitive to amikacin (n = 71, 93%). Similar rates were seen for fecal ESBL-K. pneumoniae. Resistance to first line antibiotics were also very high in fecal E. coli not producing ESBL. No sociodemographic factor was associated with EPE-carriage. Children colonized with EPE were younger than 12 months (n = 43, 48%) and often treated with antibiotics (n = 40, 44%) in the previous two months. After adjustment for age children admitted to the intensive care unit had higher odds of EPE fecal carriage compared with those in the general wards (OR = 3.9, 95%CI = 1.4–10.4). Despite comparatively high rates of fecal EPE-carriage and previous antibiotic treatment, clinical EPE cases were rare in the febrile children. The very high resistant rates for the EPE and the non-ESBL producing E. coli to commonly used antibiotics are worrying and demand implementation of antibiotic stewardship programs in all levels of health care in Tanzania.

High prevalence of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae fecal carriage among children under five years in Addis Ababa, Ethiopia

Background

Extended-spectrum beta-lactamase (ESBL) producing bacteria present an ever-growing burden in the hospital and community settings. Data on the prevalence of ESBL fecal carriage remain scarce in Ethiopia. Therefore, this study aimed to determine the prevalence of ESBL producing Escherichia coli and Klebsiella pneumoniae fecal carriage among children under five years in Addis Ababa, Ethiopia.

Methods

A facility-based cross-sectional study was conducted from April to May 2017. A total of 269 fecal/rectal swab samples were cultured on MacConkey agar. All positive cultures were characterized by colony morphology, Gram stain, and standard biochemical tests. Further, bacteria identification, antimicrobial susceptibility testing, and phenotypic detection of ESBL production were performed using VITEK 2 Compact as per the instruction of the manufacturer. Socio-demographic and risk factors data were collected using questionnaires. Data were entered by EPI INFO version 7.2.1.0 and analyzed by SPSS version 20.

Results

The overall prevalence of ESBL-producing E. coli and K. pneumoniae was 17.1% (46/269; 95% CI: 12.9%–22.7%). A total of 47 isolates were ESBL-positive, of which, 83.0% were E. coli and 17.0% were K. pneumoniae. ESBL producing E. coli and K. pneumoniae isolates were also showed high levels of MDR (93.6%) and high rates of co-resistance to aminoglycosides, fluoroquinolones, and trimethoprim-sulfamethoxazole. However, all isolates were carbapenem susceptible. In the risk factors analysis, Children’s mothers who had lower educational level (primary school) (OR: 2.472, 95% CI: 1.323–4.618, P = 0.0062) and children who used tap water for drinking (OR: 1.714, 95% CI: 1.001–3.659, P = 0.048) were found to be significantly associated with higher ESBL fecal carriage.

Conclusions

In this study, the high prevalence rate of ESBL producing E. coli and K. pneumoniae fecal carriage and high level of multidrug resistance among ESBL producing E. coli and K. pneumoniae were demonstrated. This suggested that the necessity of routine screening of ESBL is crucial for the early detection and appropriate antibiotics selection for infection caused by ESBL producing pathogens.

Antibiotic-Resistant Acinetobacter baumannii in Low-Income Countries (2000-2020): Twenty-One Years and Still below the Radar, Is It Not There or Can They Not Afford to Look for It?

Acinetobacter baumannii is an emerging pathogen, and over the last three decades it has proven to be particularly difficult to treat by healthcare services. It is now regarded as a formidable infectious agent with a genetic setup for prompt development of resistance to most of the available antimicrobial agents. Yet, it is noticed that there is a gap in the literature covering this pathogen especially in countries with limited resources. In this review, we provide a comprehensive updated overview of the available data about A. baumannii, the multi-drug resistant (MDR) phenotype spread, carbapenem-resistance, and the associated genetic resistance determinants in low-income countries (LIICs) since the beginning of the 21st century. The coverage included three major databases; PubMed, Scopus, and Web of Science. Only 52 studies were found to be relevant covering only 18 out of the 29 countries included in the LIC group. Studies about two countries, Syria and Ethiopia, contributed ~40% of the studies. Overall, the survey revealed a wide spread of MDR and alarming carbapenem-resistance profiles. Yet, the total number of studies is still very low compared to those reported about countries with larger economies. Accordingly, a discussion about possible reasons and recommendations to address the issue is presented. In conclusion, our analyses indicated that the reported studies of A. baumannii in the LICs is far below the expected numbers based on the prevailing circumstances in these countries. Lack of proper surveillance systems due to inadequate financial resources could be a major contributor to these findings.

Prevalence and risk factors associated with multi-drug resistant organisms (MDRO) carriage among pediatric patients at the time of admission in a tertiary care hospital of a developing country. A cross-sectional study

Background

The rise of Multidrug-resistant organisms (MDROs) poses a considerable burden on the healthcare systems, particularly in low-middle income countries like Pakistan. There is a scarcity of data on the carriage of MDRO particularly in the pediatrics population therefore, we aimed to determine MDRO carriage in pediatric patients at the time of admission to a tertiary care hospital in Karachi, Pakistan, and to identify the risk factors associated with it.

Methods

A cross-sectional study conducted at the pediatric department of Aga Khan University Hospital (AKUH) from May to September 2019 on 347 children aged 1–18 years. For identification of MDRO (i.e., Extended Spectrum Beta-Lactamase (ESBL) producers, Carbapenem Resistant Enterobacteriaceae (CRE), Vancomycin Resistant Enterococci (VRE), Methicillin Resistant Staphylococcus aureus (MRSA), Multidrug-resistant (MDR) Acinetobacter species and MDR Pseudomonas aeruginosa), nasal swabs and rectal swabs or stool samples were cultured on specific media within 72 h of hospitalization. Data was collected on a predesigned structured questionnaire on demographics, prior use of antibiotics for > 48 h in the last 6 months, history of vaccination in last 6 months, exposure to health care facility regardless of the time of exposure, ICU stay for > 72 h, and about the prior use of medical devices (urinary catheter, central venous lines etc.) in last 1 year. Statistical analysis was performed by Standard statistical software.

Results

Out of 347 participants, 237 (68.3%) were found to be MDRO carriers. Forty nine nasal swabs from 346 children (14.2%) showed growth of MRSA. The majority of the stool/rectal swabs (n = 222 of 322; 69%) collected were positive for MDRO. The most isolated species were ESBL Escherichia coli 174/222 (78.3%) followed by ESBL Enterobacter species 37/222 (16.7%) and ESBL Klebsiella pneumoniae 35/222 (15.8%). On univariate analysis, none of the risk factors showed statistically significant association with MDRO carriage.

Conclusion

Overall, a high prevalence of MDRO carriage was identified among admitted pediatric patients. Implementation of systematic screening may help to identify true burden of MDROs carriage in the health care settings.

