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Acinetobacter baumannii bacteria are increasingly clinically relevant due to their propensity to harbor genes conferring resistance to multiple antimicrobials, as well as their ability to persist and disseminate in hospital environments and cause difficult-to-treat nosocomial infections. Little is known about the molecular epidemiology and antimicrobial resistance profiles of these organisms in Nigeria, largely due to limited capacity for their isolation, identification, and antimicrobial susceptibility testing. Acinetobacter baumannii causes difficult-to-treat infections mostly among immunocompromised patients. Clinically relevant A. baumannii lineages and their carbapenem resistance mechanisms are sparsely described in Nigeria. This study aimed to characterize the diversity and genetic mechanisms of carbapenem resistance among A. baumannii strains isolated from hospitals in southwestern Nigeria. We sequenced the genomes of all A. baumannii isolates submitted to Nigeria’s antimicrobial resistance surveillance reference laboratory between 2016 and 2020 on an Illumina platform and performed in silico genomic characterization. Selected strains were sequenced using the Oxford Nanopore technology to characterize the genetic context of carbapenem resistance genes. The 86 A. baumannii isolates were phylogenetically diverse and belonged to 35 distinct Oxford sequence types ( oxf STs), 16 of which were novel, and 28 Institut Pasteur STs ( pas STs). Thirty-eight (44.2%) isolates belonged to none of the known international clones (ICs). Over 50% of the isolates were phenotypically resistant to 10 of 12 tested antimicrobials. The majority ( n  = 54) of the isolates were carbapenem resistant, particularly the IC7 ( pas ST25; 100%) and IC9 ( pas ST85; >91.7%) strains. bla OXA-23 (34.9%) and bla NDM-1 (27.9%) were the most common carbapenem resistance genes detected. All bla OXA-23 genes were carried on Tn 2006 or Tn 2006 -like transposons. Our findings suggest that a 10-kb Tn 125 composite transposon is the primary means of bla NDM-1 dissemination. Our findings highlight an increase in bla NDM-1 prevalence and the widespread transposon-facilitated dissemination of carbapenemase genes in diverse A. baumannii lineages in southwestern Nigeria. We make the case for improving surveillance of these pathogens in Nigeria and other understudied settings. IMPORTANCE Acinetobacter baumannii bacteria are increasingly clinically relevant due to their propensity to harbor genes conferring resistance to multiple antimicrobials, as well as their ability to persist and disseminate in hospital environments and cause difficult-to-treat nosocomial infections. Little is known about the molecular epidemiology and antimicrobial resistance profiles of these organisms in Nigeria, largely due to limited capacity for their isolation, identification, and antimicrobial susceptibility testing. Our study characterized the diversity and antimicrobial resistance profiles of clinical A. baumannii in southwestern Nigeria using whole-genome sequencing. We also identified the key genetic elements facilitating the dissemination of carbapenem resistance genes within this species. This study provides key insights into the clinical burden and population dynamics of A. baumannii in hospitals in Nigeria and highlights the importance of routine whole-genome sequencing-based surveillance of this and other previously understudied pathogens in Nigeria and other similar settings.

Salmonella enterica is a bacterial foodborne pathogen that can infect humans and animals. Proper control of Salmonella requires routine surveillance and interventions across the food-production chain. However, due to limited resources the epidemiology and transmission of non-typhoidal Salmonella serotypes remain poorly understood in several African settings, including within Ghana. Here, we employed bacterial culture and whole genome sequencing (WGS) to investigate the prevalence, virulence and antimicrobial resistance determinants of Salmonella enterica isolates from beef, cattle blood and human patient stool in Greater Tamale Metropolis, Ghana. Enrichment and culture of the specimens yielded 62 isolates in total from beef (31), bovine blood (28) and human diarrhoeal specimens (3). We identified at least 15 STs and 18 different Salmonella serovars. The most frequently detected serovars were Poona (n = 13), Montevideo (n = 10) and Poano (n = 7) with S. Montevideo being the most common from cattle blood. Thirty-two (52%) isolates belonged to novel sequence types (STs), with ST2609 (n = 9) being most common. Four raw beef isolates harboured at least one gene conferring resistance to beta-lactam ( bla TEM-1 ), chloramphenicol ( catA ), fosfomycin ( fosA7 ), quinolone ( qnrD1 ) or tetracycline ( tet(A) ). Eight isolates carried IncF, IncI and/or Col3M plasmid replicons. This study recovered Salmonella , often belonging to previously undocumented STs, at high frequencies from cattle and beef and demonstrated that isolates from human diarrhoeal patients are closely related to bovine isolates. The data highlight the need for broader and sustained surveillance and the urgent need for food safety interventions in Ghana.

