Genome analysis of multidrug resistant Enterococcus faecium and Enterococcus faecalis circulating among hospitalized patients in uMgungundlovu District, KwaZulu-Natal, South Africa.

BACKGROUND: Vancomycin-resistant enterococci (VRE) are important pathogens categorized as high-priority bacteria in the Global Priority List of Antibiotic-Resistant Bacteria to Guide Research, Discovery, and Development of New Antibiotics published by the World Health Organization. The aim of this study was to determine the risk factors, resistance, virulence, mobilomes associated with multidrug-resistant and clonal lineages of Enterococcus faecium and faecalis circulating among hospitalized patients following the health system in South Africa, using whole genome sequencing (WGS). METHODS: A cross-sectional study was conducted during a two-month periods among hospitalized patients in 2017. Rectal swabs were collected from patients admitted to medical and surgical wards in an urban tertiary hospital, and a rural district hospital in uMgungundlovu district, South Africa. Enterococci were screened for vancomycin resistance on bile esculin azide agar supplemented with 6 mg/L of vancomycin and confirmation of VRE was done using ROSCO kits. Conventional and real-time PCR methods were used to ascertain the presence of VanA, VanB, VanC-2/3 and VanC-1 genes. All six multidrug-resistant Enterococcus faecalis and faecium selected were identified using multiplexed paired-end libraries (2 × 300 bp) with the Nextera XT DNA sample preparation kit (Illumina, San Diego, CA, USA) and genome sequencing was done using Illumina MiSeq instrument with 100× coverage at the National Institute of Communicable Diseases Sequencing Core Facility, South Africa. Antibiotic resistance genes, virulence factors, plasmids, integrons and CRISPR were characterized using RAST, ResFinder, VirulenceFinder, PlasmidFinder, PHAST and ISFinder respectively. RESULTS: Sequencing analysis revealed that these strains harbouring numerous resistance genes to glycopeptides (vanC[100%], vex3[100%], vex2[83,33%] and vanG[16,66%]), macrolides, lincosamides, sterptogramine B (ermB[33,32%], Isa[16,66%], emeA[16,66%]) and tetracyclines (tetM[33,32%]) in both district and tertiary hospitals. Multidrug efflux pumps including MATE, MFS and pmrA conferring resistance to several classes of antibiotics were also identified. The main transposable elements observed were in the Tn3 family, specifically Tn1546. Four single sequence types (STs) were identified among E. faecium in the district hospital, namely ST822, ST636, ST97 along with a novel ST assigned ST1386, while one lineage, ST29 was detected in the tertiary hospital. CONCLUSION: The study reveals the genetic diversity and high pathogenicity of multidrug-resistant Enterococcus faecalis and faecium circulating among hospitalized patients. It underlines the necessity to implement routine screening of admitted patients coupled with infection control procedures, antimicrobial stewardship and awareness should be strengthened to prevent and/or contain the carriage and spread of multidrug resistant E. faecium and E. faecalis in hospitals and communities in South Africa.

High prevalence and genetic diversity of multidrug-resistant and extended-spectrum ß-lactamase-producing Escherichia coli and Klebsiella pneumoniae in mothers and neonates in a Cameroonian labor ward.