Extended-spectrum β-lactamase blaCTX-M-1 group in gram-negative bacteria colonizing patients admitted at Mazimbu hospital and Morogoro Regional hospital in Morogoro, Tanzania

Objective

The objective of this study was to determine the proportion of extended spectrum β-lactamase producing gram-negative bacteria (ESBL-GNB) colonizing patients admitted at Mazimbu hospital and Morogoro Regional hospital, in Morogoro, Tanzania. Rectal colonization with ESBL-GNB increases the risks of developing bacterial infections by extra-intestinal pathogenic ESBL-GNB.

Results

Of the 285 patients investigated, 123 (43.2%) carried ESBL-GNB in their intestines. Five of the 123 ESBL positive patients were colonized with two different bacteria, making a total of 128 ESBL producing isolates. Escherichia coli (n = 95, 74.2%) formed the majority of ESBL isolates. The proportion of CTX-M-1 group genes among ESBL isolates tested was 94.9% (93/98). History of antibiotic use (OR: 1.83, 95% CI: 1.1–3.2, P = 0.03), being on antibiotic treatment (OR: 2.61, 95% CI: 1.5–4.53, P = 0.001), duration of hospital stay (OR: 1.2, 95% CI: 1.1–1.3, P < 0.001) and history of previous admission (OR: 2.24, 95% CI: 1.2–4.1, P = 0.009) independently predicted ESBL-GNB carriage.

Epidemiology and prevalence of extended-spectrum β-lactamase- and carbapenemase-producing Enterobacteriaceae in humans, animals and the environment in West and Central Africa

Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) and carbapenemase-producing Enterobacteriaceae (CPE) are widespread. Here we used the 'One Health' approach to determine knowledge gaps on ESBL-E and CPE in West and Central Africa. We searched all articles on ESBL-E and CPE in these African regions published in PubMed, African Journals Online and Google Scholar from 2000 onwards. Among the 1201 articles retrieved, we selected 165 studies (West Africa, 118; Central Africa, 47) with data from 22 of the 26 West and Central Africa countries. Regarding the settings, 136 articles focused only on humans (carriage and/or infection), 6 articles on humans and animals, 13 on animals, 1 on humans and the environment, 8 on the environment and 1 on humans, animals and environments. ESBL-E prevalence ranged from 11-72% in humans and 7-79% in aquatic environments (wastewater). In animals, ESBL-E prevalence hugely varied: 0% in cattle, 11-36% in chickens, 20% in rats, 21-71% in pigs and 32-75% in dogs. The bla_CTX-M-15 gene was the predominant ESBL-encoding gene and was associated with plasmids of incompatibility groups F, H, K, Y, N, I1 and R. CPE were studied only in humans. Class B metallo-β-lactamases (NDM) and class D oxacillinases (OXA-48 and OXA-181) were the most common carbapenemases. Our results show major knowledge gaps, particularly on ESBL and CPE in animals and the environment, that might limit antimicrobial resistance management in these regions. The results also emphasise the urgent need to improve active surveillance programmes in each country and to support antimicrobial stewardship.

Genetic diversity and risk factors for the transmission of antimicrobial resistance across human, animals and environmental compartments in East Africa: a review

Background

The emergence and spread of antimicrobial resistance (AMR) present a challenge to disease control in East Africa. Resistance to beta-lactams, which are by far the most used antibiotics worldwide and include the penicillins, cephalosporins, monobactams and carbapenems, is reducing options for effective control of both Gram-positive and Gram-negative bacteria. The World Health Organization, Food and Agricultural Organization and the World Organization for Animal Health have all advocated surveillance of AMR using an integrated One Health approach. Regional consortia also have strengthened collaboration to address the AMR problem through surveillance, training and research in a holistic and multisectoral approach. This review paper contains collective information on risk factors for transmission, clinical relevance and diversity of resistance genes relating to extended-spectrum beta-lactamase-producing (ESBL) and carbapenemase-producing Enterobacteriaceae, and Methicillin-resistant Staphylococcus aureus (MRSA) across the human, animal and environmental compartments in East Africa.

Main body

The review of the AMR literature (years 2001 to 2019) was performed using search engines such as PubMed, Scopus, Science Direct, Google and Web of Science. The search terms included ‘antimicrobial resistance and human-animal-environment’, ‘antimicrobial resistance, risk factors, genetic diversity, and human-animal-environment’ combined with respective countries of East Africa. In general, the risk factors identified were associated with the transmission of AMR. The marked genetic diversity due to multiple sequence types among drug-resistant bacteria and their replicon plasmid types sourced from the animal, human and environment were reported. The main ESBL, MRSA and carbapenem related genes/plasmids were the ^blaCTX-Ms (45.7%), SCCmec type III (27.3%) and IMP types (23.8%), respectively.

Conclusion

The high diversity of the AMR genes suggests there may be multiple sources of resistance bacteria, or the possible exchange of strains or a flow of genes amongst different strains due to transfer by mobile genetic elements. Therefore, there should be harmonized One Health guidelines for the use of antibiotics, as well as regulations governing their importation and sale. Moreover, the trend of ESBLs, MRSA and carbapenem resistant (CAR) carriage rates is dynamic and are on rise over time period, posing a public health concern in East Africa. Collaborative surveillance of AMR in partnership with regional and external institutions using an integrated One Health approach is required for expert knowledge and technology transfer to facilitate information sharing for informed decision-making.

High fecal carriage of extended Beta Lactamase producing Enterobacteriaceae among adult patients admitted in referral hospitals in Dar es Salaam, Tanzania

BACKGROUND

Multi-drug resistance pathogens such as Extended-Spectrum Beta-Lactamase (ESBL) producing Enterobacteriaceae (ESBL-PE) are of great global health concern, since they are associated with increased morbidity and mortality. Even in the absence of infections caused by these pathogens, colonization is a great threat and can lead to cross transfer among hospitalized patients. To date data on carriage of these pathogens is still limited in Tanzania. Therefore, this study aimed to determine ESBL-PE fecal carriage rate and associated factors among hospitalized patients at Referral hospitals in Dar es Salaam.

METHODS

This was a cross sectional study conducted from May to July 2017 among patients admitted in three referral hospitals in Dar es Salaam, Tanzania. Rectal swabs were collected and screened for ESBL production using MacConkey agar supplemented with Ceftazidime 2 μg/ml. Phenotypic confirmation of ESBL-PE was done by double disk diffusion method. Statistical analysis was performed using Statistical Package for Social Sciences (SPPS) software version 20.