Salmonella enterica and Escherichia coli are well-known bacteria commonly associated with foodborne illnesses in humans and animals. Genomic characterization of these pathogens provides valuable insights into their evolution, virulence factors and resistance determinants. This study aimed to characterized previously isolated Salmonella (n = 14) and E . coli (n = 19) from milk, meat and its associated utensils in Ghana using whole-genome sequencing. Most of the Salmonella serovars (Fresno, Plymouth, Infantis, Give and Orleans) identified in this study are yet to be reported in Ghana. Most Salmonella isolates were pan-sensitive, but genes conferring resistance to fosfomycin ( fosA7 . 2 ) and tetracycline ( tet(A) ) were detected in one and three isolates, respectively. Seven of the Salmonella isolates carried the IncI1-I(Gamma) plasmid replicon. Although antimicrobial resistance was not common among Salmonella strains, most (11/19) of the E . coli strains had at least one resistance gene, with nearly half (8/19) being multidrug resistant and carried plasmids. Three of the 19 E . coli strains belonged to serovars commonly associated with enteroaggregative E . coli (EAEC) pathotype. While strains belonging to virulence-associated lineages lacked key plasmid-encoded virulence plasmids, several plasmid replicons were detected in most of the E . coli (14/19) strains. Food contaminated with these pathogens can serve as a vehicle for disease transmission, posing a significant public health risk and necessitating stringent food safety and hygiene practices to prevent outbreaks. Hence, there is need for continuous surveillance and preventive measures to stop the spread of foodborne pathogens and reduce the risk of associated illnesses in Ghana.

Background Antimicrobial resistance (AMR) poses a significant threat to global health, particularly in Western sub-Saharan Africa where 27.3 deaths per 100,000 lives are affected, and surveillance and control measures are often limited. Genomics research plays a crucial role in understanding the emergence, spread and containment measures of AMR. However, its implementation in such settings is particularly challenging due to limited human capacity. This manuscript outlines a three-day bioinformatics workshop in Cameroon, highlighting efforts to build human capacity for genomics research to support AMR surveillance using readily accessible and user-friendly web-based tools. The workshop introduced participants to basic next-generation sequencing concepts, data file formats used in bacterial genomics, data sharing procedures and considerations, as well as the use of web-based bioinformatics software to analyse genomic data, including in silico prediction of AMR, phylogenetics analyses, and a quick introduction to Linux© command line. Results Briefly, a substantial increase in participants’ confidence in bioinformatics knowledge and skills was observed before and after the workshop. Notably, before the workshop most participants lacked confidence in their ability to identify next-generation sequencing technologies or workflows (64%) and analyse genetic data using web-based bioinformatics tools (81%). After the workshop, majority of participants were extremely confident using NCBI BLAST and other web-based bioinformatics tools for data analysis with a score ≥ 5 among which 45%, 9% and 18% had a score of 8, 9, and 10, respectively. Conclusion Our findings highlight the effectiveness of this training approach in empowering local researchers and bridging the bioinformatics gap in genomics surveillance of AMR in resource-constrained settings. We provide a detailed description of the relevant training approaches used, including workshop structure, the selection and planning, and utilization of freely available web-based tools, and the evaluation methods employed. Our approach aimed to overcome limitations such as inadequate infrastructure, limited access to computational resources, and scarcity of expertise. By leveraging the power of freely available web-based tools, we demonstrated how participants can acquire fundamental bioinformatics skills, enhance their understanding of biological data analysis, and contribute to the field, even in an underprivileged environment. Building human capacity for genomics research globally, and especially in resource-constrained settings, is imperative for ensuring global health and sustainable containment of AMR.

Salmonellosis causes significant morbidity and mortality in Africa. Information on lineages of invasive Salmonella circulating in Nigeria is sparse. Salmonella enterica isolated from blood (n = 60) and cerebrospinal fluid (CSF, n = 3) between 2016 and 2020 from five tertiary hospitals in southwest Nigeria were antimicrobial susceptibility-tested and Illumina-sequenced. Genomes were analysed using publicly-available bioinformatic tools. Isolates and sequence types (STs) from blood were S. Typhi [ST1, n = 1 and ST2, n = 43] and invasive non-typhoidal Salmonella (iNTS) (S. Enteritidis [ST11, n = 7], S. Durham [ST10, n = 2], S. Rissen [ST8756, n = 2], S. Chester [ST2063, n = 1], S. Dublin [ST10, n = 1], S. Infantis [ST603, n = 1], S. Telelkebir [ST8757, n = 1] and S. Typhimurium [ST313, n = 1]). S. Typhi ST2 (n = 2) and S. Adabraka ST8757 (n = 1) were recovered from CSF. Most S. Typhi belonged to genotype 3.1.1 (n = 44), carried an IncY plasmid, had several antibiotic resistance genes (ARGs) including blaTEM-1 (n = 38), aph(6)-Id (n = 32), tet(A) (n = 33), sul2 (n = 32), dfrA14 (n = 30) as well as quinolone resistance-conferring gyrA_S83Y single-nucleotide polymorphisms (n = 37). All S. Enteritidis harboured aph(3\")-Ib, blaTEM-1, catA1, dfrA7, sul1, sul2, tet(B) genes, and a single ARG, qnrB19, was detected in S. Telelkebir. Typhoidal toxins cdtB, pltA and pltB were detected in S. Typhi, Rissen, Chester, and Telelkebir. Most invasive salmonelloses in southwest Nigeria are vaccine-preventable infections due to multidrug-resistant, West African dominant S. Typhi lineage 3.1.1. Invasive NTS serovars, including some harbouring typhoidal toxin or resistance genes, represented a third of the isolates emphasizing the need for better diagnosis and surveillance.