BACKGROUND: Escherichia coli and Klebsiella pneumoniae rank among the primary bacterial culprits in neonatal infections and fatalities in sub-Saharan Africa. This study characterized the phenotypic and genotypic features of E coli and K pneumoniae in a labor ward in Yaoundé, Cameroon. METHODS: A prospective and cross-sectional study spanning 5months, from February 21, 2022 to June 30, 2022. Rectovaginal swabs were obtained from expectant mothers, and nasopharyngeal swabs were collected from their babies. Hand swabs of health care workers and environmental samples were also collected. The samples were cultured on eosin methylene blue agar. Extended-spectrum ß-lactamase (ESBL) production was assessed using CHROMAgar ESBL and the double-disk synergy test. A polymerase chain reaction was employed to detect ß-lactamase genes. RESULTS: A total of 93 mothers and 90 neonates were collected. Almost all pregnant women (90%) were colonized by one or more multidrug-resistant (MDR) isolates with 58% being concomitantly ESBL producers. Altogether, 14 of 22 (64%) neonates were colonized by MDR isolates, while out of the 5 workers positive to Enterobacterales, all were colonized by MDR isolates. E coli predominated in pregnant women (55%) and neonates (73%), while K pneumoniae (83%) predominated in health care workers. The blaCTX-M (75%) was the leading ß-lactamase gene detected. CONCLUSIONS: Our study suggests that drug-resistant E coli and K pneumoniae are circulating at high prevalence in the labor ward in Yaoundé and emphasizes the necessity for effective infection prevention and control along with antimicrobial stewardship measures.

Phenotypic and genotypic characterization of multidrug resistant and extended-spectrum ß-lactamase-producing Enterobacterales isolated from clinical samples in the western region in Cameroon.

BACKGROUND: The 2017 World Health Organization (WHO) report has listed extended-spectrum ß-lactamase-producing Enterobacterales (ESBL-E) as critical pathogens for public health and requiring urgently new antibiotics. The aim of this study was to characterize phenotypically and genotypically ESBL-E isolated among clinical samples in Dschang, Cameroon. METHODS: A cross-sectional study was conducted during a four-month periods from February to May 2022 in the two biggest hospitals of Dschang. Clinical samples were collected and cultured on Eosin Methylene Blue agar. Suspected growing colonies were biochemically identified using the Enterosystem Kit 18R. Antimicrobial susceptibility testing (AST) was done using the Kirby Bauer disc diffusion method and interpretated according to the CA-SFM recommendations. ESBL phenotypes were double screened using CHROMagar™ ESBL and double disk synergy test (DDST). The detection of resistance genes was performed using conventional and multiplex PCR methods. Results were analyzed with SPSS (version 21) and a p-value < 0.05 was considered statistically significant. RESULTS: A total of 152 Enterobacterales were isolated among 597 clinical samples including urine, blood, cervico-vaginal, urethral swabs and wound samples. The overall prevalence of ESBL-Enterobacterales was 29.61% (45/152). The most represented ESBL species were Escherichia coli (n = 23; 51.11%), Klebsiella pneumoniae (n = 8; 17.78%) and Citrobacter freundii (n = 6; 13.33%). CONCLUSION: This study reveals the high burden of ESBL-E among clinical samples in the regional hospital in Dschang with the most common species being E. coli and K. pneumoniae. It confirmed the high occurrence of blaCTX-M and blaTEM among ESBL-E. The study suggests that implementing antimicrobial stewardship program and real-time surveillance of antimicrobial resistance are needed in the Western region of Cameroon. Moreover, the implementation of infection prevention and control measures (IPC) is essential to curb the dissemination of these bacteria from community to hospital settings. Implementation of national action plan to fight against antimicrobial resistance at the local levels is urgently needed.

Molecular epidemiology of Streptococcus agalactiae in non-pregnant populations: a systematic review.