RESULTS

Of the 196 enrolled participants, 59.7% (117/196) were confirmed to carry ESBL-PE. Diarrheic patients (57/79) had statistically significant high prevalence of ESBL colonization compared to those without diarrhea (60/117) (p = 0.01). A total of 131 ESBL-PE were isolated from 117 patients, whereby, Escherichia coli accounted for 68.7%, Klebsiella pneumoniae 28.2% and Citrobacter species 0.8%. ESBL-PE carriage was significantly higher in patients with diarrhea compared to those without diarrhea (72% vs 53.1%, p = 0.01). Recent antibiotic use was independently associated with carriage of ESBL-PE (aOR 14.65, 95%CI 3.07-69.88, p = 0.01).

CONCLUSIONS

High prevalence of fecal carriage of ESBL-PE was observed in patients admitted in tertiary hospitals in Dar es Salaam, Tanzania. The use of antibiotics was associated with carriage of ESBL producers among the study population.

High carriage rates of extended-spectrum beta-lactamase-producing enterobacteriaceae in children at admission into paediatric wards of a university teaching hospital in Lagos, Nigeria

Context

Bowel carriage has been identified as the main reservoir of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) and hospital-acquired infections. There are gaps in the knowledge of trends of these rates, which need to be filled for the development and implementation of hospital surveillance systems and antibiotic stewardship programmes in Nigeria.

Aim

This study investigated the carriage rates of ESBL-PE among 273 children admitted to the paediatric wards of a university teaching hospital, Nigeria, using a prospective cohort study design over a 6-month period.

Settings and Design

The study explored the role of new and transferred patients in introducing resistant strains of ESBLs into paediatric wards and how quickly paediatric patients that were previously free of resistant strains acquired these within the hospital environment.

Materials and Methods

E-swabs (Copan Diagnostics, Italy) were used to obtain rectal samples from participants. Positive colonies were Gram stained and subcultured onto purity plates for further identification, and antibiotic susceptibility pattern of identified ESBL-PE was obtained using a range of antibiotics.

Statistical Analysis Used

Data were analysed using SPSS statistics 20 (IBM SPSS Statistics, version 20). Statistical significance was determined using the Chi-square test and Fisher's exact test. A logistic regression analysis was also conducted to identify independent risk factors for colonisation.

Results

The findings showed that transferred patients contributed to the introduction of ESBLs into the hospital. Independent multivariate risk factors for colonisation of ESBL-PE were age >10-14 years, instrumentation (odds ratio [OR]: 0.2 [P < 0.05]) and sharing of thermometers (OR: 0.11 [P < 0.05]).

Conclusions

The carriage rate of ESBL-PE is high (25.3%) among children, and none-carriers may become colonised within 14 days of hospitalisation.

Whole genome sequencing of extended-spectrum β-lactamase genes in Enterobacteriaceae isolates from Nigeria

Extended Spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are of major concern as they are implicated in multidrug resistant nosocomial infections. They are listed on a recently published global priority list of antibiotic-resistant bacteria by the World Health Organization which raises concern in both healthcare and community settings. This study aimed at determining the frequency of ESBL genes in multidrug resistant human clinical Enterobacteriaceae isolates from Edo state Nigeria and to characterize the resistance mechanisms using whole genome sequencing. A total of 217 consecutive clinical isolates of Enterobacteriaceae, selection based on inclusion criteria, were collected from March-May 2015 from three medical microbiology laboratories of hospitals in Edo state Nigeria. All isolates were analyzed using matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Antibiotic susceptibility testing was performed by Kirby-Bauer method and minimum inhibitory concentration (MIC) determination by E-test method. Double disc synergy test was used to screen for the production of ESBL. Whole genome sequencing (WGS) was performed for isolate characterization and identification of resistance determinants. Out of 217 consecutive clinical Enterobacteriaceae isolates, 148 (68.2%) were multi-drug resistant. Of these multi-drug resistant isolates, 60 (40.5%) were positive for the ESBL phenotypic test and carried ESBL genes. CTX-M-15 was the predominant ESBL found, among 93.3% (n = 56/60). Thirty-two plasmid incompatibility groups and 28 known and two new sequence types were identified among the ESBL isolates. The high occurrence of CTX-M-15 with associated resistant determinants in multidrug resistant Enterobacteriaceae harboring different plasmid incompatibility groups and sequence types calls for the need of continuous monitoring of this resistance threat to reduce its public health impact. To our knowledge, this study presents the first genomic characterization of ESBL production mediated by blaCTX-M-15 in human clinical isolates of Enterobacter hormaechei, Citrobacter werkmanii and Atlantibacter hermannii from Nigeria.

Pharmacophore modeling, atom based 3D-QSAR, molecular docking and molecular dynamics studies on Escherichia coli ParE inhibitors

ATP dependent ParE enzyme is as an attractive target for the development of antibacterial agents. Atom based 3D-QSAR model AADHR.187 was developed based on the thirty eight Escherichia coli ParE inhibitors. The generated model showed statistically significant coefficient of determinations for the training (R² = 0.985) and test (R² = 0.86) sets. The cross-validated correlation coefficient (q2) was 0.976. The utility of the generated model was validated by the enrichment study. The model was also validated with structurally diverse external test set of ten compounds. Contour plot analysis of the generated model unveiled the chemical features necessary for the E. coli ParE enzyme inhibition. Extra-precision docking result revealed that hydrogen bonding and ionic interactions play a major role in ParE protein-ligand binding. Binding free energy was computed for the data set inhibitors to validate the binding affinity. A 30-ns molecular dynamics simulation showed high stability and effective binding of inhibitor 34 within the active site of ParE enzyme. Using the best fitted model AADHR.187, pharmacophore-based high-throughput virtual screening was performed to identify virtual hits. Based on the above studies three new molecules are proposed as E. coli ParE inhibitors with high binding affinity and favourable ADME properties.

Multi-Antibiotic Resistance and Factors Affecting Carriage of Extended Spectrum β-Lactamase-Producing Enterobacteriaceae in Pediatric Population of Enugu Metropolis, Nigeria

Extended-spectrum β-lactamase (ESBL)-producing organisms have become a serious challenge in healthcare delivery globally. The prevalence of ESBL carriage in healthy and sick children in Enugu, Nigeria, was bacteriologically investigated in this study. Four hundred and twenty-two biological samples (mid-stream urine and feces) were bacteriologically analyzed. The isolates were screened for ESBL production using Clinical and Laboratory Standards Institute (CLSI) breakpoints. The suspected ESBL producers were confirmed using double disc synergy test method. Out of the 162 isolates screened, 32 (19.8%) were confirmed as ESBL positive, with a prevalence of 25.32% among sick children in Enugu State University Teaching Hospital (ESUTH), Parklane, Enugu and 13.89% in apparently healthy children in a community setting. Klebsiella spp. and Escherichia coli had the highest prevalence of 34.6% and 28.6%, respectively; Citrobacter spp. and Enterobacter spp. were 18.2% and 16.7%, respectively. The ESBL positive isolates were resistant to sulfamethoxazole/trimethoprim (100%), tetracycline (100%), kanamycin (96.9%), nitrofurantoin (84.4%), ciprofloxacin (68.6%), and chloramphenicol (62.5%) but susceptible to meropenem (100%), colistin (56.3%), and gentamicin (50%). Klebsiella spp. had the highest ESBL occurrence among sick children while E. coli had the highest ESBL occurrence among healthy children in Enugu. All ESBL-positive isolates were multiply resistant to conventional antibiotics. The emergence and spread of β-lactamase-producing Enterobacteriaceae in hospital and community environments highlight the possibility for an infection outbreak if not checked.