are of major human health importance because they cause life-threatening nosocomial infections and often are highly resistant to antimicrobials. Specific multidrug-resistant lineages are implicated in hospital outbreaks globally. We retrospectively investigated a suspected outbreak of carbapenem-resistant (CRAB) colonizing patients in an intensive care unit (ICU) of a tertiary hospital in Southwest Nigeria where genomic surveillance of has hitherto not been conducted. A prospective observational study was conducted among all patients admitted to the ICU between August 2017 and June 2018. species were isolated from rectal swabs and verified phenotypically with the Biomerieux Vitek 2 system. Whole genome sequencing (WGS) was performed on the Illumina platform to characterize isolates from a suspected outbreak during the study period. Phylogenetic analysis, multilocus sequence typing, and antimicrobial resistance gene prediction were carried out . isolates belonging to the complex were recovered from 20 (18.5%) ICU patients. Single nucleotide polymorphism (SNP) analysis and epidemiological information revealed a putative outbreak clone comprising seven CRAB strains belonging to the globally disseminated international clone (IC) 2. These isolates had ≤2 SNP differences, identical antimicrobial resistance and virulence genes, and were all ST1114/1841. We report a carbapenem-resistant IC2 clone causing an outbreak in an ICU in Nigeria. The study findings underscore the need to strengthen the capacity to detect in human clinical samples in Nigeria and assess which interventions can effectively mitigate CRAB transmission in Nigerian hospital settings.

Antimicrobial resistance (AMR) is tracked most closely in clinical settings and high-income countries. However, resistant organisms thrive globally and are transmitted to and from healthy humans, animals and the environment, particularly in many low- and middle-income settings. The overall public health and clinical significance of these transmission opportunities remain to be completely clarified. There is thus considerable global interest in promoting a One Health view of AMR to enable a more realistic understanding of its ecology. In reality, AMR surveillance outside hospitals remains insufficient and it has been very challenging to convincingly document transmission at the interfaces between clinical specimens and other niches. In this Review, we describe AMR and its transmission in low- and middle-income-country settings, emphasizing high-risk transmission points such as urban settings and food-animal handling. In urban and food production settings, top-down and infrastructure-dependent interventions against AMR that require strong regulatory oversight are less likely to curtail transmission when used alone and should be combined with bottom-up AMR-containment approaches. We observe that the power of genomics to expose transmission channels and hotspots is largely unharnessed, and that existing and upcoming technological innovations need to be exploited towards containing AMR in low- and middle-income settings. In this Review, the authors describe the transmission of antimicrobial resistance in low- and middle-income countries from a One Health perspective, as well as the challenges and possible solutions for its containment.

Salmonella enterica is a bacterial foodborne pathogen notorious for infecting humans and animals. Proper control of Salmonella requires routine surveillance and interventions across the food-production chain. However, due to limited resources the dynamics and transmission of non-typhoidal Salmonella serotypes remain poorly understood in several African settings, including within Ghana. Here, we employed bacterial culture and whole genome sequencing (WGS) to investigate the prevalence, virulence and antimicrobial resistance determinants of Salmonella enterica isolates from beef, cattle blood and human patient stool in Greater Tamale Metropolis, Ghana. Enrichment and culture of the specimens yielded 62 isolates in total from beef (31), bovine blood (28) and human diarrhoeal specimens (3). We identified at least 15 STs and 18 different Salmonella serovars. The most common serovars detected were Poona (n=13), Montevideo (n=10) and Poano (n=7) with S. Montevideo being the most common from cattle blood. Thirty-two isolates belonged to novel sequence types (STs), with ST2609 (n=9) being most common. Four raw beef isolates harboured at least one gene conferring resistance to beta-lactam (blaTEM-1), chloramphenicol (catA), fosfomycin (fosA7), quinolone (qnrD1) or tetracycline (tet(A)). Eight isolates carried at an IncF, IncI and/orCol3M plasmid replicon. This study recovered Salmonella, often belonging to previously undocumented STs, at high frequencies from cattle and beef and demonstrated that isolates from human diarrhoeal patients are closely related to bovine isolates. The data highlight the need for broader and sustained surveillance and the urgent need for food safety interventions in Ghana.