Streptococcus agalactiae (group B Streptococcus, GBS) has recently emerged as an important pathogen among adults. However, it is overlooked in this population, with all global efforts being directed towards its containment among pregnant women and neonates. This systematic review assessed the molecular epidemiology and compared how the lineages circulating among non-pregnant populations relate to those of pregnant and neonatal populations worldwide. A systematic search was performed across nine databases from 1 January 2000 up to and including 20 September 2021, with no language restrictions. The Joanna Briggs Institute (JBI) Prevalence Critical Appraisal Tool (PCAT) was used to assess the quality of included studies. The global population structure of GBS from the non-pregnant population was analysed using in silico typing and phylogenetic reconstruction tools. Twenty-four articles out of 13 509 retrieved across 9 databases were eligible. Most studies were conducted in the World Health Organization European region (12/24, 50 %), followed by the Western Pacific region (6/24, 25 %) and the Americas region (6/24, 25 %). Serotype V (23%, 2310/10240) and clonal complex (CC) 1 (29 %, 2157/7470) were the most frequent serotype and CC, respectively. The pilus island PI1 : PI2A combination (29 %, 3931/13751) was the most prevalent surface protein gene, while the tetracycline resistance tetM (55 %, 5892/10624) was the leading antibiotic resistance gene. This study highlights that, given the common serotype distribution identified among non-pregnant populations (V, III, Ia, Ib, II and IV), vaccines including these six serotypes will provide broad coverage. The study indicates advanced molecular epidemiology studies, especially in resource-constrained settings for evidence-based decisions. Finally, the study shows that considering all at-risk populations in an inclusive approach is essential to ensure the sustainable containment of GBS.

Faecal carriage of multidrug-resistant and extended-spectrum ß-lactamase-producing Enterobacterales in people living with HIV in Yaoundé, Cameroon.

OBJECTIVES: Antibiotic resistance (AR) is a global health issue with multidimensional repercussions. There is a paucity of data regarding the molecular epidemiology of multidrug-resistant Enterobacterales (MDR-E) and extended-spectrum ß-lactamase-producing Enterobacterales (ESBL-PE) in Africa, especially among people living with HIV (PLHIV). This study aimed at determining the prevalence, risk factors, phenotypic and genotypic profiles of MDR-E and ESBL-PE isolated from PLHIV in Yaoundé, Cameroon. METHODS: In total, samples were collected from 185 PLHIV during a three-month period (April-June 2021) at the Yaoundé Central Hospital. Stool samples and rectal swabs were collected and cultured on MacConkey agar. The API 20E kit was used for the phenotypic identification of the isolates, whereas antibiotic susceptibility testing was performed using the Kirby-Bauer disk diffusion method. The ß-lactamase genes and genotypic relatedness were studied by PCR and ERIC-PCR, respectively. RESULTS: The prevalence of MDR-E among PLHIV was 81%, of which 39% were ESBL-PE. A high level of resistance to fosfomycin (89%), chloramphenicol (63%), and gentamicin (56%) was observed. Escherichia coli was the predominant MDR non-ESBL-PE (80.8%) and MDR ESBL-PE (73.77%). The principal ß-lactamases genes in MDR non-ESBL and MDR ESBL-PE were blaTEM (62.90%) and blaCTX-M (40.86%), respectively. Genetic fingerprinting revealed high genetic relatedness among E. coli isolates. CONCLUSION: This study shows a high prevalence of MDR-E and ESBL-PE in the gut of PLHIV in Yaoundé, with blaTEM and blaCTX-M being the most prevalent. It demonstrates the need to strengthen real-time surveillance of these resistant bacteria in order to improve management of infection among PLHIV.

Genome Analysis of ESBL-Producing Escherichia coli Isolated from Pigs.

The resistome, virulome and mobilome of extended spectrum ß-lactamase (ESBL)-producing Escherichia coli (ESBL-Ec) isolated from pigs in Cameroon and South Africa were assessed using whole genome sequencing (WGS). Eleven clonally related phenotypic ESBL-Ec isolates were subjected to WGS. The prediction of antibiotic resistance genes, virulence factors (VFs) and plasmids was performed using ResFinder, VirulenceFinder and PlasmidFinder, respectively. Diverse sequence types (STs) were detected with ST2144 and ST88 being predominant and blaCTX-M-15 (55%) being the principal ESBL gene. All except two isolates harboured various aminoglycoside resistance genes, including aph(3″)-Ib (6/11, 55%) and aph(6)-1d (6/11, 55%), while the qnrS1 gene was identified in four of the isolates. The ESBL-Ec isolates showed a 93.6% score of being human pathogens. The fim, ehaB, ibeB/C were the leading virulence factors detected. All isolates harboured at least three extraintestinal pathogenic E. coli (ExPEC) VFs, with one isolate harbouring up to 18 ExPEC VFs. Five isolates (45.45%) harboured the plasmid incompatibility group IncF (FII, FIB, FIC, FIA). The study revealed that there is an urgent need to implement effective strategies to contain the dissemination of resistant and virulent ESBL-Ec through the food chain in Cameroon and South Africa.