Gut mucosal colonisation with extended-spectrum beta-lactamase producing Enterobacteriaceae in sub-Saharan Africa: a systematic review and meta-analysis

Background: Extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) threaten human health; and, in areas of sub-Saharan Africa (sSA) where carbapenems are not available, may render ESBL-E infections untreatable. Gut mucosal colonisation probably occurs before infection, making prevention of colonisation an attractive target for intervention, but the epidemiology of ESBL-E in sSA is poorly described.

Objectives: Describe ESBL-E colonisation prevalence in sSA and risk factors associated with colonisation.

Methods: Studies included were prospective cross-sectional or cohort studies reporting gut mucosal ESBL-E colonisation in any population in sSA. We searched PubMed and Scopus on 18 December 2018. We summarise the range of prevalence across sites and tabulated risk factors for colonisation. The protocol was registered (Prospero ID CRD42019123559).

Results: From 2975 abstracts we identified 32 studies including a total of 8619 participants from a range of countries and settings. Six studies were longitudinal; no longitudinal studies followed patients beyond hospital discharge.  Prevalence varied between 5 and 84% with a median of 31%, with a relationship to setting: pooled ESBL-E colonisation in community studies was 18% (95% CI 12 to 28, 12 studies); in studies recruiting people at admission to hospital colonisation was 32% (95% CI 24 to 41% 8 studies); and for inpatients, colonisation was 55% (95% CI 49 to 60%, 7 studies). Antimicrobial use was associated with increased risk of ESBL-E colonisation, and protected water sources or water treatment by boiling may reduce risk.

Conclusions: ESBL-E colonisation is common in sSA, but how people become carriers and why is not well understood. To inform the design of interventions to interrupt transmission in this setting requires longitudinal, community studies.

Gut mucosal colonisation with extended-spectrum beta-lactamase producing Enterobacteriaceae in sub-Saharan Africa: a systematic review and meta-analysis

Background: Extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) threaten human health; and, in areas of sub-Saharan Africa (sSA) where carbapenems are not available, may render ESBL-E infections untreatable. Gut mucosal colonisation probably occurs before infection, making prevention of colonisation an attractive target for intervention, but the epidemiology of ESBL-E in sSA is poorly described. Objectives: Describe ESBL-E colonisation prevalence in sSA and risk factors associated with colonisation. Methods: Studies included were prospective cross-sectional or cohort studies reporting gut mucosal ESBL-E colonisation in any population in sSA. We searched PubMed and Scopus on 18 December 2018. We summarise the range of prevalence across sites and tabulated risk factors for colonisation. The protocol was registered (Prospero ID CRD42019123559). Results: From 2975 abstracts we identified 32 studies including a total of 8619 participants from a range of countries and settings. Six studies were longitudinal; no longitudinal studies followed patients beyond hospital discharge.  Prevalence varied between 5 and 84% with a median of 31%, with a relationship to setting: pooled ESBL-E colonisation in community studies was 18% (95% CI 12 to 28, 12 studies); in studies recruiting people at admission to hospital colonisation was 32% (95% CI 24 to 41% 8 studies); and for inpatients, colonisation was 55% (95% CI 49 to 60%, 7 studies). Antimicrobial use was associated with increased risk of ESBL-E colonisation, and protected water sources or water treatment by boiling may reduce risk. Conclusions: ESBL-E colonisation is common in sSA, but how people become carriers and why is not well understood. To inform the design of interventions to interrupt transmission in this setting requires longitudinal, community studies.

Multiplex PCR reveals a high prevalence of multiple pathogens in traveller's diarrhoea in children

OBJECTIVE

Traveller's diarrhoea (TD) is one of the most frequent illnesses affecting children returning from tropical countries. The purpose of this study was to assess the distribution of pathogens associated with TD in children using a multiplex PCR assay on stool samples.

DESIGN

All the children admitted for TD in two university hospitals from 1 August to 15October during 2014 and 2015 were included in a prospective study. Stool samples were tested by a multiplex PCR FilmArray GI panel detecting 22 pathogens. Performances for the detection of major enteropathogenic bacteria (Salmonella, Shigella and Campylobacter spp) by multiplex PCR and conventional culture methods were compared. The prevalence of extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae was also determined.

RESULTS

Fifty-nine children were included. In 58 cases (98%), at least one pathogen was identified, including 9 different enteropathogenic bacteria, 5 viruses and 2 parasites. Multiplex PCR enhanced the enteropathogenic bacteria detection by 25%. The most frequent pathogens were enteroaggregative Escherichia coli (n=32), enteropathogenic E. coli (n=26), enterotoxigenic E. coli (n=19), Salmonella enterica, enteroinvasive E. coli/Shigella (n=16 each), Cryptosporidium, sapovirus (n=11 each), Campylobacter jejuni, norovirus (n=10 each), rotavirus (n=9), Giardia (n=8) and Shiga-toxin-producing E. coli (n=4). Fifty-two coinfections were observed, notably including bacteria and viruses (n=21), multiple bacteria (n=14), or bacteria and parasites (n=10). ESBL were detected in 28 cases. Multiplex PCR could optimise the number of treated patients by 27% compared with stool cultures.

CONCLUSION

Multiplex PCR on stools revealed a high prevalence of diverse enteric pathogens and coinfections in children with TD. Major enteropathogenic bacteria were more frequently detected by multiplex PCR compared with conventional culture. Finally, this technique allows the start of appropriate and early antibiotic treatment and seems to optimise the number of correctly treated patients.

Isolation of Extended-Spectrum β-lactamase- (ESBL-) Producing Escherichia coli and Klebsiella pneumoniae from Patients with Community-Onset Urinary Tract Infections in Jimma University Specialized Hospital, Southwest Ethiopia

Background

Klebsiella pneumoniae and Escherichia coli are the major extended-spectrum β-lactamase- (ESBL-) producing organisms increasingly isolated as causes of complicated urinary tract infections and remain an important cause of failure of therapy with cephalosporins and have serious infection control consequence.