Multidrug-Resistant and Extended-Spectrum ß-Lactamase (ESBL) - Producing Enterobacterales Isolated from Carriage Samples among HIV Infected Women in Yaoundé, Cameroon.

The exacerbation of antimicrobial resistance (AMR) is a major public health threat worldwide. In sub-Saharan Africa, there is a scarcity of data regarding multidrug-resistant (resistance to at least one antibiotic of three or more families of antibiotics) as well as extended spectrum ß-lactamase-producing Enterobacterales (ESBL-PE), isolated among clinical and asymptomatically healthy patients, especially in women living with HIV (WLHIV) despite their immunocompromised status. The overarching aim of this study was set to determine the prevalence and characterize genotypically multi-drug resistant Enterobacterales (MDR-E) and ESBL- PE isolated from vaginal swabs of WLHIV attending the Yaoundé Central Hospital, Yaoundé, Cameroon. A cross-sectional study was conducted among WLHIV during a four-month periods from 1 February to 31 May 2021. A total of 175 WLHIV, of childbearing age and under antiretroviral treatment were contacted. One hundred and twenty participants (120) were recruited and vaginal swabs were collected from them. After culture on Eosine-Methylen Blue (EMB) agar, the identification of Enterobacterales was performed using API 20E kit. A double-screening of ESBL-PE was performed using a combined disc diffusion method and ROSCO Diagnostica kits. An antibiotic susceptibility test was carried out by disc diffusion as per the Kirby-Bauer method and the ß-lactamase resistance genes, blaCTX-M, blaCTX-M-group1-2-9, blaTEM were molecularly characterized using a conventional Polymerase Chain Reaction (PCR). Overall, 30.83% (37/120) of the included WLHIV were colonized with Enterobacterales and the prevalence of vaginal carriage of MDR Enterobacterales among them was 62.16% (23/37). Among MDR-E isolates, the most prevalent species were E. coli (56.0%; 14/25) and K. pneumoniae (20.0%; 5/25). High rates of resistance to trimethoprim-sulfamethoxazole (96.0%; 24/25), amoxicillin-clavulanic acid (88.0%; 22/25) and gentamicin (72%; 18/25) were observed. The resistance mechanisms detected among these isolates were ESBL (48.0%; 12/25), ESBL+ porin loss (8.0%; 2/25), ESBL+AmpC (24%; 6/25), with blaCTX-M, blaCTX-M-group-1,2,9 being identified at 48.0% (12/25) for each of them and blaTEM at 72.0% (18/25). Our findings confirm the high-prevalence of MDR as well as ESBL-PE isolated in WLHIV, and suggest that a real time monitoring system of antimicrobial resistant bacteria coupled with the reinforcement of infection prevention control (IPC) strategies are needed to sustainably contain these life-threatening pathogens especially in the most vulnerable populations.

Methicillin resistant staphylococci isolated in clinical samples: a 3-year retrospective study analysis.

AIM: To determine the prevalence and describe the antimicrobial resistance patterns of circulating methicillin-resistant staphylococci (MRS) isolated from clinical specimens during a 3-year period in Yaoundé, Cameroon. MATERIALS & METHODS: From January 2017 to December 2019, 1683 clinical samples were plated onto Mannitol salt agar. Bacterial identification was performed followed by antibiotic susceptibility testing. Data were analyzed using R program. RESULTS: Staphylococci were identified in 90 (5.35%) of the 1683 clinical samples. Among these, 83.33% were MRS with 78.67% being methicillin-resistant Staphylococcus aureus (MRSA). The prevalence of MRS infection increased significantly with age. CONCLUSION: The study offers a good baseline for surveillance intervention to contain antimicrobial resistance and highlights the need to strengthen antimicrobial stewardship and infection, prevention and control programs in the country.

Draft genome sequence of a clinical Acinetobacter haemolyticus isolate from South Africa.

OBJECTIVES: Here we describe the draft genome sequence of a clinical Acinetobacter haemolyticus isolate (A109R1B4) from a rectal swab of a hospitalised patient in South Africa. METHODS: Genomic DNA from the isolate was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using Qiagen CLC Genomics Workbench. The assembled contigs were annotated and antimicrobial resistance genes and sequence type were identified. RESULTS: The genome comprised 281 contigs with a total assembly length of 3 371 389bp, a G+C content of 39.9% and an N50 value of 58 196bp, and reference coverage was 93.08 while the coverage was 88.08. A total of 3387 genes, 3292 coding sequences (CDS), 3175 coding genes and 95 RNA genes were detected. The antimicrobial resistance genes blaOXA-264 and aac(6')-Ig were detected. CONCLUSION: The genome sequence reported will serve as a reference point for molecular epidemiological studies of antibiotic-resistant A. haemolyticus in Africa.

Genome analysis of methicillin-resistant Staphylococcus aureus isolated from pigs: Detection of the clonal lineage ST398 in Cameroon and South Africa.

Food animals are considered reservoirs of methicillin-resistant Staphylococcus aureus (MRSA) and are implicated in their zoonotic transmission in the farm-to-plate continuum. LA-MRSA has been reported as a zoonotic agent that has the potential to spread to humans and may cause infections in at-risk groups. In this study, whole genome sequencing was used to describe the genetic environment (resistance mechanisms, virulence factors and mobile genetic elements) and investigate the genetic lineages of MRSA isolates from pigs in Cameroonian and South African abattoirs. During March-October 2016, 288 nasal and rectal pooled samples from 432 pigs as well as nasal and hand swabs from 82 humans were collected. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were de novo-assembled using the Qiagen CLC Genomics Workbench and SPAdes. The assembled contigs were annotated, and antibiotic resistance genes, virulence factors, plasmids, SCCmec and phage elements were identified with ResFinder, Virulence Finder, PlasmidFinder, SCCmec Finder and PHAST, respectively. Core genome single nucleotide analysis was undertaken to assess clonal relatedness among isolates. A lower MRSA prevalence was observed in pigs in Cameroon (n = 1/13; 0.07%) compared with South Africa (n = 4/22; 18.18%), and none of the workers were colonized by MRSA. Genome analysis identified various antibiotic resistance genes along with six virulence factors in all isolates. All MRSA isolates belonged to the clonal lineage ST398 (spa-type t011) and harboured the type Vc SCCmec and several plasmids. Our study shows that the livestock-associated MRSA clonal lineage ST398 is already present in both Cameroon and South Africa and is probably underestimated in the absence of molecular epidemiological studies. It reveals the serious food safety and public health threat associated with this animal strain and underscores the need for interventions to contain this resistant clone.

Whole Genome Sequencing of Extended Spectrum ß-lactamase (ESBL)-producing Klebsiella pneumoniae Isolated from Hospitalized Patients in KwaZulu-Natal, South Africa.