Objective

To assess the prevalence and antibiotics resistance patterns of ESBL-producing Escherichia coli and Klebsiella pneumoniae from community-onset urinary tract infections in Jimma University Specialized hospital, Southwest Ethiopia, 2016.

Methodology

A hospital-based cross-sectional study was conducted, and a total of 342 urine samples were cultured on MacConkey agar for the detection of etiologic agents. Double-disk synergy (DDS) methods were used for detection of ESBL-producing strains. A disc of amoxicillin + clavulanic acid (20/10 µg) was placed in the center of the Mueller–Hinton agar plate, and cefotaxime (30 µg) and ceftazidime (30 µg) were placed at a distance of 20 mm (center to center) from the amoxicillin + clavulanic acid disc. Enhanced inhibition zone of any of the cephalosporin discs on the side facing amoxicillin + clavulanic acid was considered as ESBL producer.

Results

In the current study, ESBL-producing phenotypes were detected in 23% (n = 17) of urinary isolates, of which Escherichia coli accounts for 76.5% (n = 13) and K. pneumoniae for 23.5% (n = 4). ESBL-producing phenotypes showed high resistance to cefotaxime (100%), ceftriaxone (100%), and ceftazidime (70.6%), while both ESBL-producing and non-ESBL-producing isolates showed low resistance to amikacin (9.5%), and no resistance was seen with imipenem. In the risk factors analysis, previous antibiotic use more than two cycles in the previous year (odds ratio (OR), 6.238; 95% confidence interval (CI), 1.257–30.957; p = 0.025) and recurrent UTI more than two cycles in the last 6 months or more than three cycles in the last year (OR, 7.356; 95% CI, 1.429–37.867; p = 0.017) were found to be significantly associated with the ESBL-producing groups.

Conclusion

Extended-spectrum β-lactamases- (ESBL-)producing strain was detected in urinary tract isolates. The occurrence of multidrug resistance to the third-generation cephalosporins, aminoglycosides, fluoroquinolones, trimethoprim-sulfamethoxazole, and tetracyclines is more common among ESBL producers. Thus, detecting and reporting of ESBL-producing organisms have paramount importance in the clinical decision-making.

Extended spectrum beta-lactamase mediated resistance in carriage and clinical gram-negative ESKAPE bacteria: a comparative study between a district and tertiary hospital in South Africa

Background

Gram-negative ESKAPE bacteria are increasingly implicated in several difficult-to-treat infections in developed and developing countries. They are listed by the World Health Organization as resistant bacteria of critical priority in research.

Objectives

To determine the risk factors, prevalence, phenotypic profiles, genetic diversity and clonal relatedness of extended-spectrum β-lactamase (ESBL)-producing multi-drug resistant (MDR) Gram-negative ESKAPE bacteria in the faecal carriage and clinical samples from patients in an urban, tertiary and a rural, district hospital in uMgungundlovu District, KwaZulu-Natal, South Africa.

Methods

This study took place in a district and tertiary hospital during a two-months period from May to June 2017 in uMgungundlovu district, South Africa. Rectal swabs collected from hospitalized patients, at admission, after 48 h and at discharge (whenever possible) formed the carriage sample while clinical isolates routinely processed in the microbiological laboratory during the sampling period were also collected and formed the clinical sample. Gram-negative ESKAPE bacteria were screened for ESBL production on selective MacConkey agar and confirmed using ROSCO kits. Minimum inhibitory concentrations were determined, and real-time and multiplex polymerase chain reaction were used to ascertain the presence of bla _CTX-M group-1-2-9, bla _CTX-M group 8/25, bla _SHV, bla _TEM, bla _OXA-1-like, bla _KPC, bla _VIM, bla _IMP, bla _GES and AmpC genes. Genomic fingerprinting was also performed using ERIC-PCR. Risk factors for ESBL-mediating MDR Gram-negative ESKAPE colonization were ascertained by univariate and multivariate logistic regression analyses.

Results

Overall prevalence of carriage of ESBL-mediating MDR Gram-negative ESKAPE was 37.21% (16/43), 42.31% (11/26) and 57.14% (4/7) at admission, after 48 h and at discharge respectively. The prevalence of ESBL-mediating MDR Gram-negative ESKAPE bacteria in faecal carriage (46%) was higher than clinical samples (28%). Colonization was mainly associated with the referral from district to tertiary hospital with high statistical significance (OR: 14.40, 95% CI 0.98-210.84). bla _{CTX-M-group-9}, bla _{CTX-M-group-1} and bla _SHV were the main resistance genes identified. Several patients carried more than two different isolates. A Klebsiella pneumoniae (K1) clone was circulating within wards and between hospitals.

Conclusion

The study highlights the high prevalence of ESBL-mediating MDR Gram-negative ESKAPE bacteria in carriage and clinical samples among hospitalized patients in uMgungundlovu, South Africa. The wide dissemination of these resistant ESKAPE bacteria in hospitals necessitates improvements in routine screening and reinforcement of infection, prevention and control measures.

Incidence and Risk Factors for Acquisition of Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae in Newborns in Seville, Spain: A Prospective Cohort Study

BACKGROUND

ESBL-producing Enterobacteriaceae (ESBL-E) are an emerging cause of infections in children. Data are scarce on incidence rates and risk factors for acquisition of colonisation with ESBL-E.

METHODS

A total of 46 and 50 newborns from colonised and non-colonised mothers, respectively, were followed during one year after birth. Rectal swabs were performed every 3 months to detect ESBL-E; bla_ESBL were characterised and isolates were typed for comparison. Multivariate analysis for risk factors was performed using Cox regression.

RESULTS

Incidence density of any new acquisition and of first acquisition of ESBL-E was 2.7 and 1.9 episodes per 100 children-month, respectively, among children whose mothers were colonised, and 1.2 and 1.3, respectively, among children whose mothers were not. The weighted average prevalence of colonisation rates during the first year were 15.9% and 8%, respectively. No infections due to ESBL-E were detected. Living with pets at home, breastfeeding, sterilisation of feeding bottles and out-of-home childcare were protective for ESBL-E acquisition; having a colonised mother increased the risk. The most frequent ESBL types were CTX-M-14 and CTX-M-1. In 5/19 (26.3%) children with acquisition of new clones, the acquired ESBL-E was shared with their mothers.

CONCLUSIONS

Acquisition of ESBL-E colonisation is not rare during the first year of life. Breastfeeding and out-of-home childcare were protective for acquisition, and colonised mothers were associated with increased risk. However, the same clone was shared by mother and child in only a subset of acquisition episodes.

Intestinal Carriage of Third-Generation Cephalosporin-Resistant and Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae in Healthy US Children

BACKGROUND

The epidemiology of antibiotic-resistant Enterobacteriaceae intestinal carriage in healthy US children has not been well characterized.