Extended spectrum ß-lactamase (ESBL)-producing Klebsiella pneumoniae remain a critical clinical concern worldwide. The aim of this study was to characterize ESBL-producing K. pneumoniae detected within and between two hospitals in uMgungundlovu district, South Africa, using whole genome sequencing (WGS). An observational period prevalence study on antibiotic-resistant ESKAPE (i.e. Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) bacteria was carried out in hospitalized patients during a two-month period in 2017. Rectal swabs and clinical specimens were collected from patients hospitalized and were screened for ESBL-producing, Gram-negative ESKAPE bacteria using cefotaxime-containing MacConkey agar and ESBL combination disk tests. Nine confirmed ESBL-K. pneumoniae isolated from six patients and two hospitals were whole genome sequenced using an Illumina MiSeq platform. Genome sequences were screened for presence of integrons, insertion sequences, plasmid replicons, CRISPR regions, resistance genes and virulence genes using different software tools. Of the 159 resistant Gram-negative isolates collected, 31 (19.50%) were ESBL-producers, of which, nine (29.03%) were ESBL-K. pneumoniae. The nine K. pneumoniae isolates harboured several ß-lactamase genes, including blaCTX-M-15, blaTEM-1b, blaSHV-1, blaOXA-1 concomitantly with many other resistance genes e.g. acc(6')-lb-cr, aadAI6, oqxA and oqxB that confer resistance to aminoglycosides and/or fluoroquinolones, respectively. Three replicon plasmid types were detected in both clinical and carriage isolates, namely ColRNAI, IncFIB(K), IncF(II). Sequence type ST152 was confirmed in two patients (one carriage isolate detected on admission and one isolate implicated in infection) in one hospital. In contrast, ST983 was confirmed in a clinical and a carriage isolate of two patients in two different hospitals. Our data indicate introduction of ESBL-producing K. pneumoniae isolates into hospitals from the community. We also found evidence of nosocomial transmission within a hospital and transmission between different hospitals. The Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-associated cas3 genes were further detected in two of the nine ESBL-KP isolates. This study showed that both district and tertiary hospital in uMgungundlovu District were reservoirs for several resistance determinants and highlighted the necessity to efficiently and routinely screen patients, particularly those receiving extensive antibiotic treatment and long-term hospitalization stay. It also reinforced the importance of infection, prevention and control measures to reduce the dissemination of antibiotic resistance within the hospital referral system in this district.

Emergence and Spread of Extended Spectrum ß-Lactamase Producing Enterobacteriaceae (ESBL-PE) in Pigs and Exposed Workers: A Multicentre Comparative Study between Cameroon and South Africa.

Extended spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-PE) represent a significant public health concern globally and are recognized by the World Health Organization as pathogens of critical priority. However, the prevalence of ESBL-PE in food animals and humans across the farm-to-plate continuum is yet to be elucidated in Sub-Saharan countries including Cameroon and South Africa. This work sought to determine the risk factors, carriage, antimicrobial resistance profiles and genetic relatedness of extended spectrum ß-lactamase producing Enterobacteriaceae (ESBL-PE) amid pigs and abattoir workers in Cameroon and South Africa. ESBL-PE from pooled samples of 432 pigs and nasal and hand swabs of 82 humans were confirmed with VITEK 2 system. Genomic fingerprinting was performed by ERIC-PCR. Logistic regression (univariate and multivariate) analyses were carried out to identify risk factors for human ESBL-PE carriage using a questionnaire survey amongst abattoir workers. ESBL-PE prevalence in animal samples from Cameroon were higher than for South Africa and ESBL-PE carriage was observed in Cameroonian workers only. Nasal ESBL-PE colonization was statistically significantly associated with hand ESBL-PE (21.95% vs. 91.67%; p = 0.000; OR = 39.11; 95% CI 2.02⁻755.72; p = 0.015). Low level of education, lesser monthly income, previous hospitalization, recent antibiotic use, inadequate handwashing, lack of training and contact with poultry were the risk factors identified. The study highlights the threat posed by ESBL-PE in the food chain and recommends the implementation of effective strategies for antibiotic resistance containment in both countries.

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 ß-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 blaCTX-M group-1-2-9, blaCTX-M group 8/25, blaSHV, blaTEM, blaOXA-1-like, blaKPC, blaVIM, blaIMP, blaGES 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). blaCTX-M-group-9, blaCTX-M-group-1 and blaSHV 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.

Draft genome sequence of a methicillin-resistant Staphylococcus epidermidis isolate from swine.

OBJECTIVES: Here we report the draft genome sequence of a methicillin-resistant Staphylococcus epidermidis strain (sequence type 59) isolated from a pooled rectal sample from pigs collected in an abattoir in South Africa. METHODS: Genomic DNA of S. epidermidis PR246B0 was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using CLC Genomics Workbench (QIAGEN). The assembled contigs were annotated and antimicrobial resistance genes, plasmids and the sequence type were identified. RESULTS: The genome comprised a circular chromosome of 2537769bp, with a G-C content of 32.32% and various antimicrobial resistance genes associated with resistance to ß-lactams, fluoroquinolones, aminoglycosides, fosfomycin, macrolides, lincosamides and tetracycline. Genome analysis also revealed the presence of seven plasmid replicon types. CONCLUSION: The genome sequence reported herein will provide useful information for a better understanding of the genetic structure of the S. epidermidis genome in Africa.

Mannitol-fermenting methicillin-resistant staphylococci (MRS) in pig abattoirs in Cameroon and South Africa: A serious food safety threat.

Food animals can be reservoirs of methicillin-resistant staphylococci (MRS) and are involved in their zoonotic transmission through the food chain. In Africa, there is a dearth of information about the food safety issues associated with their dissemination in the farm-to-plate continuum. This study sought to determine and compare the carriage, antimicrobial resistance profiles and clonal relatedness of circulating MRS strains among pigs and exposed workers in Cameroon and South Africa. A total of 288 nasal and rectal pooled samples collected from 432 pigs as well as nasal and hand swabs from 82 humans were cultured on mannitol salt agar supplemented with 6 mg/l cefoxitin. Presumptive MRS were screened for methicillin resistance using the cefoxitin disc test and confirmed with the VITEK 2 system. Selected isolates underwent genomic fingerprinting via REP-PCR. Univariate and multivariate logistic regression analyses were performed to identify risk factors for MRS carriage in humans from a questionnaire survey among slaughterhouse workers. Overall, 75% and 70% of nasal and rectal pooled samples were respectively positive for MRS. The MRS prevalence in all pooled pig samples from Cameroon was higher than that of South Africa. MRS prevalence of carriage (nasal and hand) was higher in Cameroonian exposed workers compared to those from South Africa, with high statistical significance. Nasal MRS colonization was highly statistically associated with hand MRS (31.58% vs 86.21%; p = 0.000; OR = 13.54; 95% CI 3.99-45.95; p = 0.015). Recent antibiotic use, previous hospitalization, occupation of relatives, years in the employment and contact with poultry were the main risk factors identified in the emergence and spread of MRS. MRS are emerging as serious foodborne pathogens and present a food safety threat. There is an urgent need to implement stringent and effective prevention and containment measures to curb antibiotic resistance in the farm-to-plate continuum in Cameroon and South Africa.

Draft genome sequences of extended-spectrum ß-lactamase-producing Enterobacter aerogenes isolated from swine and human.

OBJECTIVES: The draft genome sequences of two Enterobacter aerogenes strains (HN503E2II and PN108E5IIB) isolated from two Cameroonian abattoirs are reported. METHODS: Bacterial genomic DNA of the two isolates was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using CLC Genomics Workbench and SPAdes. The assembled contigs were annotated, and antibiotic resistance genes, virulence factors and plasmids were identified. RESULTS: Whole-genome sequencing revealed that both strains were similar, with genomes of 4878638bp and 4794257bp, encoding several resistance genes associated with resistance to ß-lactams, fluoroquinolones, aminoglycosides, fosfomycin, phenicols, sulphonamides, trimethoprim, macrolides and tetracycline. In silico analysis also revealed chromosomal integration of one plasmid in the genome of PN108E5IIB. CONCLUSION: The genome sequences reported here will provide useful information for a better understanding of the genetic structure of E. aerogenes in Africa.