METHODS

Children between 14 days and 14 years of age were enrolled during well-child visits in Oakland, California, Kansas City, Kansas, and Nashville, Tennessee, between December 2013 and March 2015. Data on recent antibiotic use by the child and travel and hospitalization history of all members of each child's household were obtained with a risk-factor survey. Stool specimens collected from the subjects were screened for extended-spectrum β-lactamase-producing (ESBL-P) bacteria using CHROMagar ESBL medium. Putative ESBL-P Escherichia coli and Klebsiella colonies underwent phenotypic confirmation by double-disk synergy testing; confirmed third-generation cephalosporin-resistant (3GCR) isolates underwent additional antibiotic-susceptibility testing.

RESULTS

In 519 subjects, the overall 3GCR Enterobacteriaceae carriage rate was 4.4% (n = 23) and ranged from 3.4% to 5.1% among the study sites. The ESBL-P Enterobacteriaceae carriage rate was 3.5% (n = 18). The rates of 3GCR Enterobacteriaceae carriage was highest in 1 to <2 year olds at 6.5%, and was 5.2% in <5 year-olds vs 1.7% in ≥5-year-olds (P = .11). 3GCR and ESBL-P Enterobacteriaceae carriage was associated with international travel within the previous year; 11.1% of ESBL-P Enterobacteriaceae carriers reported this history compared with 1.6% of noncarriers (P = .004). No other queried factor was found to increase risk. Of the 24 analyzed 3GCR isolates, 58% were multidrug resistant.

CONCLUSIONS

The 3GCR Enterobacteriaceae carriage rate exceeds 5% in healthy US children <5 years of age. International travel within the previous year increased the risk of 3GCR and ESBL-P Enterobacteriaceae carriage. In contrast, we found no differences in the rates of hospitalization or recent antibiotic exposure between carriers and noncarriers. Young children, who have the highest prevalence of colonization, might be a sentinel population to study to gain a better understanding of community sources of antibiotic-resistant Enterobacteriaceae.

Prevalence and risk factors for faecal carriage of Extended Spectrum β-lactamase producing Enterobacteriaceae among food handlers in lower basic schools in West Coast Region of The Gambia

BACKGROUND

The isolation of Extended spectrum βlactamase (ESBLs) producing Enterobacteriaceae among food handlers and their implication as sources of food borne outbreaks are a public health concern. This study seeks to investigate the prevalence of faecal carriage of these bacteria among food handlers in the West Coast Region of The Gambia.

METHOD

This study enrolled 600 participants from 60 Lower Basic Schools in West Coast Region of the country. Stool samples collected from the participants were presumptively screened for the ESBLs producing Enterobacteriaceae, using Drigalski agar, supplemented with 2mg/L cefotaxime. The bacterial colonies that grew on each Drigalski agar were tested for ESBL production by the double disk synergy test as recommended by Clinical and Laboratory Standard Institute (CLSI-2015). The confirmatory analysis for ESBL was determined as the zone of inhibition of cefotaxime and/or ceftazidime to ≥5mm from that of cefotaxime /clavulanicacid and/or ceftazidime/clavulanic acid. The presumptive screening of isolates for AmpC phenotypes was done by testing the organism against cefoxitin. The prevalence of the ESBL carriage was presented in percentages. The association of risk factors to the faecal carriage of ESBLs producing Enterobacteriaceae was performed by Pearson Chi-squared and Fishers Exact at (p ≤ 0.05).

RESULT

The prevalence of faecal carriage ESBL producing Enterobacteriaceae among food handlers was 5.0% (28/565). We found50% (14/28) and3.57% (1/28) ESBL producing bacteria were presumptive AmpC and carbapenemase resistance phenotype. Themost abundant ESBL producing Enterobacteriaceae were Klebsiella spp 32.1% (9/28) and Escherichia spp 28.6% (8/28). The use of antibiotics in the last 3 months was found to be significantly associated (P = 0.012) with the faecal carriage of ESBLs producing Enterobacteriaceae.

CONCLUSION

The prevalence of faecal carriage of ESBLs producing Enterobacteriaceae among food handlers in the Gambia is low. The history to use of the antibiotics in the last three months was found to be significantly associated with this prevalence. Therefore, the institution of a robust antimicrobial surveillance and treatment of patients with such infections are necessary to curb the spread of these multidrug resistant bacteria in the country. Rational prescription and usage of the antibiotics especially cephalosporin should be advocated both in public and private health facilities.

Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) among travellers to Africa: destination-specific data pooled from three European prospective studies

BACKGROUND

One third of travellers to low- and middle-income regions of the tropics and subtropics become colonized by extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE). The risk varies by destination and, for each traveller, may be substantially further increased by travellers' diarrhoea (TD) and antibiotic use. Despite the risk of TD in Africa, ESBL-PE acquisition rates in all studies are lower there than in Asia. Africa has become increasingly popular as a destination for international travellers, yet minimal data are available from the continent's subregions and countries.

METHODS

We analysed subregion- and country-specific data on carriage and risk factors for ESBL-PE colonization pooled from three prospective studies conducted between 2009 and 2013 among Finnish and Dutch travellers. The data were subjected to multivariable analysis of risk factors. In addition, we compared our data to two recent large investigations reporting data by subregion and country.

RESULTS

Our joint analysis comprised data on 396 travellers. The ESBL-PE colonization rate was highest in Northern Africa, followed by Middle and Eastern Africa, and lowest in Southern and Western Africa. Of individual countries with more than 15 visitors, the highest rates were seen for Egypt (12/17; 70.6%), Ghana (6/23; 26.1%), and Tanzania (14/81; 17.3%); the rates among travellers to Egypt were comparable to those reported in South and Southeast Asia. In a pooled multivariable analysis, travel destination, age, overnight hospitalisation abroad, TD, and use of fluoroquinolones were independently associated with increased ESBL-PE colonization rates.

CONLUSIONS

Even in areas with relatively low risk of colonization, antimicrobials clearly predispose to colonization with ESBL-PE. Travellers to Africa should be cautioned against unnecessary use of antibiotics.

Multidrug resistance among Escherichia coli and Klebsiella pneumoniae carried in the gut of out-patients from pastoralist communities of Kasese district, Uganda

Background

Antimicrobial resistance is a worldwide public health emergency that requires urgent attention. Most of the effort to prevent this coming catastrophe is occurring in high income countries and we do not know the extent of the problem in low and middle-income countries, largely because of low laboratory capacity coupled with lack of effective surveillance systems. We aimed at establishing the magnitude of antimicrobial resistance among Escherichia coli and Klebsiella pneumoniae carried in the gut of out-patients from pastoralist communities of rural Western Uganda.