Draft genome sequence of an extended-spectrum ß-lactamase (CTX-M-15)-producing Escherichia coli ST10 isolated from a nasal sample of an abattoir worker in Cameroon.

OBJECTIVES: Here we report the draft genome sequence of Escherichia coli strain HN503E1II isolated from a nasal sample of an abattoir worker in Cameroon. METHODS: Bacterial genomic DNA of E. coli HN503E1II was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using the Qiagen CLC Genomics Workbench. The assembled contigs were annotated and antibiotic resistance genes, virulence factors, plasmids and the sequence type (ST) were identified. RESULTS: The genome comprised a circular chromosome of 4 674201bp, with a 50.78% G+C content and several resistance genes associated with resistance to ß-lactams, fluoroquinolones, aminoglycosides, sulphonamides, trimethoprim, macrolides and tetracycline. The isolate was assigned to ST10 with 100% identity among the seven housekeeping genes. In silico analysis also revealed the presence six plasmid types and one virulence factor. CONCLUSION: The genome sequence reported here will provide valuable information for a better understanding of the genetic structure of the E. coli genome in Africa.

Antibiotic Resistance in Food Animals in Africa: A Systematic Review and Meta-Analysis.

OBJECTIVES: This study critically reviewed the published literature and performed a meta-analysis to determine the overall burden of antibiotic-resistant bacteria in food animals in Africa. METHODS: English and French published articles indexed in EBSCOhost, PubMed, Web of Science, and African Journals Online were retrieved, with searches being conducted up to August, 2015. Data were pooled and meta-analysis performed using a random-effects model, and the results are described as event rates. RESULTS: According to the predefined inclusion and exclusion criteria, 17 articles out of the 852 retrieved were eligible for the qualitative and quantitative analysis. The studies included were mainly conducted in Nigeria, with Escherichia coli, Salmonella spp., and Campylobacter spp. being the main bacteria. The pooled estimates showed high level of antibiotic resistance (ABR) (86%; p < 0.001) and multidrug resistance (73%; p = 0.003). CONCLUSION: Our results suggest that ABR is substantively prevalent and poses a serious threat for food safety and security in Africa. These findings shed light on areas for future research concerning antibiotic-resistant and multidrug-resistant bacteria in food animals as etiological agents of infectious diseases in humans. They further yielded some interesting findings on the burden of ABR that could be useful in developing measures to contain this threat in the farm-to-plate continuum in Africa.

Clinical and economic impact of antibiotic resistance in developing countries: A systematic review and meta-analysis.

INTRODUCTION: Despite evidence of the high prevalence of antibiotic resistant infections in developing countries, studies on the clinical and economic impact of antibiotic resistance (ABR) to inform interventions to contain its emergence and spread are limited. The aim of this study was to analyze the published literature on the clinical and economic implications of ABR in developing countries. METHODS: A systematic search was carried out in Medline via PubMed and Web of Sciences and included studies published from January 01, 2000 to December 09, 2016. All papers were considered and a quality assessment was performed using the Newcastle-Ottawa quality assessment scale (NOS). RESULTS: Of 27 033 papers identified, 40 studies met the strict inclusion and exclusion criteria and were finally included in the qualitative and quantitative analysis. Mortality was associated with resistant bacteria, and statistical significance was evident with an odds ratio (OR) 2.828 (95%CI, 2.231-3.584; p = 0.000). ESKAPE pathogens was associated with the highest risk of mortality and with high statistical significance (OR 3.217; 95%CIs; 2.395-4.321; p = 0.001). Eight studies showed that ABR, and especially antibiotic-resistant ESKAPE bacteria significantly increased health care costs. CONCLUSION: ABR is associated with a high mortality risk and increased economic costs with ESKAPE pathogens implicated as the main cause of increased mortality. Patients with non-communicable disease co-morbidities were identified as high-risk populations.