Methods

A cross-sectional study was carried out among pastoralists living in and around the Queen Elizabeth Protected Area (QEPA). Stool samples were collected from individuals from pastoralist communities who presented to the health facilities with fever and/or diarrhea without malaria and delivered to the microbiology laboratory of College of Health Sciences-Makerere University for processing, culture and drug susceptibility testing.

Results

A total of 300 participants fulfilling the inclusion criteria were recruited into the study. Three hundred stool samples were collected, with 209 yielding organisms of interest. Out of 209 stool samples that were positive, 181 (89%) grew E. coli, 23 (11%) grew K. pneumoniae and five grew Shigella. Generally, high antibiotic resistance patterns were detected among E. coli and K. pneumoniae isolated. High resistance against cotrimoxazole 74%, ampicillin 67%, amoxicillin/clavulanate 37%, and ciprofloxacin 31% was observed among the E. coli. In K. pneumoniae, cotrimoxazole 68% and amoxicillin/clavulanate 46%, were the most resisted antimicrobials. Additionally, 57% and 82% of the E. coli and K. pneumoniae respectively were resistant to at least three classes of the antimicrobials tested. Resistance to carbapenems was not detected among K. pneumoniae and only 0.6% of the E. coli were resistant to carbapenems. Isolates producing ESBLs comprised 12% and 23% of E. coli and K. pneumoniae respectively.

Conclusion

We demonstrated high antimicrobial resistance, including multidrug resistance, among E. coli and K. pneumoniae isolates from pastoralist out-patients. We recommend a One Health approach to establish the sources and drivers of this problem to inform public health.

Fecal carriage of multidrug-resistant Escherichia coli by community children in southern Taiwan

BACKGROUND

The emergence of multidrug-resistant (MDR) Escherichia coli (E. coli), particularly E. coli sequence type ST131, is becoming a global concern. Commensal bacteria, an important reservoir of antibiotic resistance genes, facilitate the spread of such genes to pathogenic bacterial strains. The objective of the study is to investigate the fecal carriage of MDR E. coli and ST131 E. coli in community children in Southern Taiwan.

METHODS

In this prospective study, stool samples from children aged 0-18 years were obtained within 3 days of hospitalization from October 2013 to September 2014. Children with a history of underlying diseases, antibiotic treatment, or hospitalization in the 3 months before specimen collection were excluded. E. coli colonies were selected and tested for antimicrobial susceptibility, and O25b-ST131, multilocus sequence typing, and blaCTX-M gene groups were detected.

RESULTS

Among 157 E. coli isolates, the rates of nonsusceptibility to ampicillin, amoxycillin + clavulanate, trimethoprim-sulfamethoxazole, and cefazolin were 70, 65.6, 47.1, and 32.5%, respectively. Twenty-nine (18.5%) isolates were nonsusceptible to ciprofloxacin. MDR E. coli accounted for 58 (37%) of all isolates. Thirteen (8.3%) isolates produced extended-spectrum β-lactamase (ESBL). Furthermore, 26 (16.6%) and 13 (8.3%) isolates were O25b and ST131 positive, respectively. Five (38.5%) of the 13 ESBL-producing E. coli belonged to blaCTX-M group 9, among which were CTXM-14 and 4 (80%) were O25b-ST131 positive. Compared with the non-ESBL and ciprofloxacin-susceptible groups, the ESBL and ciprofloxacin-nonsusceptible groups showed significantly higher rates of O25b-ST131 positivity.

CONCLUSIONS

The prevalence of the fecal carriage of nonsusceptible E. coli in children was high; among these E. coli, 37% were MDR, 18.5% were nonsusceptible to ciprofloxacin, and 8.3% produced ESBL. O25b-ST131 was the most common ESBL-producing E. coli clonal group present in the feces of children, and the ESBL and ciprofloxacin-nonsusceptible groups showed significantly higher rates of O25b-ST131 positivity.

Faecal colonization of E. coli and Klebsiella spp. producing extended-spectrum beta-lactamases and plasmid-mediated AmpC in Mozambican university students

Background

In recent years, the world has seen a surge in Enterobacteriaceae resistant to broad-spectrum beta-lactam antibiotics due to the production of extended-spectrum beta-lactamases (ESBLs) or plasmid-mediated AmpC (pAmpC) enzymes. Data on the epidemiology of cephalosporin-resistant Enterobacteriaceae in Sub-Saharan Africa are still limited.

Methods

Two hundred seventy-five non-repetitive stool samples were collected from Mozambican university students of both sexes. Samples were cultured on MacConkey agar with and without ceftriaxone (1 mg/L) for selection of third-generation cephalosporin-resistant isolates, which were subjected to antimicrobial susceptibility testing by disc diffusion, characterization of resistance genes by PCR and ERIC-PCR analysis for strain clonality.

Results

Among the 275 students, 55 (20%) carried a total of 56 E. coli (n = 35) and Klebsiella spp. (n = 21) isolates resistant to ceftriaxone and phenotypically positive for ESBL- and/or pAmpC-production. Forty-three percent of the isolates (24/56) contained only ESBL genes, 11% (6/56) only pAmpC genes, and 36% (20/56) both ESBL and pAmpC genes. The remaining six isolates were negative for the CTX-M/pAmpC genes included in the test panel. E. coli and Klebsiella spp. combined demonstrated 70% resistance to tetracycline and co-trimoxazole, 63% to ceftazidime and 34% to ciprofloxacin. In total, 89% of ESBL/pAmpC-positive isolates were defined as multi-resistant by being resistant to three or more antibiotic classes. ERIC-PCR fingerprinting demonstrated low similarity among isolates. None of the participants reported recent hospitalization and just 12.5% had taken antibiotics 3 months prior to the study.

Conclusion

This study demonstrated 20% colonization with multi-resistant E. coli and Klebsiella spp. among Mozambican students with a diversity of ESBL and pAmpC genes. Colonization was not related to prior hospitalization or antimicrobial consumption.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3154-1) contains supplementary material, which is available to authorized users.

High carriage rate of extended-spectrum beta-lactamase-producing Enterobacteriaceae among patients admitted for surgery in Tanzanian hospitals with a low rate of endogenous surgical site infections

INTRODUCTION

Despite the high reported rates of surgical site infections (SSIs) caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae (EPE) in low-income countries, including Tanzania, the role of EPE carriage in subsequent occurrence of SSIs is not known. This study investigated the rates of EPE carriage among surgical patients at the time of admission and discharge, and linked EPE genotype with SSIs.

METHODS

EPE were confirmed among isolates from rectal and wound/pus swabs using VITEK-2. Polymerase chain reaction and sequencing were performed to detect beta-lactamase genes. Multi-locus sequence typing was used to determine the genotypes of EPE isolates.

RESULTS

Among 930 patients enrolled, EPE carriage was significantly higher on discharge than admission (36.4% vs 23.7%, P<0.001). Of 272 patients who tested negative on admission, 78 (28.7%) acquired EPE during hospitalization. History of hospital stay within the previous three months was an independent predictor of EPE acquisition [hazard ratio 2, 95% confidence interval (CI) 1.04-3.98, P=0.038]. Of the 536 patients who were successfully followed-up after surgery, 78 (14.6%, 95% CI 11.6-17.5) developed SSIs. Of 57 SSIs investigated, 33 (58%) were caused by enteric Gram-negative bacteria, of which 63.6% (21/33) were EPE. Escherichia coli sequence type (ST)131 pandemic clone and Klebsiella pneumoniae ST391 predominated among wound isolates. The bla_CTX-M-15 gene was detected in 37 (97.3%) of 38 ESBL isolates. Male sex was an independent predictor of SSI (odds ratio 2.92, 95% CI 1.73-4.91, P<0.001).

CONCLUSION

These findings warrant implementation of strict infection control measures, antimicrobial stewardship and exploration of the transmission dynamics of EPE in surgical wards.

Prevalence and risk factors for CTX-M gram-negative bacteria in hospitalized patients at a tertiary care hospital in Kilimanjaro, Tanzania

Emergence and spread of extended spectrum beta-lactamase (ESBL)-producing gram-negative bacteria, mainly due to CTX-M, is a major global public health problem. Patients infected with ESBL-producing gram-negative bacteria have an increased risk of treatment failure and death. We investigated the prevalence and risk factors for CTX-M gram-negative bacteria isolated from clinical specimens of patients hospitalized at a tertiary care hospital in Kilimanjaro, Tanzania. Isolated gram-negative bacteria from inpatients admitted at Kilimanjaro Christian Medical Centre (KCMC) between August 2013 and August 2015 were fully genome sequenced. The prevalence of ESBL-producing gram-negative bacteria was determined based on the presence of bla_CTX-M. The odds ratio (OR) and risk factors for ESBL-producing gram-negative bacteria due to CTX-M were assessed using logistic regression models. The overall CTX-M prevalence (95% CI) was 13.6% (10.1–18.1). Adjusted for other factors, the OR of CTX-M gram-negative bacteria for patients previously hospitalized was 0.26 (0.08–0.88), p = 0.031; the OR for patients currently on antibiotics was 4.02 (1.29–12.58), p = 0.017; the OR for patients currently on ceftriaxone was 0.14 (0.04–0.46), p = 0.001; and the OR for patients with wound infections was 0.24 (0.09–0.61), p = 0.003. The prevalence of ESBL-producing gram-negative bacteria due to CTX-M in this setting is relatively low compared to other previous reports in similar settings. However, to properly stop further spread in the hospital, we recommend setting up a hospital surveillance system that takes full advantage of the available next-generation sequencing facility to routinely screen for all types of bacterial resistance genes.

Correlates of multi-drug non-susceptibility in enteric bacteria isolated from Kenyan children with acute diarrhea

BACKGROUND

Reduced antimicrobial susceptibility threatens treatment efficacy in sub-Saharan Africa, where data on the burden and correlates of antibiotic resistance among enteric pathogens are limited.

METHODS

Fecal samples from children aged 6 mos-15 yrs presenting with acute diarrhea in western Kenya were cultured for bacterial pathogens. HIV-uninfected children with identified Shigella or Salmonella species or pathogenic Escherichia coli (EPEC, ETEC, EAEC or EIEC) were included in this cross-sectional sub-study. Non-susceptibility to ampicillin, ceftriaxone, ciprofloxacin, cotrimoxazole, and tetracycline was determined using MicroScan Walkaway40 Plus. Multivariable log-binomial regression was used to identify correlates of multi-drug non-susceptibility (MDNS, non-susceptibility to ≥ 3 of these antibiotics).

RESULTS

Of 292 included children, median age was 22.5 mos. MDNS was identified in 62.5% of 318 isolates. Non-susceptibility to cotrimoxazole (92.8%), ampicillin (81.3%), and tetracycline (75.0%) was common. Young age (6-24 mos vs. 24-59 mos adjusted prevalence ratio [aPR] = 1.519 [95% confidence interval: 1.19, 1.91]), maternal HIV (aPR = 1.29 [1.01, 1.66]); and acute malnutrition (aPR = 1.28 [1.06, 1.55]) were associated with higher prevalence of MDNS, as were open defecation (aPR = 2.25 [1.13, 4.50]), household crowding (aPR = 1.29 [1.08, 1.53]) and infrequent caregiver hand-washing (aPR = 1.50 [1.15, 1.95]).

CONCLUSIONS

Young age, HIV exposure, acute malnutrition and poor sanitation may increase risk of antibiotic non-susceptible enteric pathogen infections among children in Kenya.

Faecal carriage of CTX-M extended-spectrum beta-lactamase-producing Enterobacteriaceae among street children dwelling in Mwanza city, Tanzania

BACKGROUND

Data on ESBL carriage of healthy people including children are scarce especially in developing countries. We analyzed the prevalence and genotypes of ESBL-producing Enterobacteriaceae (EPE) in Tanzanian street children with rare contact to healthcare facilities but significant interactions with the environment, animals and other people.

METHODOLOGY/ PRINCIPLE FINDINGS

Between April and July 2015, stool samples of 107 street children, who live in urban Mwanza were analyzed for EPE. Intestinal carriage of EPE was found in 34 (31.8%, 95% CI; 22.7-40.3) children. Of the 36 isolates from 34 children, 30 (83.3%) were Escherichia coli (E. coli) and six Klebsiella pneumoniae (K. pneumoniae). Out of 36 isolates, 36 (100%), 35 (97%), 25 (69%) and 16 (44%) were resistant to tetracycline, trimethoprim-sulfamethoxazole, ciprofloxacin and gentamicin, respectively. Beta-lactamase genes and the multilocus sequence types of E. coli and K. pneumoniae were characterized. ESBL gene blaCTX-M-15 was detected in 75% (27/36) of ESBL isolates. Sequence types (STs) 131, 10, 448 and 617 were the most prevalent in E. coli. Use of local herbs (OR: 3.5, 95% CI: 1.51-8.08, P = 0.003) and spending day and night on streets (OR: 3.6, 95% CI: 1.44-8.97, P = 0.005) were independent predictors of ESBL carriage.

CONCLUSIONS/ SIGNIFICANCE

We observed a high prevalence of blaCTX-M-15 in EPE collected from street children in Tanzania. Detection of E. coli STs 131, 10, 38 and 648, which have been observed worldwide in animals and people, highlights the need for multidisciplinary approaches to understand the epidemiology and drivers of antimicrobial resistance in low-income countries.